Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
135  structures 8602  species 0  interactions 31696  sequences 241  architectures

Family: SMC_N (PF02463)

Summary: RecF/RecN/SMC N terminal domain

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

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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.

RecF/RecN/SMC N terminal domain Provide feedback

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics [1]. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.

Literature references

  1. Strunnikov AV, Jessberger R; , Eur J Biochem 1999;263:6-13.: Structural maintenance of chromosomes (SMC) proteins: conserved molecular properties for multiple biological functions. PUBMED:10429180 EPMC:10429180

  2. Hirano T; , Curr Opin Cell Biol 1998;10:317-322.: SMC protein complexes and higher-order chromosome dynamics. PUBMED:9640531 EPMC:9640531


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003395

This domain is found at the N terminus of structural maintenance of chromosomes (SMC) proteins, which function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair and epigenetic silencing of gene expression [ PUBMED:11983169 ]. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics [ PUBMED:10429180 ]. This domain is also found in RecF and RecN proteins, which are involved in DNA metabolism and recombination.

Domain organisation

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

Loading domain graphics...

Pfam Clan

This family is a member of clan P-loop_NTPase (CL0023), which has the following description:

AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes [2].

The clan contains the following 243 members:

6PF2K AAA AAA-ATPase_like AAA_10 AAA_11 AAA_12 AAA_13 AAA_14 AAA_15 AAA_16 AAA_17 AAA_18 AAA_19 AAA_2 AAA_21 AAA_22 AAA_23 AAA_24 AAA_25 AAA_26 AAA_27 AAA_28 AAA_29 AAA_3 AAA_30 AAA_31 AAA_32 AAA_33 AAA_34 AAA_35 AAA_5 AAA_6 AAA_7 AAA_8 AAA_9 AAA_PrkA ABC_ATPase ABC_tran ABC_tran_Xtn Adeno_IVa2 Adenylsucc_synt ADK AFG1_ATPase AIG1 APS_kinase Arf ArsA_ATPase ATP-synt_ab ATP_bind_1 ATP_bind_2 ATPase ATPase_2 Bac_DnaA BCA_ABC_TP_C Beta-Casp bpMoxR Cas_Csn2 Cas_St_Csn2 CbiA CBP_BcsQ CDC73_C CENP-M CFTR_R CLP1_P CMS1 CoaE CobA_CobO_BtuR CobU cobW CPT CSM2 CTP_synth_N Cytidylate_kin Cytidylate_kin2 DAP3 DBINO DEAD DEAD_2 DLIC DNA_pack_C DNA_pack_N DNA_pol3_delta DNA_pol3_delta2 DnaB_C dNK DO-GTPase1 DO-GTPase2 DUF1611 DUF1726 DUF2075 DUF2326 DUF2478 DUF257 DUF2791 DUF2813 DUF3584 DUF463 DUF5906 DUF6079 DUF815 DUF853 DUF87 DUF927 Dynamin_N Dynein_heavy Elong_Iki1 ELP6 ERCC3_RAD25_C Exonuc_V_gamma FeoB_N Fer4_NifH Flavi_DEAD FTHFS FtsK_SpoIIIE G-alpha Gal-3-0_sulfotr GBP GBP_C GTP_EFTU Gtr1_RagA Guanylate_kin GvpD HDA2-3 Helicase_C Helicase_C_2 Helicase_C_4 Helicase_RecD Herpes_Helicase Herpes_ori_bp Herpes_TK HSA HydF_dimer HydF_tetramer Hydin_ADK IIGP IPPT IPT iSTAND IstB_IS21 KAP_NTPase KdpD Kinase-PPPase Kinesin KTI12 LAP1C Lon_2 LpxK MCM MeaB MEDS Mg_chelatase Microtub_bd MipZ MMR_HSR1 MMR_HSR1_C MobB MukB Mur_ligase_M MutS_V Myosin_head NACHT NAT_N NB-ARC NOG1 NTPase_1 NTPase_P4 OPA1_C ORC3_N P-loop_TraG ParA Parvo_NS1 PAXNEB PduV-EutP PhoH PIF1 Ploopntkinase1 Ploopntkinase2 Ploopntkinase3 Podovirus_Gp16 Polyoma_lg_T_C Pox_A32 PPK2 PPV_E1_C PRK PSY3 Rad17 Rad51 Ras RecA ResIII RHD3 RhoGAP_pG1_pG2 RHSP RNA12 RNA_helicase Roc RsgA_GTPase RuvB_N SbcCD_C SecA_DEAD Septin Sigma54_activ_2 Sigma54_activat SKI SMC_N SNF2-rel_dom Spore_III_AA Spore_IV_A SRP54 SRPRB SulA Sulfotransfer_1 Sulfotransfer_2 Sulfotransfer_3 Sulfotransfer_4 Sulfotransfer_5 Sulphotransf SWI2_SNF2 T2SSE T4SS-DNA_transf Terminase_1 Terminase_3 Terminase_6N Terminase_GpA Thymidylate_kin TIP49 TK TniB Torsin TraG-D_C tRNA_lig_kinase TrwB_AAD_bind TsaE UvrB UvrD-helicase UvrD_C UvrD_C_2 Viral_helicase1 VirC1 VirE YqeC Zeta_toxin Zot

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(28)
Full
(31696)
Representative proteomes UniProt
(120929)
RP15
(5078)
RP35
(15359)
RP55
(29894)
RP75
(47453)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(28)
Full
(31696)
Representative proteomes UniProt
(120929)
RP15
(5078)
RP35
(15359)
RP55
(29894)
RP75
(47453)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(28)
Full
(31696)
Representative proteomes UniProt
(120929)
RP15
(5078)
RP35
(15359)
RP55
(29894)
RP75
(47453)
Raw Stockholm Download   Download   Download   Download   Download      
Gzipped Download   Download   Download   Download   Download      

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

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: [1]
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 28
Number in full: 31696
Average length of the domain: 741.10 aa
Average identity of full alignment: 15 %
Average coverage of the sequence by the domain: 92.10 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 40.0 40.0
Trusted cut-off 40.0 40.0
Noise cut-off 39.9 39.9
Model length: 220
Family (HMM) version: 21
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

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...

Loading sunburst data...

Tree controls

Hide

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

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

Structures

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_N domain has been found. There are 135 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.

Loading structure mapping...

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
A0A0G2K4T5 View 3D Structure Click here
A0A0N7KEM6 View 3D Structure Click here
A0A0N7KUG0 View 3D Structure Click here
A0A0P0WP88 View 3D Structure Click here
A0A0R0HP07 View 3D Structure Click here
A0A0R0I695 View 3D Structure Click here
A0A1D6GTS1 View 3D Structure Click here
A0A1D6IXQ6 View 3D Structure Click here
A0A1D6KLM4 View 3D Structure Click here
A0A1D6M7C7 View 3D Structure Click here
A0A1D6M7C7 View 3D Structure Click here
A0A1D6MEC8 View 3D Structure Click here
A0A1D6N452 View 3D Structure Click here
A0A1D6N452 View 3D Structure Click here
A0A1D8PI59 View 3D Structure Click here
A0A1D8PJK7 View 3D Structure Click here
A0A1D8PSI8 View 3D Structure Click here
A0A2R8QCL7 View 3D Structure Click here
A4HSG2 View 3D Structure Click here
A4HTF1 View 3D Structure Click here
A4HZD1 View 3D Structure Click here
A4IBP1 View 3D Structure Click here
A5PN27 View 3D Structure Click here
B2FDA8 View 3D Structure Click here
B8A5K9 View 3D Structure Click here
C0PG09 View 3D Structure Click here
D3ZE73 View 3D Structure Click here
D4A5Q2 View 3D Structure Click here
D4AB26 View 3D Structure Click here
E7F0X6 View 3D Structure Click here
E7F0X6 View 3D Structure Click here
E7FGC2 View 3D Structure Click here
F1MAD9 View 3D Structure Click here
G5EG17 View 3D Structure Click here
I1JIN1 View 3D Structure Click here
I1L5P0 View 3D Structure Click here
I1LVC8 View 3D Structure Click here
I1LVC8 View 3D Structure Click here
I1LWK5 View 3D Structure Click here
I1LYK3 View 3D Structure Click here
I1M0W9 View 3D Structure Click here
I1M0W9 View 3D Structure Click here
I1M7D7 View 3D Structure Click here
I1N651 View 3D Structure Click here
I1NHX5 View 3D Structure Click here
O01789 View 3D Structure Click here
O42649 View 3D Structure Click here
O94383 View 3D Structure Click here
O95347 View 3D Structure Click here
O95347 View 3D Structure Click here
P05824 View 3D Structure Click here
P0A7H0 View 3D Structure Click here
P32908 View 3D Structure Click here
P38989 View 3D Structure Click here
P38989 View 3D Structure Click here
P41003 View 3D Structure Click here
P41004 View 3D Structure Click here
P47037 View 3D Structure Click here
P48996 View 3D Structure Click here
P48996 View 3D Structure Click here
P53692 View 3D Structure Click here
P97690 View 3D Structure Click here
P9WGF3 View 3D Structure Click here
P9WHI7 View 3D Structure Click here
P9WHI9 View 3D Structure Click here
Q08204 View 3D Structure Click here
Q09591 View 3D Structure Click here
Q12267 View 3D Structure Click here
Q14683 View 3D Structure Click here
Q18237 View 3D Structure Click here
Q18616 View 3D Structure Click here
Q1LVV8 View 3D Structure Click here
Q20060 View 3D Structure Click here
Q2FY50 View 3D Structure Click here
Q2FZ49 View 3D Structure Click here
Q2FZ49 View 3D Structure Click here
Q2G275 View 3D Structure Click here
Q4CKD6 View 3D Structure Click here
Q4CUA8 View 3D Structure Click here
Q4D0W6 View 3D Structure Click here
Q4D2P9 View 3D Structure Click here
Q4D5A9 View 3D Structure Click here
Q4DL10 View 3D Structure Click here
Q4DUB1 View 3D Structure Click here
Q4E1T5 View 3D Structure Click here
Q54E85 View 3D Structure Click here
Q54E85 View 3D Structure Click here
Q54FE3 View 3D Structure Click here
Q54I56 View 3D Structure Click here
Q54LV0 View 3D Structure Click here
Q54PK4 View 3D Structure Click here
Q552D9 View 3D Structure Click here
Q552D9 View 3D Structure Click here
Q56YN8 View 3D Structure Click here
Q59037 View 3D Structure Click here
Q59037 View 3D Structure Click here
Q59UE8 View 3D Structure Click here
Q5A4Y2 View 3D Structure Click here
Q5KQG5 View 3D Structure Click here
Q5N6W1 View 3D Structure Click here
Q5N6W1 View 3D Structure Click here
Q6Q1P4 View 3D Structure Click here
Q7KK96 View 3D Structure Click here
Q8CG46 View 3D Structure Click here
Q8CG47 View 3D Structure Click here
Q8CG48 View 3D Structure Click here
Q8I1U7 View 3D Structure Click here
Q8I413 View 3D Structure Click here
Q8IED2 View 3D Structure Click here
Q8II57 View 3D Structure Click here
Q8IPT2 View 3D Structure Click here
Q8IY18 View 3D Structure Click here
Q8NDV3 View 3D Structure Click here
Q920F6 View 3D Structure Click here
Q96SB8 View 3D Structure Click here
Q9C5Y4 View 3D Structure Click here
Q9CU62 View 3D Structure Click here
Q9CW03 View 3D Structure Click here
Q9FJL0 View 3D Structure Click here
Q9FLR5 View 3D Structure Click here
Q9LFS8 View 3D Structure Click here
Q9NTJ3 View 3D Structure Click here
Q9SN90 View 3D Structure Click here
Q9UQE7 View 3D Structure Click here
Q9V3A7 View 3D Structure Click here
Q9VCB8 View 3D Structure Click here
Q9VCD8 View 3D Structure Click here
Q9VXE9 View 3D Structure Click here
Q9Z1M9 View 3D Structure Click here
X1WEJ1 View 3D Structure Click here