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15  structures 5653  species 0  interactions 6628  sequences 7  architectures

Family: SMC_ScpB (PF04079)

Summary: Segregation and condensation complex subunit ScpB

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Condensin". More...

Condensin Edit Wikipedia article

An interphase nucleus (left) and a set of mitotic chromosomes (right) from human tissue culture cells. Bar, 10 μm.

Condensins are large protein complexes that play a central role in chromosome assembly and segregation during mitosis and meiosis.[1][2]

Subunit composition

Eukaryotic condensins

Subunit composition of condensin complexes

Many eukaryotic cells possess two different types of condensin complexes, known as condensin I and condensin II, each of which is composed of five subunits.[3][4] Condensins I and II share the same pair of core subunits, SMC2 and SMC4, both belonging to a large family of chromosomal ATPases, known as SMC proteins (SMC stands for Structural Maintenance of Chromosomes).[5][6] Each of the complexes contains a distinct set of non-SMC regulatory subunits (a kleisin subunit[7] and a pair of HEAT-repeat subunits[8][9]). The nematode Caenorhabditis elegans possesses a third complex (closely related to condensin I) that participates in chromosome-wide gene regulation, i.e., dosage compensation.[10] In this complex, known as condensin IDC, the authentic SMC4 subunit is replaced with its variant, DPY-27.

Complex Subunit Classification S. cerevisiae S. pombe C. elegans D. melanogaster Vertebrates (human genes)
condensin I & II SMC2 ATPase Smc2 Cut14 MIX-1 DmSmc2 CAP-E (SMC2)
condensin I & II SMC4 ATPase Smc4 Cut3 SMC-4 DmSmc4 CAP-C (SMC4)
condensin I CAP-D2 HEAT Ycs4 Cnd1 DPY-28 Cap-D2 CAP-D2 (NCAPD2)
condensin I CAP-G HEAT Ycg1 Cnd3 CAP-G1 cap-g CAP-G (NCAPG)
condensin I CAP-H kleisin Brn1 Cnd2 DPY-26 barren CAP-H (NCAPH)
condensin II CAP-D3 HEAT - - HCP-6 Cap-D3 CAP-D3 (NCAPD3)
condensin II CAP-G2 HEAT - - CAP-G2 -? CAP-G2 (NCAPG2)
condensin II CAP-H2 kleisin - - KLE-2 Cap-H2 CAP-H2 (NCAPH2)
condensin IDC SMC4 variant ATPase - - DPY-27 - -

The structure and function of condensin I are conserved from yeast to humans, but yeast has no condensin II.[11][12] There is no apparent relationship between the occurrence of condensin II and the size of eukaryotic genomes. In fact, the primitive red alga Cyanidioschyzon merolae has both condensins I and II although its genome size is small and comparable to that of yeast.[13]

Prokaryotic condensins

Prokaryotic species also have condensin-like complexes that play an important role in chromosome organization and segregation. The prokaryotic condensins can be classified into two types: SMC-ScpAB[14] and MukBEF.[15] Many eubacterial and archaeal species have SMC-ScpAB, whereas a subgroup of eubacteria (known as gamma-proteobacteria) has MukBEF. ScpA and MukF belong to a family of proteins called "kleisins",[7] whereas ScpB and MukF have recently been classified into a new family of proteins named "kite".[16]

Complex Subunit Classification B. subtilis Caulobacter E.coli
SMC-ScpAB ScpA kleisin ScpA ScpA -
SMC-ScpAB ScpB kite ScpB ScpB -
MukBEF MukB ATPase - - MukB
MukBEF MukE kite - - MukE
MukBEF MukF kleisin - - MukF

Molecular mechanisms

Molecular activities

Purified condensin I introduces positive superhelical tension into double-stranded DNA in an ATP-hydrolysis-dependent manner.[17] It also displays a DNA-stimulated ATPase activity in vitro. An SMC2-SMC4 dimer has an ability to reanneal complementary single-stranded DNA.[18] This activity does not require ATP.

In preparation for the mitosis, it was hypothesized that condensin plays a key role in compaction and segregation of the sister chromatids. The same was demonstrated by the polymer physics simulations[19]. However, the direct evidence for the DNA loop extrusion activity was provided by single-molecule experiments [20]. In those experiments, the activity of individual condensin complexes on DNA was visualized by real-time fluorescence imaging revealing that condensin indeed is a fast loop-extruding motor and single condensin complex can extrude 1500 bp of DNA per second in a strictly ATP dependent manner[21]. Furthermore, these results showed that condensin anchors DNA between kleisin-Ycg1 subunits and pulls DNA asymmetrically to form large loops.

Molecular structures

SMC dimers that act as the core subunits of condensins display a highly unique V-shape (see SMC proteins for details).[22] The holocomplex of condensin I has been visualized by electron microscopy.[23]

Mitotic functions

Distribution of condensin I (green) and condensin II (red) in human metaphase chromosomes. Bar, 1 μm.

In human tissue culture cells, the two condensin complexes are regulated differently during the cell cycle.[24][25] Condensin II is present within the cell nucleus during interphase and is involved in an early stage of chromosome condensation within the prophase nucleus. On the other hand, condensin I is present in the cytoplasm during interphase, and gains access to chromosomes only after the nuclear envelope breaks down at the end of prophase. During prometaphase and metaphase, both condensin I and condensin II contribute to the assembly of condensed chromosomes, in which two sister chromatids are fully resolved.[4] The two complexes apparently stay associated with chromosomes after the sister chromatids separate from each other in anaphase. At least one of the subunits of condensin I is known to be a direct target of a cyclin-dependent kinase (Cdk).[26]

Chromosomal functions outside of mitosis

Recent studies have shown that condensins participate in a wide variety of chromosome functions outside of mitosis or meiosis.[27] In budding yeast, for instance, condensin I (the sole condensin in this organism) is involved in copy number regulation of the rDNA repeat[28] as well as in clustering of the tRNA genes.[29] In Drosophila, condensin II subunits contribute to the dissolution of polytene chromosomes[30] and the formation of chromosome territories[31] in ovarian nurse cells. Evidence is also available that they negatively regulate transvection in diploid cells. In A. thaliana, condensin II is essential for tolerance of excess boron stress, possibly by alleviating DNA damage.[32] It has been shown that, in human cells, condensin II’s contribution to resolving sister chromatids initiates as early as in S phase.[33]


Eukaryotic cells have two additional classes of SMC protein complexes. Cohesin contains SMC1 and SMC3 and is involved in sister chromatid cohesion. The SMC5/6 complex contains SMC5 and SMC6 and is implicated in recombinational repair.

See also


  1. ^ Hirano T (2016). "Condensin-based chromosome organization from bacteria to vertebrates". Cell. 164 (5): 847–857. doi:10.1016/j.cell.2016.01.033. PMID 26919425.
  2. ^ Wood AJ, Severson AF, Meyer BJ (2010). "Condensin and cohesin complexity: the expanding repertoire of functions". Nat Rev Genet. 11 (6): 391–404. doi:10.1038/nrg2794. PMC 3491780. PMID 20442714.
  3. ^ Hirano T, Kobayashi R, Hirano M (1997). "Condensins, chromosome condensation complex containing XCAP-C, XCAP-E and a Xenopus homolog of the Drosophila Barren protein". Cell. 89 (4): 511–21. doi:10.1016/S0092-8674(00)80233-0. PMID 9160743.
  4. ^ a b Ono T, Losada A, Hirano M, Myers MP, Neuwald AF, Hirano T (2003). "Differential contributions of condensin I and condensin II to mitotic chromosome architecture in vertebrate cells". Cell. 115 (1): 109–21. doi:10.1016/S0092-8674(03)00724-4. PMID 14532007.
  5. ^ Jeppsson K, Kanno T, Shirahige K, Sjögren C (2014). "The maintenance of chromosome structure: positioning and functioning of SMC complexes". Nat. Rev. Mol. Cell Biol. 15 (9): 601–614. doi:10.1038/nrm3857. PMID 25145851.
  6. ^ Uhlmann F (2016). "SMC complexes: from DNA to chromosomes". Nat. Rev. Mol. Cell Biol. 17 (7): 399–412. doi:10.1038/nrm.2016.30. PMID 27075410.
  7. ^ a b Schleiffer A, Kaitna S, Maurer-Stroh S, Glotzer M, Nasmyth K, Eisenhaber F (2003). "Kleisins: a superfamily of bacterial and eukaryotic SMC protein partners". Mol. Cell. 11 (3): 571–5. doi:10.1016/S1097-2765(03)00108-4. PMID 12667442.
  8. ^ Neuwald AF, Hirano T (2000). "HEAT repeats associated with condensins, cohesins, and other complexes involved in chromosome-related functions". Genome Res. 10 (10): 1445–52. doi:10.1101/gr.147400. PMC 310966. PMID 11042144.
  9. ^ Yoshimura SH, Hirano T (2016). "HEAT repeats - versatile arrays of amphiphilic helices working in crowded environments?". J. Cell Sci. 129 (21): 3963–3970. doi:10.1242/jcs.185710. PMID 27802131.
  10. ^ Csankovszki G, Collette K, Spahl K, Carey J, Snyder M, Petty E, Patel U, Tabuchi T, Liu H, McLeod I, Thompson J, Sarkeshik A, Yates J, Meyer BJ, Hagstrom K (2009). "Three distinct condensin complexes control C. elegans chromosome dynamics". Curr. Biol. 19 (1): 9–19. doi:10.1016/j.cub.2008.12.006. PMC 2682549. PMID 19119011.
  11. ^ Sutani T, Yuasa T, Tomonaga T, Dohmae N, Takio K, Yanagida M (1999). "Fission yeast condensin complex: essential roles of non-SMC subunits for condensation and Cdc2 phosphorylation of Cut3/SMC4". Genes Dev. 13 (17): 2271–83. doi:10.1101/gad.13.17.2271. PMC 316991. PMID 10485849.
  12. ^ Freeman L, Aragon-Alcaide L, Strunnikov A (2000). "The condensin complex governs chromosome condensation and mitotic transmission of rDNA". J. Cell Biol. 149 (4): 811–824. doi:10.1083/jcb.149.4.811. PMC 2174567. PMID 10811823.
  13. ^ Fujiwara T, Tanaka K, Kuroiwa T, Hirano T (2013). "Spatiotemporal dynamics of condensins I and II: evolutionary insights from the primitive red alga Cyanidioschyzon merolae". Mol. Biol. Cell. 24 (16): 2515–27. doi:10.1091/mbc.E13-04-0208. PMC 3744952. PMID 23783031.
  14. ^ Mascarenhas J, Soppa J, Strunnikov AV, Graumann PL (2002). "Cell cycle-dependent localization of two novel prokaryotic chromosome segregation and condensation proteins in Bacillus subtilis that interact with SMC protein". EMBO J. 21 (12): 3108–18. doi:10.1093/emboj/cdf314. PMC 126067. PMID 12065423.
  15. ^ Yamazoe M, Onogi T, Sunako Y, Niki H, Yamanaka K, Ichimura T, Hiraga S (1999). "Complex formation of MukB, MukE and MukF proteins involved in chromosome partitioning in Escherichia coli". EMBO J. 18 (21): 5873–84. doi:10.1093/emboj/18.21.5873. PMC 1171653. PMID 10545099.
  16. ^ Palecek JJ, Gruber S (2015). "Kite proteins: a superfamily of SMC/kleisin partners conserved across Bacteria, Archaea, and Eukaryotes". Structure. 23 (12): 2183–2190. doi:10.1016/j.str.2015.10.004. PMID 26585514.
  17. ^ Kimura K, Hirano T (1997). "ATP-dependent positive supercoiling of DNA by 13S condensin: a biochemical implication for chromosome condensation". Cell. 90 (4): 625–634. doi:10.1016/s0092-8674(00)80524-3. PMID 9288743.
  18. ^ Sutani T, Yanagida M (1997). "DNA renaturation activity of the SMC complex implicated in chromosome condensation". Nature. 388 (6644): 798–801. doi:10.1038/42062. PMID 9285594.
  19. ^ Goloborodko, Anton; Imakaev, Maxim V; Marko, John F; Mirny, Leonid (2016-05-18). "Compaction and segregation of sister chromatids via active loop extrusion". eLife. 5. doi:10.7554/eLife.14864. ISSN 2050-084X. PMC 4914367. PMID 27192037.
  20. ^ Ganji, Mahipal; Shaltiel, Indra A.; Bisht, Shveta; Kim, Eugene; Kalichava, Ana; Haering, Christian H.; Dekker, Cees (2018-04-06). "Real-time imaging of DNA loop extrusion by condensin". Science. 360 (6384): 102–105. doi:10.1126/science.aar7831. ISSN 0036-8075. PMC 6329450. PMID 29472443.
  21. ^ Ganji, Mahipal; Shaltiel, Indra A.; Bisht, Shveta; Kim, Eugene; Kalichava, Ana; Haering, Christian H.; Dekker, Cees (2018-04-06). "Real-time imaging of DNA loop extrusion by condensin". Science. 360 (6384): 102–105. doi:10.1126/science.aar7831. ISSN 0036-8075. PMC 6329450. PMID 29472443.
  22. ^ Melby TE, Ciampaglio CN, Briscoe G, Erickson HP (1998). "The symmetrical structure of structural maintenance of chromosomes (SMC) and MukB proteins: long, antiparallel coiled coils, folded at a flexible hinge". J. Cell Biol. 142 (6): 1595–1604. doi:10.1083/jcb.142.6.1595. PMC 2141774. PMID 9744887.
  23. ^ Anderson DE, Losada A, Erickson HP, Hirano T (2002). "Condensin and cohesin display different arm conformations with characteristic hinge angles". J. Cell Biol. 156 (6): 419–424. doi:10.1083/jcb.200111002. PMC 2173330. PMID 11815634.
  24. ^ Ono T, Fang Y, Spector DL, Hirano T (2004). "Spatial and temporal regulation of Condensins I and II in mitotic chromosome assembly in human cells". Mol. Biol. Cell. 15 (7): 3296–308. doi:10.1091/mbc.E04-03-0242. PMC 452584. PMID 15146063.
  25. ^ Hirota T, Gerlich D, Koch B, Ellenberg J, Peters JM (2004). "Distinct functions of condensin I and II in mitotic chromosome assembly". J. Cell Sci. 117 (Pt 26): 6435–45. doi:10.1242/jcs.01604. PMID 15572404.
  26. ^ Kimura K, Hirano M, Kobayashi R, Hirano T (1998). "Phosphorylation and activation of 13S condensin by Cdc2 in vitro". Science. 282 (5388): 487–490. doi:10.1126/science.282.5388.487. PMID 9774278.
  27. ^ Hirano T (2012). "Condensins: universal organizers of chromosomes with diverse functions". Genes Dev. 26 (15): 1659–1678. doi:10.1101/gad.194746.112. PMC 3418584. PMID 22855829.
  28. ^ Johzuka K, Terasawa M, Ogawa H, Ogawa T, Horiuchi T (2006). "Condensin loaded onto the replication fork barrier site in the rRNA gene repeats during S phase in a FOB1-dependent fashion to prevent contraction of a long repetitive array in Saccharomyces cerevisiae". Mol Cell Biol. 26 (6): 2226–2236. doi:10.1128/MCB.26.6.2226-2236.2006. PMC 1430289. PMID 16507999.
  29. ^ Haeusler RA, Pratt-Hyatt M, Good PD, Gipson TA, Engelke DR (2008). "Clustering of yeast tRNA genes is mediated by specific association of condensin with tRNA gene transcription complexes". Genes Dev. 22 (16): 2204–2214. doi:10.1101/gad.1675908. PMC 2518813. PMID 18708579.
  30. ^ Hartl TA, Smith HF, Bosco G (2008). "Chromosome alignment and transvection are antagonized by condensin II". Science. 322 (5906): 1384–1387. doi:10.1126/science.1164216. PMID 19039137.
  31. ^ Bauer CR, Hartl TA, Bosco G (2012). "Condensin II promotes the formation of chromosome territories by inducing axial compaction of polyploid interphase chromosomes". PLoS Genet. 8 (8): e1002873. doi:10.1371/journal.pgen.1002873. PMC 3431300. PMID 22956908.
  32. ^ Sakamoto T, Inui YT, Uraguchi S, Yoshizumi T, Matsunaga S, Mastui M, Umeda M, Fukui K, Fujiwara T (2011). "Condensin II alleviates DNA damage and is essential for tolerance of boron overload stress in Arabidopsis". Plant Cell. 23 (9): 3533–3546. doi:10.1105/tpc.111.086314. PMC 3203421. PMID 21917552.
  33. ^ Ono T, Yamashita D, Hirano T (2013). "Condensin II initiates sister chromatid resolution during S phase". J. Cell Biol. 200 (4): 429–441. doi:10.1083/jcb.201208008. PMC 3575537. PMID 23401001.

External links

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Segregation and condensation complex subunit ScpB Provide feedback

This is a family of prokaryotic proteins that form one of the subunits, ScpB, of the segregation and condensation complex, condensin, that plays a key role in the maintenance of the chromosome. In prokaryotes the complex consists of three proteins, SMC, ScpA (kleisin) and ScpB. ScpB dimerises and binds to ScpA. As originally predicted, ScpB is structurally a winged-helix at both its N- and C-terminal halves. IN Bacillus subtilis,one Smc dimer is bridged by a single ScpAB to generate asymmetric tripartite rings analogous to eukaryotic SMC complex ring-shaped assemblies [1,2].

Literature references

  1. Burmann F, Shin HC, Basquin J, Soh YM, Gimenez-Oya V, Kim YG, Oh BH, Gruber S;, Nat Struct Mol Biol. 2013;20:371-379.: An asymmetric SMC-kleisin bridge in prokaryotic condensin. PUBMED:23353789 EPMC:23353789

  2. Kamada K, Miyata M, Hirano T;, Structure. 2013;21:581-594.: Molecular basis of SMC ATPase activation: role of internal structural changes of the regulatory subcomplex ScpAB. PUBMED:23541893 EPMC:23541893

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR005234

This family represents ScpB, which along with ScpA ( INTERPRO ) interacts with SMC in vivo forming a complex that is required for chromosome condensation and segregation [ PUBMED:12065423 , PUBMED:12897137 ]. The SMC-Scp complex appears to be similar to the MukB-MukE-Muk-F complex in Escherichia coli [ PUBMED:10545099 ], where MukB ( INTERPRO ) is the homologue of SMC. ScpA and ScpB have little sequence similarity to MukE ( INTERPRO ) or MukF ( INTERPRO ), they are predicted to be structurally similar, being predominantly alpha-helical with coiled coil regions.

In general scpA and scpB form an operon in most bacterial genomes. Flanking genes are highly variable suggesting that the operon has moved throughout evolution. Bacteria containing an smc gene also contain scpA or scpB but not necessarily both. An exception is found in Deinococcus radiodurans, which contains scpB but neither smc nor scpA. In the archaea the gene order SMC-ScpA is conserved in nearly all species, as is the very short distance between the two genes, indicating co-transcription of the both in different archaeal genera and arguing that interaction of the gene products is not confined to the homologues in Bacillus subtilis. It would seem probable that, in light of all the studies, SMC, ScpA and ScpB proteins or homologues act together in chromosome condensation and segregation in all prokaryotes [ PUBMED:12100548 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan HTH (CL0123), which has the following description:

This family contains a diverse range of mostly DNA-binding domains that contain a helix-turn-helix motif.

The clan contains the following 353 members:

AbiEi_3_N AbiEi_4 ANAPC2 AphA_like AraR_C Arg_repressor ARID ArsR B-block_TFIIIC B5 Bac_DnaA_C Baculo_PEP_N BetR BHD_3 BLACT_WH Bot1p BrkDBD BsuBI_PstI_RE_N C_LFY_FLO CaiF_GrlA CarD_CdnL_TRCF CDC27 Cdc6_C Cdh1_DBD_1 CDT1 CDT1_C CENP-B_N Costars CPSase_L_D3 Cro Crp CSN4_RPN5_eIF3a CSN8_PSD8_EIF3K CtsR Cullin_Nedd8 CUT CUTL CvfB_WH DBD_HTH DDRGK DEP Dimerisation Dimerisation2 DNA_meth_N DpnI_C DprA_WH DsrC DsrD DUF1016_N DUF1133 DUF1153 DUF1323 DUF134 DUF1441 DUF1492 DUF1495 DUF1670 DUF1804 DUF1819 DUF1836 DUF1870 DUF2089 DUF2250 DUF2316 DUF2513 DUF2582 DUF3116 DUF3253 DUF3853 DUF3860 DUF3908 DUF433 DUF4364 DUF4423 DUF4447 DUF480 DUF4817 DUF5635 DUF573 DUF6088 DUF6262 DUF6362 DUF6432 DUF6462 DUF6471 DUF722 DUF739 DUF742 DUF977 E2F_TDP EAP30 eIF-5_eIF-2B ELL ESCRT-II Ets EutK_C Exc F-112 FaeA Fe_dep_repr_C Fe_dep_repress FeoC FokI_C FokI_N Forkhead FtsK_gamma FUR GcrA GerE GntR GP3_package HARE-HTH HemN_C HNF-1_N Homeobox_KN Homeodomain Homez HPD HrcA_DNA-bdg HSF_DNA-bind HTH_1 HTH_10 HTH_11 HTH_12 HTH_13 HTH_15 HTH_16 HTH_17 HTH_18 HTH_19 HTH_20 HTH_21 HTH_22 HTH_23 HTH_24 HTH_25 HTH_26 HTH_27 HTH_28 HTH_29 HTH_3 HTH_30 HTH_31 HTH_32 HTH_33 HTH_34 HTH_35 HTH_36 HTH_37 HTH_38 HTH_39 HTH_40 HTH_41 HTH_42 HTH_43 HTH_45 HTH_46 HTH_47 HTH_48 HTH_49 HTH_5 HTH_50 HTH_51 HTH_52 HTH_53 HTH_54 HTH_55 HTH_56 HTH_57 HTH_58 HTH_59 HTH_6 HTH_7 HTH_8 HTH_9 HTH_ABP1_N HTH_AraC HTH_AsnC-type HTH_CodY HTH_Crp_2 HTH_DeoR HTH_IclR HTH_Mga HTH_micro HTH_OrfB_IS605 HTH_PafC HTH_ParB HTH_psq HTH_SUN2 HTH_Tnp_1 HTH_Tnp_1_2 HTH_Tnp_4 HTH_Tnp_IS1 HTH_Tnp_IS630 HTH_Tnp_ISL3 HTH_Tnp_Mu_1 HTH_Tnp_Mu_2 HTH_Tnp_Tc3_1 HTH_Tnp_Tc3_2 HTH_Tnp_Tc5 HTH_WhiA HxlR IBD IF2_N IRF KicB KilA-N Kin17_mid KORA KorB La LacI LexA_DNA_bind Linker_histone LZ_Tnp_IS481 MADF_DNA_bdg MAGE MARF1_LOTUS MarR MarR_2 MerR MerR-DNA-bind MerR_1 MerR_2 Mga Mnd1 MogR_DNAbind Mor MotA_activ MqsA_antitoxin MRP-L20 MukE Myb_DNA-bind_2 Myb_DNA-bind_3 Myb_DNA-bind_4 Myb_DNA-bind_5 Myb_DNA-bind_6 Myb_DNA-bind_7 Myb_DNA-binding Neugrin NFRKB_winged NOD2_WH NUMOD1 ORC_WH_C OST-HTH P22_Cro PaaX PadR PapB PAX PCI Penicillinase_R Phage_AlpA Phage_antitermQ Phage_CI_repr Phage_CII Phage_NinH Phage_Nu1 Phage_rep_O Phage_rep_org_N Phage_terminase PheRS_DBD1 PheRS_DBD2 PheRS_DBD3 Pou Pox_D5 PqqD PRC2_HTH_1 PUFD PuR_N Put_DNA-bind_N pXO2-72 Raf1_HTH Rap1-DNA-bind Rep_3 RepA_C RepA_N RepC RepL Replic_Relax RFX_DNA_binding Ribosomal_S18 Ribosomal_S19e Ribosomal_S25 Rio2_N RNA_pol_Rpc34 RNA_pol_Rpc82 RNase_H2-Ydr279 ROQ_II RP-C RPA RPA_C RQC Rrf2 RTP RuvB_C S10_plectin SAC3_GANP SANT_DAMP1_like SatD SelB-wing_1 SelB-wing_2 SelB-wing_3 SgrR_N Sigma54_CBD Sigma54_DBD Sigma70_ECF Sigma70_ner Sigma70_r2 Sigma70_r3 Sigma70_r4 Sigma70_r4_2 SinI Ski_Sno SLIDE Slx4 SMC_Nse1 SMC_ScpB SoPB_HTH SpoIIID SRP19 SRP_SPB STN1_2 Sulfolobus_pRN Suv3_N Swi6_N SWIRM Tau95 TBPIP TEA Terminase_5 TetR_N TFA2_Winged_2 TFIIE_alpha TFIIE_beta TFIIF_alpha TFIIF_beta Tn7_Tnp_TnsA_C Tn916-Xis TraI_2_C Trans_reg_C TrfA TrmB tRNA_bind_2 tRNA_bind_3 Trp_repressor UPF0122 UPF0175 Vir_act_alpha_C YdaS_antitoxin YjcQ YokU z-alpha


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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: TIGRFAMs (release 2.0);
Previous IDs: DUF387;
Type: Family
Sequence Ontology: SO:0100021
Author: TIGRFAMs, Finn RD
Number in seed: 94
Number in full: 6628
Average length of the domain: 158.70 aa
Average identity of full alignment: 35 %
Average coverage of the sequence by the domain: 71.09 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.4 27.4
Trusted cut-off 27.4 27.5
Noise cut-off 27.3 27.3
Model length: 159
Family (HMM) version: 18
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Archea Archea Eukaryota Eukaryota
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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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The tree shows the occurrence of this domain across different species. More...


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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the SMC_ScpB domain has been found. There are 15 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
I6XCB2 View 3D Structure Click here
Q2FY77 View 3D Structure Click here