8GXQ

PIC-Mediator in complex with +1 nucleosome (T40N) in MH-binding state

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.04 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

Structures of +1 nucleosome-bound PIC-Mediator complex.

Chen, X., Wang, X., Liu, W., Ren, Y., Qu, X., Li, J., Yin, X., Xu, Y.

(2022) Science 378: 62-68

  • DOI: 10.1126/science.abn8131
  • Primary Citation of Related Structures:  
    8GXQ, 8GXS

  • PubMed Abstract: 

    • RNA polymerase II-mediated eukaryotic transcription starts with the assembly of the preinitiation complex (PIC) on core promoters. The +1 nucleosome is well positioned about 40 base pairs downstream of the transcription start site (TSS) and is commonly known as a barrier of transcription ...

    RNA polymerase II-mediated eukaryotic transcription starts with the assembly of the preinitiation complex (PIC) on core promoters. The +1 nucleosome is well positioned about 40 base pairs downstream of the transcription start site (TSS) and is commonly known as a barrier of transcription. The +1 nucleosome-bound PIC-Mediator structures show that PIC-Mediator prefers binding to T40N nucleosome located 40 base pairs downstream of TSS and contacts T50N but not the T70N nucleosome. The nucleosome facilitates the organization of PIC-Mediator on the promoter by binding TFIIH subunit p52 and Mediator subunits MED19 and MED26 and may contribute to transcription initiation. PIC-Mediator exhibits multiple nucleosome-binding patterns, supporting a structural role of the +1 nucleosome in the coordination of PIC-Mediator assembly. Our study reveals the molecular mechanism of PIC-Mediator organization on chromatin and underscores the significance of the +1 nucleosome in regulating transcription initiation.

    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: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIBC [auth BA]316Homo sapiensMutation(s): 0 
Gene Names: GTF2B, TF2B, TFIIB
EC: 2.3.1.48
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 1D [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: 5
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIE subunit 1E [auth EA]439Homo sapiensMutation(s): 0 
Gene Names: GTF2E1, TF2E1
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIF subunit 1F [auth FA]517Homo sapiensMutation(s): 0 
Gene Names: GTF2F1, RAP74
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH helicase subunit XPDG [auth HA]760Homo sapiensMutation(s): 0 
Gene Names: ERCC2, XPD, XPDC
EC: 3.6.4.12
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3H [auth NA],
BC [auth NE]		136Xenopus laevisMutation(s): 0 
Gene Names: XELAEV_18002543mg, LOC121398065, LOC108703785, LOC121398067
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Entity ID: 9
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DNA-directed RNA polymerase subunitI [auth PA]1,970Sus scrofaMutation(s): 0 
Gene Names: POLR2A
EC: 2.7.7.6
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Transcription initiation factor TFIID subunit 2J [auth DB]1,199Homo sapiensMutation(s): 0 
Gene Names: TAF2, CIF150, TAF2B
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Transcription initiation factor IIE subunit betaK [auth EB]291Homo sapiensMutation(s): 0 
Gene Names: GTF2E2, TF2E2
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General transcription factor IIF subunit 2L [auth FB]249Homo sapiensMutation(s): 0 
Gene Names: GTF2F2, RAP30
EC: 3.6.4.12
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General transcription factor IIH subunit 1M [auth HB]548Homo sapiensMutation(s): 0 
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Histone H4N [auth NB],
CC [auth NF]		103Xenopus laevisMutation(s): 0 
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DNA-directed RNA polymerase subunit betaO [auth PB]1,174Sus scrofaMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 16
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General transcription factor IIH subunit 4P [auth HC]462Homo sapiensMutation(s): 0 
Gene Names: GTF2H4
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DNA-directed RNA polymerase II subunit RPB3Q [auth PC]275Sus scrofaMutation(s): 0 
Gene Names: POLR2C
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DNA-directed RNA polymerase II subunit ER [auth PE]210Sus scrofaMutation(s): 0 
Gene Names: POLR2E
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DNA-directed RNA polymerase II subunit FS [auth PF]127Sus scrofaMutation(s): 0 
Gene Names: POLR2F
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DNA-directed RNA polymerases I, II, and III subunit RPABC3T [auth PH]150Sus scrofaMutation(s): 0 
Gene Names: POLR2H
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DNA-directed RNA polymerase II subunit RPB9U [auth PI]125Sus scrofaMutation(s): 0 
Gene Names: POLR2I
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DNA-directed RNA polymerases I, II, and III subunit RPABC5V [auth PJ]67Sus scrofaMutation(s): 0 
Gene Names: POLR2L
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RNA_pol_L_2 domain-containing proteinW [auth PK]117Sus scrofaMutation(s): 0 
Gene Names: POLR2J
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Entity ID: 24
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RPB12X [auth PL]58Sus scrofaMutation(s): 0 
Gene Names: POLR2K
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TATA-box-binding proteinY [auth DP]339Homo sapiensMutation(s): 0 
Gene Names: TBP, GTF2D1, TF2D, TFIID
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Transcription initiation factor IIA subunit 1Z [auth DQ]376Homo sapiensMutation(s): 0 
Gene Names: GTF2A1, TF2A1
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Transcription initiation factor IIA subunit 2AA [auth DO]109Homo sapiensMutation(s): 0 
Gene Names: GTF2A2, TF2A2
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Transcription initiation factor TFIID subunit 3BA [auth Dc]929Homo sapiensMutation(s): 0 
Gene Names: TAF3
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Transcription initiation factor TFIID subunit 4JA [auth DD],
CA [auth Dd]		1,085Homo sapiensMutation(s): 0 
Gene Names: TAF4, TAF2C, TAF2C1, TAF4A, TAFII130, TAFII135
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Entity ID: 30
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Transcription initiation factor TFIID subunit 5LA [auth DE],
DA [auth De]		800Homo sapiensMutation(s): 0 
Gene Names: TAF5, TAF2D
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Entity ID: 31
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Transcription initiation factor TFIID subunit 6MA [auth DF],
EA [auth Df]		677Homo sapiensMutation(s): 0 
Gene Names: TAF6, TAF2E, TAFII70
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Entity ID: 32
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Transcription initiation factor TFIID subunit 9PA [auth DI],
FA [auth Di]		264Homo sapiensMutation(s): 0 
Gene Names: TAF9, TAF2G, TAFII31
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 10QA [auth DJ],
GA [auth Dj]		218Homo sapiensMutation(s): 0 
Gene Names: TAF10, TAF2A, TAF2H, TAFII30
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Entity ID: 34
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Transcription initiation factor TFIID subunit 11HA [auth Dk]211Homo sapiensMutation(s): 0 
Gene Names: TAF11, TAF2I, PRO2134
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Transcription initiation factor TFIID subunit 12RA [auth DL],
IA [auth Dl]		161Homo sapiensMutation(s): 0 
Gene Names: TAF12, TAF15, TAF2J, TAFII20
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Transcription initiation factor TFIID subunit 13KA [auth Dm]124Homo sapiensMutation(s): 0 
Gene Names: TAF13, TAF2K, TAFII18
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Transcription initiation factor TFIID subunit 7NA [auth DG]349Homo sapiensMutation(s): 0 
Gene Names: TAF7, TAF2F, TAFII55
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Entity ID: 38
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Transcription initiation factor TFIID subunit 8OA [auth DH]310Homo sapiensMutation(s): 0 
Gene Names: TAF8, TAFII43, TBN
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Entity ID: 39
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CDK-activating kinase assembly factor MAT1SA [auth HD]309Homo sapiensMutation(s): 0 
Gene Names: MNAT1, CAP35, MAT1, RNF66
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General transcription factor IIH subunit 3TA [auth HE]308Homo sapiensMutation(s): 0 
Gene Names: GTF2H3
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIH subunit 2UA [auth HG]395Homo sapiensMutation(s): 0 
Gene Names: GTF2H2, BTF2P44
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH helicase subunit XPBVA [auth HH]782Homo sapiensMutation(s): 0 
Gene Names: ERCC3, XPB, XPBC
EC: 3.6.4.12
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIH subunit 5WA [auth HF]71Homo sapiensMutation(s): 0 
Gene Names: GTF2H5, C6orf175, TTDA
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclin-dependent kinase 7XA [auth HI]346Homo sapiensMutation(s): 1 
Gene Names: CDK7, CAK, CAK1, CDKN7, MO15, STK1
EC: 2.7.11.22 (UniProt), 2.7.11.23 (UniProt)
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclin-HYA [auth HJ]323Homo sapiensMutation(s): 0 
Gene Names: CCNH
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Entity ID: 46
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DNA-directed RNA polymerase II subunit RPB4ZA [auth PD]142Sus scrofaMutation(s): 0 
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7AB [auth PG]172Sus scrofaMutation(s): 0 
Gene Names: POLR2G
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 7BB [auth g]233Homo sapiensMutation(s): 0 
Gene Names: MED7, ARC34, CRSP9
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Entity ID: 49
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Mediator of RNA polymerase II transcription subunit 10CB [auth j]135Homo sapiensMutation(s): 0 
Gene Names: MED10, L6, TRG17, TRG20
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 14DB [auth n]1,454Homo sapiensMutation(s): 0 
Gene Names: MED14, ARC150, CRSP2, CXorf4, DRIP150, EXLM1, RGR1, TRAP170
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 19EB [auth s]244Homo sapiensMutation(s): 0 
Gene Names: MED19, LCMR1
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Entity ID: 52
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Mediator of RNA polymerase II transcription subunit 21FB [auth u]144Homo sapiensMutation(s): 0 
Gene Names: MED21, SRB7, SURB7
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Entity ID: 53
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Mediator of RNA polymerase II transcription subunit 1GB [auth a]1,581Homo sapiensMutation(s): 0 
Gene Names: 
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 4HB [auth d]270Homo sapiensMutation(s): 0 
Gene Names: MED4, ARC36, DRIP36, VDRIP, HSPC126
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 6IB [auth f]246Homo sapiensMutation(s): 0 
Gene Names: MED6, ARC33
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Entity ID: 56
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Mediator of RNA polymerase II transcription subunit 9JB [auth i]146Homo sapiensMutation(s): 0 
Gene Names: MED9, MED25
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Entity ID: 57
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Mediator of RNA polymerase II transcription subunit 31KB [auth m]131Homo sapiensMutation(s): 0 
Gene Names: MED31, SOH1, CGI-125
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Entity ID: 58
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Mediator of RNA polymerase II transcription subunit 17LB [auth q]651Homo sapiensMutation(s): 0 
Gene Names: MED17, ARC77, CRSP6, DRIP77, DRIP80, TRAP80
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Entity ID: 59
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Mediator of RNA polymerase II transcription subunit 26MB [auth z]600Homo sapiensMutation(s): 0 
Gene Names: MED26, ARC70, CRSP7
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Entity ID: 60
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Mediator of RNA polymerase II transcription subunit 29NB [auth b]200Homo sapiensMutation(s): 0 
Gene Names: MED29, IXL
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Entity ID: 61
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Mediator of RNA polymerase II transcription subunit 27OB [auth c]311Homo sapiensMutation(s): 0 
Gene Names: MED27, CRSP34, CRSP8
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Entity ID: 62
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Mediator of RNA polymerase II transcription subunit 28PB [auth e]178Homo sapiensMutation(s): 0 
Gene Names: MED28, EG1, FKSG20
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Entity ID: 63
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Mediator of RNA polymerase II transcription subunit 30QB [auth l]178Homo sapiensMutation(s): 0 
Gene Names: MED30, THRAP6, TRAP25
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Entity ID: 64
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Mediator of RNA polymerase II transcription subunit 15RB [auth o]788Homo sapiensMutation(s): 0 
Gene Names: MED15, ARC105, CTG7A, PCQAP, TIG1, TNRC7
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Entity ID: 65
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Isoform 2 of Mediator of RNA polymerase II transcription subunit 8SB [auth h]268Homo sapiensMutation(s): 0 
Gene Names: MED8
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Entity ID: 66
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Mediator of RNA polymerase II transcription subunit 11TB [auth k]117Homo sapiensMutation(s): 0 
Gene Names: MED11, HSPC296
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Entity ID: 67
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Mediator of RNA polymerase II transcription subunit 18UB [auth r]208Homo sapiensMutation(s): 0 
Gene Names: MED18
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Entity ID: 68
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Mediator of RNA polymerase II transcription subunit 20VB [auth t]212Homo sapiensMutation(s): 0 
Gene Names: MED20, TRFP
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Entity ID: 69
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Mediator of RNA polymerase II transcription subunit 22WB [auth v]200Homo sapiensMutation(s): 0 
Gene Names: MED22, SURF5
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Entity ID: 70
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Isoform 2 of Mediator of RNA polymerase II transcription subunit 16XB [auth p]841Homo sapiensMutation(s): 0 
Gene Names: MED16, DRIP92, THRAP5
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