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: https://doi.org/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. 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

    Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIBC [auth BA]316Homo sapiensMutation(s): 0 
Gene Names: GTF2BTF2BTFIIB
EC: 2.3.1.48
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GTEx:  ENSG00000137947 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 1D [auth DA]1,872Homo sapiensMutation(s): 0 
Gene Names: TAF1BA2RCCG1CCGSTAF2A
EC: 2.3.1.48 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
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GTEx:  ENSG00000147133 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIE subunit 1E [auth EA]439Homo sapiensMutation(s): 0 
Gene Names: GTF2E1TF2E1
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GTEx:  ENSG00000153767 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIF subunit 1F [auth FA]517Homo sapiensMutation(s): 0 
Gene Names: GTF2F1RAP74
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GTEx:  ENSG00000125651 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH helicase subunit XPDG [auth HA]760Homo sapiensMutation(s): 0 
Gene Names: ERCC2XPDXPDC
EC: 3.6.4.12
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GTEx:  ENSG00000104884 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3BC [auth NE],
H [auth NA]
136Xenopus laevisMutation(s): 0 
Gene Names: XELAEV_18002543mg
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunitI [auth PA]1,970Sus scrofaMutation(s): 0 
Gene Names: POLR2A
EC: 2.7.7.6
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 2J [auth DB]1,199Homo sapiensMutation(s): 0 
Gene Names: TAF2CIF150TAF2B
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIE subunit betaK [auth EB]291Homo sapiensMutation(s): 0 
Gene Names: GTF2E2TF2E2
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GTEx:  ENSG00000197265 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIF subunit 2L [auth FB]249Homo sapiensMutation(s): 0 
Gene Names: GTF2F2RAP30
EC: 3.6.4.12
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GTEx:  ENSG00000188342 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIH subunit 1M [auth HB]548Homo sapiensMutation(s): 0 
Gene Names: GTF2H1BTF2
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GTEx:  ENSG00000110768 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4CC [auth NF],
N [auth NB]
103Xenopus laevisMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
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
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIH subunit 4P [auth HC]462Homo sapiensMutation(s): 0 
Gene Names: GTF2H4
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GTEx:  ENSG00000213780 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3Q [auth PC]275Sus scrofaMutation(s): 0 
Gene Names: POLR2C
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit ER [auth PE]210Sus scrofaMutation(s): 0 
Gene Names: POLR2E
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit FS [auth PF]127Sus scrofaMutation(s): 0 
Gene Names: POLR2F
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3T [auth PH]150Sus scrofaMutation(s): 0 
Gene Names: POLR2H
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9U [auth PI]125Sus scrofaMutation(s): 0 
Gene Names: POLR2I
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC5V [auth PJ]67Sus scrofaMutation(s): 0 
Gene Names: POLR2L
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
RNA_pol_L_2 domain-containing proteinW [auth PK]117Sus scrofaMutation(s): 0 
Gene Names: POLR2J
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
RPB12X [auth PL]58Sus scrofaMutation(s): 0 
Gene Names: POLR2K
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
TATA-box-binding proteinY [auth DP]339Homo sapiensMutation(s): 0 
Gene Names: TBPGTF2D1TF2DTFIID
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GTEx:  ENSG00000112592 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIA subunit 1Z [auth DQ]376Homo sapiensMutation(s): 0 
Gene Names: GTF2A1TF2A1
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GTEx:  ENSG00000165417 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIA subunit 2AA [auth DO]109Homo sapiensMutation(s): 0 
Gene Names: GTF2A2TF2A2
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GTEx:  ENSG00000140307 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 3BA [auth Dc]929Homo sapiensMutation(s): 0 
Gene Names: TAF3
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GTEx:  ENSG00000165632 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 4CA [auth Dd],
JA [auth DD]
1,085Homo sapiensMutation(s): 0 
Gene Names: TAF4TAF2CTAF2C1TAF4ATAFII130TAFII135
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GTEx:  ENSG00000130699 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 5DA [auth De],
LA [auth DE]
800Homo sapiensMutation(s): 0 
Gene Names: TAF5TAF2D
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GTEx:  ENSG00000148835 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 6EA [auth Df],
MA [auth DF]
677Homo sapiensMutation(s): 0 
Gene Names: TAF6TAF2ETAFII70
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GTEx:  ENSG00000106290 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 9FA [auth Di],
PA [auth DI]
264Homo sapiensMutation(s): 0 
Gene Names: TAF9TAF2GTAFII31
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GTEx:  ENSG00000273841 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 10GA [auth Dj],
QA [auth DJ]
218Homo sapiensMutation(s): 0 
Gene Names: TAF10TAF2ATAF2HTAFII30
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GTEx:  ENSG00000166337 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 11HA [auth Dk]211Homo sapiensMutation(s): 0 
Gene Names: TAF11TAF2IPRO2134
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GTEx:  ENSG00000064995 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 12IA [auth Dl],
RA [auth DL]
161Homo sapiensMutation(s): 0 
Gene Names: TAF12TAF15TAF2JTAFII20
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GTEx:  ENSG00000120656 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 13KA [auth Dm]124Homo sapiensMutation(s): 0 
Gene Names: TAF13TAF2KTAFII18
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GTEx:  ENSG00000197780 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 7NA [auth DG]349Homo sapiensMutation(s): 0 
Gene Names: TAF7TAF2FTAFII55
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GTEx:  ENSG00000178913 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 8OA [auth DH]310Homo sapiensMutation(s): 0 
Gene Names: TAF8TAFII43TBN
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GTEx:  ENSG00000137413 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
CDK-activating kinase assembly factor MAT1SA [auth HD]309Homo sapiensMutation(s): 0 
Gene Names: MNAT1CAP35MAT1RNF66
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GTEx:  ENSG00000020426 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIH subunit 3TA [auth HE]308Homo sapiensMutation(s): 0 
Gene Names: GTF2H3
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GTEx:  ENSG00000111358 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIH subunit 2UA [auth HG]395Homo sapiensMutation(s): 0 
Gene Names: GTF2H2BTF2P44
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GTEx:  ENSG00000145736 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH helicase subunit XPBVA [auth HH]782Homo sapiensMutation(s): 0 
Gene Names: ERCC3XPBXPBC
EC: 3.6.4.12
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GTEx:  ENSG00000163161 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIH subunit 5WA [auth HF]71Homo sapiensMutation(s): 0 
Gene Names: GTF2H5C6orf175TTDA
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GTEx:  ENSG00000272047 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-dependent kinase 7XA [auth HI]346Homo sapiensMutation(s): 1 
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GTEx:  ENSG00000134058 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-HYA [auth HJ]323Homo sapiensMutation(s): 0 
Gene Names: CCNH
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GTEx:  ENSG00000134480 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB4ZA [auth PD]142Sus scrofaMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7AB [auth PG]172Sus scrofaMutation(s): 0 
Gene Names: POLR2G
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 7BB [auth g]233Homo sapiensMutation(s): 0 
Gene Names: MED7
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GTEx:  ENSG00000155868 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 10CB [auth j]135Homo sapiensMutation(s): 0 
Gene Names: MED10
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GTEx:  ENSG00000133398 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 14DB [auth n]1,454Homo sapiensMutation(s): 0 
Gene Names: MED14
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GTEx:  ENSG00000180182 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 19EB [auth s]244Homo sapiensMutation(s): 0 
Gene Names: MED19
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GTEx:  ENSG00000156603 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 21FB [auth u]144Homo sapiensMutation(s): 0 
Gene Names: MED21
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GTEx:  ENSG00000152944 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 1GB [auth a]1,581Homo sapiensMutation(s): 0 
Gene Names: MED1
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GTEx:  ENSG00000125686 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 4HB [auth d]270Homo sapiensMutation(s): 0 
Gene Names: MED4
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Find proteins for Q9NPJ6 (Homo sapiens)
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GTEx:  ENSG00000136146 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 6IB [auth f]246Homo sapiensMutation(s): 0 
Gene Names: MED6
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GTEx:  ENSG00000133997 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 9JB [auth i]146Homo sapiensMutation(s): 0 
Gene Names: MED9
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GTEx:  ENSG00000141026 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 31KB [auth m]131Homo sapiensMutation(s): 0 
Gene Names: MED31
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Find proteins for Q9Y3C7 (Homo sapiens)
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GTEx:  ENSG00000108590 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 17LB [auth q]651Homo sapiensMutation(s): 0 
Gene Names: MED17
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Find proteins for Q9NVC6 (Homo sapiens)
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GTEx:  ENSG00000042429 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 26MB [auth z]600Homo sapiensMutation(s): 0 
Gene Names: MED26
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Find proteins for O95402 (Homo sapiens)
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GTEx:  ENSG00000105085 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 29NB [auth b]200Homo sapiensMutation(s): 0 
Gene Names: MED29
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GTEx:  ENSG00000063322 
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