5IYA

Human core-PIC in the closed state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Near-atomic resolution visualization of human transcription promoter opening.

He, Y.Yan, C.Fang, J.Inouye, C.Tjian, R.Ivanov, I.Nogales, E.

(2016) Nature 533: 359-365

  • DOI: 10.1038/nature17970
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • In eukaryotic transcription initiation, a large multi-subunit pre-initiation complex (PIC) that assembles at the core promoter is required for the opening of the duplex DNA and identification of the start site for transcription by RNA polymerase II. ...

    In eukaryotic transcription initiation, a large multi-subunit pre-initiation complex (PIC) that assembles at the core promoter is required for the opening of the duplex DNA and identification of the start site for transcription by RNA polymerase II. Here we use cryo-electron microscropy (cryo-EM) to determine near-atomic resolution structures of the human PIC in a closed state (engaged with duplex DNA), an open state (engaged with a transcription bubble), and an initially transcribing complex (containing six base pairs of DNA-RNA hybrid). Our studies provide structures for previously uncharacterized components of the PIC, such as TFIIE and TFIIH, and segments of TFIIA, TFIIB and TFIIF. Comparison of the different structures reveals the sequential conformational changes that accompany the transition from each state to the next throughout the transcription initiation process. This analysis illustrates the key role of TFIIB in transcription bubble stabilization and provides strong structural support for a translocase activity of XPB.


    Organizational Affiliation

    Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB1A1970Homo sapiensMutation(s): 0 
Gene Names: POLR2APOLR2
EC: 2.7.7.6 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
Find proteins for P24928 (Homo sapiens)
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PHAROS  P24928
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB2B1174Homo sapiensMutation(s): 0 
Gene Names: POLR2B
EC: 2.7.7.6
Find proteins for P30876 (Homo sapiens)
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PHAROS  P30876
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB3C275Homo sapiensMutation(s): 0 
Gene Names: POLR2CA-152E5.7
Find proteins for P19387 (Homo sapiens)
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PHAROS  P19387
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB5E210Homo sapiensMutation(s): 0 
Gene Names: POLR2E
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PHAROS  P19388
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB7G172Homo sapiensMutation(s): 0 
Gene Names: POLR2GRPB7
Find proteins for P62487 (Homo sapiens)
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PHAROS  P62487
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB8H150Homo sapiensMutation(s): 0 
Gene Names: POLR2H
Find proteins for P52434 (Homo sapiens)
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PHAROS  P52434
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB10J67Homo sapiensMutation(s): 0 
Gene Names: POLR2L
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PHAROS  P62875
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB11-aK117Homo sapiensMutation(s): 0 
Gene Names: POLR2JPOLR2J1
Find proteins for P52435 (Homo sapiens)
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Transcription initiation factor IIBM316Homo sapiensMutation(s): 0 
Gene Names: GTF2BTF2BTFIIB
EC: 2.3.1.48
Find proteins for Q00403 (Homo sapiens)
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PHAROS  Q00403
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Transcription initiation factor IIA subunit 1N376Homo sapiensMutation(s): 0 
Gene Names: GTF2A1TF2A1
Find proteins for P52655 (Homo sapiens)
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PHAROS  P52655
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
TATA-box-binding proteinP339Homo sapiensMutation(s): 0 
Gene Names: TBPGTF2D1TF2DTFIID
Find proteins for P20226 (Homo sapiens)
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PHAROS  P20226
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Transcription elongation factor A protein 1U301Homo sapiensMutation(s): 0 
Gene Names: TCEA1GTF2STFIIS
Find proteins for P23193 (Homo sapiens)
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PHAROS  P23193
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB12L58Homo sapiensMutation(s): 0 
Gene Names: POLR2K
Find proteins for P53803 (Homo sapiens)
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PHAROS  P53803
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Transcription initiation factor IIA subunit 2O109Homo sapiensMutation(s): 0 
Gene Names: GTF2A2TF2A2
Find proteins for P52657 (Homo sapiens)
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PHAROS  P52657
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
General transcription factor IIE subunit 1Q439Homo sapiensMutation(s): 0 
Gene Names: GTF2E1TF2E1
Find proteins for P29083 (Homo sapiens)
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PHAROS  P29083
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Transcription initiation factor IIE subunit betaR291Homo sapiensMutation(s): 0 
Gene Names: GTF2E2TF2E2
Find proteins for P29084 (Homo sapiens)
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PHAROS  P29084
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
General transcription factor IIF subunit 1S517Homo sapiensMutation(s): 0 
Gene Names: GTF2F1RAP74
Find proteins for P35269 (Homo sapiens)
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PHAROS  P35269
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
General transcription factor IIF subunit 2T249Homo sapiensMutation(s): 0 
Gene Names: GTF2F2RAP30
EC: 3.6.4.12
Find proteins for P13984 (Homo sapiens)
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PHAROS  P13984
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB4D142Homo sapiensMutation(s): 0 
Gene Names: POLR2D
Find proteins for O15514 (Homo sapiens)
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PHAROS  O15514
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB6F127Homo sapiensMutation(s): 0 
Gene Names: POLR2FPOLRF
Find proteins for P61218 (Homo sapiens)
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PHAROS  P61218
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB9I125Homo sapiensMutation(s): 0 
Gene Names: POLR2I
Find proteins for P36954 (Homo sapiens)
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PHAROS  P36954
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  • Reference Sequence

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Entity ID: 22
MoleculeChainsLengthOrganism
SCP-XX59Homo sapiens

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Entity ID: 23
MoleculeChainsLengthOrganism
SCP-YY59Homo sapiens
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
A, B, C, I, J, L, M, Q, U
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM63072
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM110387
National Science Foundation (NSF, United States)United StatesMCB-1149521
Howard Hughes Medical Institute (HHMI)United States--

Revision History 

  • Version 1.0: 2016-05-18
    Type: Initial release
  • Version 1.1: 2016-05-25
    Changes: Database references
  • Version 1.2: 2016-06-22
    Changes: Database references
  • Version 1.3: 2017-09-13
    Changes: Author supporting evidence, Database references
  • Version 1.4: 2019-11-20
    Changes: Author supporting evidence