7ENC

TFIID-based PIC-Mediator holo-complex in fully-assembled state (hPIC-MED)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.13 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structures of the human Mediator and Mediator-bound preinitiation complex.

Chen, X., Yin, X., Li, J., Wu, Z., Qi, Y., Wang, X., Liu, W., Xu, Y.

(2021) Science 372

  • DOI: https://doi.org/10.1126/science.abg0635
  • Primary Citation of Related Structures:  
    7EMF, 7ENA, 7ENC, 7ENJ

  • PubMed Abstract: 

    The 1.3-megadalton transcription factor IID (TFIID) is required for preinitiation complex (PIC) assembly and RNA polymerase II (Pol II)-mediated transcription initiation on almost all genes. The 26-subunit Mediator stimulates transcription and cyclin-dependent kinase 7 (CDK7)-mediated phosphorylation of the Pol II C-terminal domain (CTD). We determined the structures of human Mediator in the Tail module-extended (at near-atomic resolution) and Tail-bent conformations and structures of TFIID-based PIC-Mediator (76 polypeptides, ~4.1 megadaltons) in four distinct conformations. PIC-Mediator assembly induces concerted reorganization (Head-tilting and Middle-down) of Mediator and creates a Head-Middle sandwich, which stabilizes two CTD segments and brings CTD to CDK7 for phosphorylation; this suggests a CTD-gating mechanism favorable for phosphorylation. The TFIID-based PIC architecture modulates Mediator organization and TFIIH stabilization, underscoring the importance of TFIID in orchestrating PIC-Mediator assembly.

    • Organizational Affiliation: 

    Human Phenome Institute, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 1A [auth a]1,581Homo sapiensMutation(s): 0 
Gene Names: 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 31B [auth m]131Homo sapiensMutation(s): 0 
Gene Names: MED31, SOH1, CGI-125
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 4C [auth d]270Homo sapiensMutation(s): 0 
Gene Names: MED4, ARC36, DRIP36, VDRIP, HSPC126
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 6D [auth f]246Homo sapiensMutation(s): 0 
Gene Names: MED6, ARC33
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 7E [auth g]233Homo sapiensMutation(s): 0 
Gene Names: MED7, ARC34, CRSP9
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2 of Mediator of RNA polymerase II transcription subunit 8F [auth h]268Homo sapiensMutation(s): 0 
Gene Names: MED8
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 18G [auth r]208Homo sapiensMutation(s): 0 
Gene Names: MED18
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 20H [auth t]212Homo sapiensMutation(s): 0 
Gene Names: MED20, TRFP
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 10I [auth j]135Homo sapiensMutation(s): 0 
Gene Names: MED10, L6, TRG17, TRG20
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 11J [auth k]117Homo sapiensMutation(s): 0 
Gene Names: MED11, HSPC296
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 14K [auth n]1,454Homo sapiensMutation(s): 0 
Gene Names: MED14, ARC150, CRSP2, CXorf4, DRIP150, EXLM1, RGR1, TRAP170
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 17L [auth q]651Homo sapiensMutation(s): 0 
Gene Names: MED17, ARC77, CRSP6, DRIP77, DRIP80, TRAP80
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 19M [auth s]244Homo sapiensMutation(s): 0 
Gene Names: MED19, LCMR1
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 21N [auth u]144Homo sapiensMutation(s): 0 
Gene Names: MED21, SRB7, SURB7
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 22O [auth v]200Homo sapiensMutation(s): 0 
Gene Names: MED22, SURF5
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 26P [auth z]600Homo sapiensMutation(s): 0 
Gene Names: MED26, ARC70, CRSP7
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 27Q [auth c]311Homo sapiensMutation(s): 0 
Gene Names: MED27, CRSP34, CRSP8
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 28R [auth e]178Homo sapiensMutation(s): 0 
Gene Names: MED28, EG1, FKSG20
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 29S [auth b]200Homo sapiensMutation(s): 0 
Gene Names: MED29, IXL
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 30T [auth l]178Homo sapiensMutation(s): 0 
Gene Names: MED30, THRAP6, TRAP25
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 15U [auth o]788Homo sapiensMutation(s): 0 
Gene Names: MED15, ARC105, CTG7A, PCQAP, TIG1, TNRC7
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 9V [auth i]146Homo sapiensMutation(s): 0 
Gene Names: MED9, MED25
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
CDK-activating kinase assembly factor MAT1W [auth 0]309Homo sapiensMutation(s): 0 
Gene Names: MNAT1, CAP35, MAT1, RNF66
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-dependent kinase 7X [auth 8]346Homo sapiensMutation(s): 0 
Gene Names: CDK7, CAK, CAK1, CDKN7, MO15, STK1
EC: 2.7.11.22 (PDB Primary Data), 2.7.11.23 (PDB Primary Data)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-HY [auth 9]323Homo sapiensMutation(s): 0 
Gene Names: CCNH
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIH subunit 1Z [auth 1]548Homo sapiensMutation(s): 0 
Gene Names: GTF2H1, BTF2
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIH subunit 2AA [auth 2]395Homo sapiensMutation(s): 0 
Gene Names: GTF2H2, BTF2P44
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIH subunit 3BA [auth 3]308Homo sapiensMutation(s): 0 
Gene Names: GTF2H3
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIH subunit 4CA [auth 4]462Homo sapiensMutation(s): 0 
Gene Names: GTF2H4
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIH subunit 5DA [auth 5]71Homo sapiensMutation(s): 0 
Gene Names: GTF2H5, C6orf175, TTDA
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH helicase subunit XPBEA [auth 6]782Homo sapiensMutation(s): 0 
Gene Names: ERCC3, XPB, XPBC
EC: 3.6.4.12
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH helicase subunit XPDFA [auth 7]760Homo sapiensMutation(s): 0 
Gene Names: ERCC2, XPD, XPDC
EC: 3.6.4.12
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIE subunit 1GA [auth EA]439Homo sapiensMutation(s): 0 
Gene Names: GTF2E1, TF2E1
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIE subunit betaHA [auth EB]291Homo sapiensMutation(s): 0 
Gene Names: GTF2E2, TF2E2
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 1IA [auth DA]1,872Homo sapiensMutation(s): 0 
Gene Names: TAF1, BA2R, CCG1, CCGS, TAF2A
EC: 2.3.1.48 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 2JA [auth DB]1,199Homo sapiensMutation(s): 0 
Gene Names: TAF2, CIF150, TAF2B
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 4KA [auth DD],
TA [auth Dd]		1,085Homo sapiensMutation(s): 0 
Gene Names: TAF4, TAF2C, TAF2C1, TAF4A, TAFII130, TAFII135
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 5LA [auth DE],
UA [auth De]		800Homo sapiensMutation(s): 0 
Gene Names: TAF5, TAF2D
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 6MA [auth DF],
VA [auth Df]		677Homo sapiensMutation(s): 0 
Gene Names: TAF6, TAF2E, TAFII70
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 7NA [auth DG]349Homo sapiensMutation(s): 0 
Gene Names: TAF7, TAF2F, TAFII55
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 8OA [auth DH]310Homo sapiensMutation(s): 0 
Gene Names: TAF8, TAFII43, TBN
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 9PA [auth DI],
WA [auth Di]		264Homo sapiensMutation(s): 0 
Gene Names: TAF9, TAF2G, TAFII31
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 10QA [auth DJ],
XA [auth Dj]		218Homo sapiensMutation(s): 0 
Gene Names: TAF10, TAF2A, TAF2H, TAFII30
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 12RA [auth DL],
ZA [auth Dl]		161Homo sapiensMutation(s): 0 
Gene Names: TAF12, TAF15, TAF2J, TAFII20
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 3SA [auth Dc]929Homo sapiensMutation(s): 0 
Gene Names: TAF3
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 11YA [auth Dk]211Homo sapiensMutation(s): 0 
Gene Names: TAF11, TAF2I, PRO2134
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 13AB [auth Dm]124Homo sapiensMutation(s): 0 
Gene Names: TAF13, TAF2K, TAFII18
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIA subunit 2BB [auth DO]109Homo sapiensMutation(s): 0 
Gene Names: GTF2A2, TF2A2
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
TATA-box-binding proteinCB [auth DP]339Homo sapiensMutation(s): 0 
Gene Names: TBP, GTF2D1, TF2D, TFIID
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
TFIIA-aDB [auth DQ]307Homo sapiensMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIBEB [auth BA]316Homo sapiensMutation(s): 0 
Gene Names: GTF2B, TF2B, TFIIB
EC: 2.3.1.48
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIF subunit 2249Homo sapiensMutation(s): 0 
Gene Names: GTF2F2, RAP30
EC: 3.6.4.12
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
RPB1IB [auth PA]1,970Sus scrofaMutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaJB [auth PB]1,174Sus scrofaMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3KB [auth PC]275Sus scrofaMutation(s): 0 
Gene Names: POLR2C
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB4LB [auth PD]142Sus scrofaMutation(s): 0 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit EMB [auth PE]210Sus scrofaMutation(s): 0 
Gene Names: POLR2E
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit FNB [auth PF]127Sus scrofaMutation(s): 0 
Gene Names: POLR2F
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7OB [auth PG]172Sus scrofaMutation(s): 0 
Gene Names: POLR2G
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3PB [auth PH]150Sus scrofaMutation(s): 0 
Gene Names: POLR2H
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9QB [auth PI]125Sus scrofaMutation(s): 0 
Gene Names: POLR2I
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
RPB10RB [auth PJ]67Sus scrofaMutation(s): 0 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
RNA_pol_L_2 domain-containing proteinSB [auth PK]117Sus scrofaMutation(s): 0 
Gene Names: POLR2J
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
RPB12TB [auth PL]58Sus scrofaMutation(s): 0 
Gene Names: POLR2K
UniProt
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIF subunit 1UB [auth FA]517Homo sapiensMutation(s): 0 
Gene Names: GTF2F1, RAP74
UniProt
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 23VB [auth w]1,368Homo sapiensMutation(s): 0 
Gene Names: MED23, ARC130, CRSP3, DRIP130, KIAA1216, SUR2
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 24WB [auth x]989Homo sapiensMutation(s): 0 
Gene Names: MED24, ARC100, CRSP4, DRIP100, KIAA0130, THRAP4, TRAP100
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Find proteins for O75448 (Homo sapiens)
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