Summary: WD domain, G-beta repeat
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WD40 repeat Edit Wikipedia article
WD domain, G-beta repeat | |||||||||
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![]() Ribbon diagram of the C-terminal WD40 domain of Tup1 (a transcriptional corepressor in yeast), which adopts a 7-bladed beta-propeller fold. Ribbon is colored from blue (N-terminus) to red (C-terminus).[1]
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Identifiers | |||||||||
Symbol | WD40 | ||||||||
Pfam | PF00400 | ||||||||
Pfam clan | CL0186 | ||||||||
InterPro | IPR001680 | ||||||||
PROSITE | PDOC00574 | ||||||||
SCOP | 1gp2 | ||||||||
SUPERFAMILY | 1gp2 | ||||||||
CDD | cd00200 | ||||||||
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The WD40 repeat (also known as the WD or beta-transducin repeat) is a short structural motif of approximately 40 amino acids, often terminating in a tryptophan-aspartic acid (W-D) dipeptide.[2] Tandem copies of these repeats typically fold together to form a type of circular solenoid protein domain called the WD40 domain.
Structure
WD40 domain-containing proteins have 4 to 16 repeating units, all of which are thought to form a circularised beta-propeller structure (see figure to the right).[3][4] The WD40 domain is composed of several repeats, a variable region of around 20 residues at the beginning followed by a more common repeated set of residues. These repeats typically form a four stranded anti-parallel beta sheet or blade. These blades come together to form a propeller with the most common being a 7 bladed beta propeller. The blades interlock so that the last beta strand of one repeat forms with the first three of the next repeat to form the 3D blade structure.
Function
WD40-repeat proteins are a large family found in all eukaryotes and are implicated in a variety of functions ranging from signal transduction and transcription regulation to cell cycle control, autophagy and apoptosis.[5] The underlying common function of all WD40-repeat proteins is coordinating multi-protein complex assemblies, where the repeating units serve as a rigid scaffold for protein interactions. The specificity of the proteins is determined by the sequences outside the repeats themselves. Examples of such complexes are G proteins (beta subunit is a beta-propeller), TAFII transcription factor, and E3 ubiquitin ligase.[3][4]
Examples
According to the initial analysis of the human genome WD40 repeats are the eighth largest family of proteins. In all 277 proteins were identified to contain them.[6] Human genes encoding proteins containing this domain include:
- AAAS, AAMP, AHI1, AMBRA1, APAF1, ARPC1A, ARPC1B, ATG16L1,
- BOP1, BRWD1, BRWD2, BRWD3, BTRC, BUB3,
- C6orf11, CDC20, CDC40, CDRT1, CHAF1B, CIAO1, CIRH1A, COPA, COPB2, CORO1A, CORO1B, CORO1C, CORO2A, CORO2B, CORO6, CORO7, CSTF1,
- DDB2, DENND3, DMWD, DMXL1, DMXL2, DNAI1, DNAI2, DNCI1, DTL, DYNC1I1, DYNC1I2, EDC4,
- EED, EIF3S2, ELP2, EML1, EML2, EML3, EML4, EML4-ALK, EML5, ERCC8,
- FBXW10, FBXW11, FBXW2, FBXW4, FBXW5, FBXW7, FBXW8, FBXW9, FZR1,
- GBL, GEMIN5, GNB1, GNB1L, GNB2, GNB2L1, GNB3, GNB4, GNB5, GRWD1, GTF3C2,
- HERC1, HIRA, HZGJ,
- IFT121, IFT122, IFT140, IFT172, IFT80, IQWD1,
- KATNB1, KIAA1336, KIF21A, KIF21B, KM-PA-2,
- KEAP1,
- LLGL1, LLGL2, LRBA, LRRK1, LRRK2, LRWD1, LYST,
- MAPKBP1, MED16, MORG1,
- NBEA, NBEAL1, NEDD1, NLE1, NSMAF, NUP37, NUP43, NWD1,
- PAAF1, PAFAH1B1, PAK1IP1, PEX7, PHIP, PIK3R4, PLAA, PLRG1, PPP2R2A, PPP2R2B, PPP2R2C, PPP2R2D, PPWD1, PREB, PRPF19, PRPF4, PWP1, PWP2,
- RAE1, RPTOR, RBBP4, RBBP5, RBBP7, RFWD2, RFWD3, RRP9,
- SCAP, SEC13, SEC31A, SEC31B, SEH1L, SHKBP1, SMU1, SPAG16, SPG, STRAP, STRN, STRN3, STRN4, STXBP5, STXBP5L,
- TAF5, TAF5L, TBL1X, TBL1XR1, TBL1Y, TBL2, TBL3, TEP1, THOC3, THOC6, TLE1, TLE2, TLE3, TLE4, TLE6, TRAF7, TSSC1, TULP4, TUWD12,
- UTP15, UTP18,
- WAIT1, WDF3, WDFY1, WDFY2, WDFY3, WDFY4, WDHD1, WDR1, WDR10, WDR12, WDR13, WDR16, WDR17, WDR18, WDR19, WDR20, WDR21A, WDR21C, WDR22, WDR23, WDR24, WDR25, WDR26, WDR27, WDR3, WDR31, WDR32, WDR33, WDR34, WDR35, WDR36, WDR37, WDR38, WDR4, WDR40A, WDR40B, WDR40C, WDR41, WDR42A, WDR42B, WDR43, WDR44, WDR46, WDR47, WDR48, WDR49, WDR5, WDR51A, WDR51B, WDR52, WDR53, WDR54, WDR55, WDR57, WDR59, WDR5B, WDR6, WDR60, WDR61, WDR62, WDR63, WDR64, WDR65, WDR66, WDR67, WDR68, WDR69, WDR7, WDR70, WDR72, WDR73, WDR74, WDR75, WDR76, WDR77, WDR78, WDR79, WDR8, WDR81, WDR82, WDR85, WDR86, WDR88, WDR89, WDR90, WDR91, WDR92, WDSOF1, WDSUB1, WDTC1, WSB1, WSB2,
- ZFP106
WDR gene | other gene names | NCBI Entrez Gene ID |
Human disease associated with mutations |
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WDR1 | AIP1; NORI-1; HEL-S-52 | 9948 | |
WDR2 | CORO2A; IR10; CLIPINB | 7464 | |
WDR3 | DIP2; UTP12 | 10885 | |
WDR4 | TRM82; TRMT82 | 10785 | |
WDR5 | SWD3; BIG-3; CFAP89 | 11091 | |
WDR6 | 11180 | ||
WDR7 | TRAG; KIAA0541; Rabconnectin 3 beta | 23335 | |
WDR8 | WRAP73 | 49856 | |
WDR9 | BRWD1; N143; C21orf107 | 54014 | |
WDR10 | IFT122; CED; SPG; CED1; WDR10p; WDR140 | 55764 | Sensenbrenner syndrome |
WDR11 | DR11; HH14; BRWD2; WDR15 | 55717 | Kallmann syndrome |
WDR12 | YTM1 | 55759 | |
WDR13 | MG21 | 64743 | |
WDR14 | GNB1L; GY2; FKSG1; WDVCF; DGCRK3 | 54584 | |
WDR15 | WDR11 | ||
WDR16 | CFAP52; WDRPUH | 146845 | |
WDR17 | 116966 | ||
WDR18 | Ipi3 | 57418 | |
WDR19 | ATD5; CED4; DYF-2; ORF26; Oseg6; PWDMP; SRTD5; IFT144; NPHP13 | 57728 | Sensenbrenner syndrome, Jeune syndrome |
WDR20 | DMR | 91833 | |
WDR21 | DCAF4; WDR21A | 26094 | |
WDR22 | DCAF5; BCRG2; BCRP2 | 8816 | |
WDR23 | DCAF11; GL014; PRO2389 | 80344 | |
WDR24 | JFP7; C16orf21 | 84219 | |
WDR25 | C14orf67 | 79446 | |
WDR26 | CDW2; GID7; MIP2 | 80232 | |
WDR27 | 253769 | ||
WDR28 | GRWD1; CDW4; GRWD; RRB1 | 83743 | |
WDR29 | SPAG16; PF20 | 79582 | |
WDR30 | ATG16L1; IBD10; APG16L; ATG16A; ATG16L | 55054 | Crohn’s disease |
WDR31 | 114987 | ||
WDR32 | DCAF10 | 79269 | |
WDR33 | NET14; WDC146 | 55339 | |
WDR34 | DIC5; FAP133; SRTD11 | 89891 | Jeune syndrome |
WDR35 | CED2; IFTA1; SRTD7; IFT121 | 57539 | Sensenbrenner syndrome |
WDR36 | GLC1G; UTP21; TAWDRP; TA-WDRP | 134430 | Primary Open Angle Glaucoma |
WDR37 | 22884 | ||
WDR38 | 401551 | ||
WDR39 | CIAO1; CIA1 | 9391 | |
WDR40A | DCAF12; CT102; TCC52; KIAA1892 | 25853 | |
WDR41 | MSTP048 | 55255 | |
WDR43 | UTP5; NET12 | 23160 | |
WDR44 | RPH11; RAB11BP | 54521 | |
WDR45 | JM5; NBIA4; NBIA5; WDRX1; WIPI4; WIPI-4 | 11152 | Beta-propeller protein-associated neurodegeneration (BPAN) |
WDR46 | UTP7; BING4; FP221; C6orf11 | 9277 | |
WDR47 | NEMITIN; KIAA0893 | 22911 | |
WDR48 | P80; UAF1; SPG60 | 57599 | |
WDR49 | 151790 | ||
WDR50 | UTP18; CGI-48 | 51096 | |
WDR52 | CFAP44 | 55779 | |
WDR53 | 348793 | ||
WDR54 | 84058 | ||
WDR55 | 54853 | ||
WDR56 | IFT80; ATD2; SRTD2 | 57560 | Jeune syndrome |
WDR57 | SNRNP40; SPF38; PRP8BP; HPRP8BP; PRPF8BP | 9410 | |
WDR58 | THOC6; BBIS; fSAP35 | 79228 | |
WDR59 | FP977 | 79726 | |
WDR60 | SRPS6; SRTD8; FAP163 | 55112 | Jeune syndrome |
WDR61 | SKI8; REC14 | 80349 | |
WDR62 | MCPH2; C19orf14 | 284403 | microcephaly |
WDR63 | DIC3; NYD-SP29 | 126820 | |
WDR64 | 128025 | ||
WDR65 | CFAP57; VWS2 | 149465 | Van der Woude syndrome |
WDR66 | CaM-IP4 | 144406 | |
WDR67 | TBC1D31; Gm85 | 93594 | |
WDR68 | DCAF7; AN11; HAN11; SWAN-1 | 10238 | |
WDR69 | DAW1; ODA16 | 164781 | |
WDR70 | 55100 | ||
WDR71 | PAAF1; PAAF; Rpn14 | 80227 | |
WDR72 | AI2A3 | 256764 | Amelogenesis imperfecta |
WDR73 | HSPC264 | 84942 | |
WDR74 | 54663 | ||
WDR75 | NET16; UTP17 | 84128 | |
WDR76 | CDW14 | 79968 | |
WDR77 | p44; MEP50; MEP-50; HKMT1069; Nbla10071; p44/Mep50 | 79084 | |
WDR78 | DIC4 | 79819 | |
WDR79 | WRAP53; DKCB3; TCAB1 | 55135 | |
WDR80 | ATG16L; ATG16B | 89849 | |
WDR81 | CAMRQ2; PPP1R166 | 124997 | cerebellar ataxia, mental retardation, and dysequilibrium syndrome-2 |
WDR82 | SWD2; MST107; WDR82A; MSTP107; PRO2730; TMEM113; PRO34047 | 80335 | |
WDR83 | MORG1 | 84292 | |
WDR84 | PAK1IP1; PIP1; MAK11 | 55003 | |
WDR85 | DPH7; RRT2; C9orf112 | 92715 | |
WDR86 | 349136 | ||
WDR87 | NYD-SP11 | 83889 | |
WDR88 | PQWD | 126248 | |
WDR89 | MSTP050; C14orf150 | 112840 | |
WDR90 | C16orf15; C16orf16; C16orf17; C16orf18; C16orf19 | 197335 | |
WDR91 | HSPC049 | 29062 | |
WDR92 | MONAD | 116143 | |
WDR93 | 56964 | ||
WDR94 | AMBRA1; DCAF3 | 55626 | |
WDR96 | CFAP43; C10orf79 | 80217 |
See also
- Beta-propeller
- Tomosyn, a protein two WD40 domains
References
- ^ PDB: 1erj​; Sprague ER, Redd MJ, Johnson AD, Wolberger C (June 2000). "Structure of the C-terminal domain of Tup1, a corepressor of transcription in yeast". EMBO J. 19 (12): 3016–27. doi:10.1093/emboj/19.12.3016. PMC 203344 
. PMID 10856245.
- ^ Neer EJ, Schmidt CJ, Nambudripad R, Smith TF (September 1994). "The ancient regulatory-protein family of WD-repeat proteins". Nature. 371 (6495): 297–300. doi:10.1038/371297a0. PMID 8090199.
- ^ a b Smith TF, Gaitatzes C, Saxena K, Neer EJ (May 1999). "The WD40 repeat: a common architecture for diverse functions". Trends Biochem. Sci. 24 (5): 181–5. doi:10.1016/S0968-0004(99)01384-5. PMID 10322433.
- ^ a b Li D, Roberts R (December 2001). "WD-repeat proteins: structure characteristics, biological function, and their involvement in human diseases". Cell. Mol. Life Sci. 58 (14): 2085–97. doi:10.1007/PL00000838. PMID 11814058.
- ^ Stirnimann CU, Petsalaki E, Russell RB, Müller CW (May 2010). "WD40 proteins propel cellular networks". Trends Biochem. Sci. 35 (10): 565–74. doi:10.1016/j.tibs.2010.04.003. PMID 20451393.
- ^ Lander ES, Linton LM, Birren B, et al. (February 2001). "Initial sequencing and analysis of the human genome". Nature. 409 (6822): 860–921. doi:10.1038/35057062. PMID 11237011.
External links
- Eukaryotic Linear Motif resource motif class LIG_APCC_Dbox_1
- Eukaryotic Linear Motif resource motif class LIG_APCC_KENbox_2
- Eukaryotic Linear Motif resource motif class LIG_COP1
- Eukaryotic Linear Motif resource motif class LIG_CRL4_Cdt2_1
- Eukaryotic Linear Motif resource motif class LIG_CRL4_Cdt2_2
- Eukaryotic Linear Motif resource motif class LIG_EH1_1
- Eukaryotic Linear Motif resource motif class LIG_GLEBS_BUB3_1
- Eukaryotic Linear Motif resource motif class LIG_RAPTOR_TOS_1
- Eukaryotic Linear Motif resource motif class LIG_SCF_FBW7_1
- Eukaryotic Linear Motif resource motif class LIG_SCF_FBW7_2
- Eukaryotic Linear Motif resource motif class LIG_SCF-TrCP1_1
- Eukaryotic Linear Motif resource motif class LIG_WRPW_1
- Eukaryotic Linear Motif resource motif class LIG_WRPW_2
- Eukaryotic Linear Motif resource motif class TRG_ER_diArg_1
- Eukaryotic Linear Motif resource motif class TRG_ER_diLys_1
- Eukaryotic Linear Motif resource motif class TRG_Golgi_diPhe_1
- Eukaryotic Linear Motif resource motif class TRG_PTS2
This article incorporates text from the public domain Pfam and InterPro IPR001680
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.
WD domain, G-beta repeat Provide feedback
No Pfam abstract.
Literature references
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Neer EJ, Schmidt CJ, Nambudripad R, Smith TF; , Nature 1994;371:297-300.: The ancient regulatory-protein family of WD-repeat proteins. PUBMED:8090199 EPMC:8090199
Internal database links
SCOOP: | ANAPC4_WD40 CEP19 Coatomer_WDAD Cytochrom_D1 eIF2A Frtz Ge1_WD40 Gmad1 IKI3 Nucleoporin_N Nup160 PQQ_2 RAB3GAP2_N SGL Utp8 VID27 WD40_like |
Similarity to PfamA using HHSearch: | eIF2A ANAPC4_WD40 Ge1_WD40 |
External database links
HOMSTRAD: | WD40 |
PRINTS: | PR00320 |
PROSITE: | PDOC00574 |
SCOP: | 1gp2 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR001680
WD-40 repeats (also known as WD or beta-transducin repeats) are short ~40 amino acid motifs, often terminating in a Trp-Asp (W-D) dipeptide. WD40 repeats usually assume a 7-8 bladed beta-propeller fold, but proteins have been found with 4 to 16 repeated units, which also form a circularised beta-propeller structure. WD-repeat proteins are a large family found in all eukaryotes and are implicated in a variety of functions ranging from signal transduction and transcription regulation to cell cycle control and apoptosis. Repeated WD40 motifs act as a site for protein-protein interaction, and proteins containing WD40 repeats are known to serve as platforms for the assembly of protein complexes or mediators of transient interplay among other proteins. The specificity of the proteins is determined by the sequences outside the repeats themselves. Examples of such complexes are G proteins (beta subunit is a beta-propeller), TAFII transcription factor, and E3 ubiquitin ligase [PUBMED:11814058, PUBMED:10322433]. In Arabidopsis spp., several WD40-containing proteins act as key regulators of plant-specific developmental events.
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | protein binding (GO:0005515) |
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 Beta_propeller (CL0186), which has the following description:
This large clan contains proteins that contain beta propellers. These are composed of between 6 and 8 repeats. The individual repeats are composed of a four stranded sheet. The clan includes families such as WD40 Pfam:PF00400 where the individual repeats are modeled. The clan also includes families where the entire propeller is modeled such as Pfam:PF02239 usually because the individual repeats are not discernible. These proteins carry out a very wide diversity of functions including catalysis.
The clan contains the following 74 members:
ANAPC4_WD40 Arylesterase Arylsulfotran_2 Arylsulfotrans BBS2_Mid Beta_propel Coatomer_WDAD CPSF_A CyRPA Cytochrom_D1 DPPIV_N DUF1513 DUF1668 DUF2415 DUF4221 DUF4934 DUF5046 DUF5050 DUF5122 DUF5128 DUF839 eIF2A FG-GAP FG-GAP_2 Frtz Ge1_WD40 Glu_cyclase_2 Gmad1 GSDH IKI3 Itfg2 Kelch_1 Kelch_2 Kelch_3 Kelch_4 Kelch_5 Kelch_6 Lactonase Ldl_recept_b Lgl_C LVIVD Me-amine-dh_H MRJP Nbas_N Neisseria_PilC NHL Nucleoporin_N Nup160 PALB2_WD40 PD40 Pectate_lyase22 Peptidase_S9_N PHTB1_N Phytase-like PQQ PQQ_2 PQQ_3 RAG2 RCC1 RCC1_2 Reg_prop SBBP SBP56 SdiA-regulated SGL Str_synth TcdB_toxin_midN TolB_like VCBS VID27 WD40 WD40_3 WD40_4 WD40_likeAlignments
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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
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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 (1465) |
Full (540137) |
Representative proteomes | UniProt (788245) |
NCBI (1096175) |
Meta (4365) |
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RP15 (159138) |
RP35 (312603) |
RP55 (438651) |
RP75 (528851) |
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Jalview | |||||||||
HTML | |||||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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Seed (1465) |
Full (540137) |
Representative proteomes | UniProt (788245) |
NCBI (1096175) |
Meta (4365) |
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RP15 (159138) |
RP35 (312603) |
RP55 (438651) |
RP75 (528851) |
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Raw Stockholm | |||||||||
Gzipped |
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
Seed source: | Pfam-B_2 (release 1.0) |
Previous IDs: | G-beta; |
Type: | Repeat |
Sequence Ontology: | SO:0001068 |
Author: |
Finn RD |
Number in seed: | 1465 |
Number in full: | 540137 |
Average length of the domain: | 39.40 aa |
Average identity of full alignment: | 24 % |
Average coverage of the sequence by the domain: | 19.56 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 38 | ||||||||||||
Family (HMM) version: | 32 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
There are 54 interactions for this family. More...
Mad3_BUB1_II SBP_bac_1 7tm_1 Ribosomal_S8 G-gamma Ribosomal_S17e Lipase_GDSL_2 CPSF_A PRMT5 G-alpha IRK Nucleopor_Nup85 Ribosomal_S17e Trimer_CC Ribosomal_S9 EZH2_WD-Binding DUF1899 Nup96 Ribosomal_S2 Lipase_GDSL_2 Nup96 Ribosomal_S6e Ribosomal_S4e ARPC4 Sec16_C HORMA PI3_PI4_kinase MMS1_N WD40 Ribosomal_S5 Ribosomal_S2 Ribosomal_S9 Cofilin_ADF G-gamma Phosducin DEP Coatomer_WDAD RGS PH Sec16 Methyltransf_4 Actin CAF1C_H4-bd Sec16 NB-ARC Cytochrom_C CAF1C_H4-bd N-SET Nucleopor_Nup85 P16-Arc Sec16_C Histone FATC MMS1_NStructures
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 WD40 domain has been found. There are 4237 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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