5IVW

Human core TFIIH bound to DNA within the PIC

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 10.0 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: https://doi.org/10.1038/nature17970
  • Primary Citation of Related Structures:  
    5IVW, 5IY6, 5IY7, 5IY8, 5IY9, 5IYA, 5IYB, 5IYC, 5IYD

  • 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. 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) ...

    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 LengthOrganismDetailsImage
TFIIH basal transcription factor complex helicase XPB subunitA [auth V]782Homo sapiensMutation(s): 0 
Gene Names: ERCC3, XPB, XPBC
EC: 3.6.4.12
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Find proteins for P19447 (Homo sapiens)
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PHAROS:  P19447
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UniProt GroupP19447
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
TFIIH basal transcription factor complex helicase XPD subunitB [auth W]760Homo sapiensMutation(s): 0 
Gene Names: ERCC2, XPD, XPDC
EC: 3.6.4.12
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Find proteins for P18074 (Homo sapiens)
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UniProt GroupP18074
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIH subunit 2C [auth 0]395Homo sapiensMutation(s): 0 
Gene Names: GTF2H2, BTF2P44
UniProt
Find proteins for Q13888 (Homo sapiens)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIH subunit 5D [auth 1]71Homo sapiensMutation(s): 0 
Gene Names: GTF2H5, C6orf175, TTDA
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PHAROS:  Q6ZYL4
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIH subunit 4E [auth 2]462Homo sapiensMutation(s): 0 
Gene Names: GTF2H4
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PHAROS:  Q92759
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIH subunit 3F [auth 3]308Homo sapiensMutation(s): 0 
Gene Names: GTF2H3
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Entity ID: 7
MoleculeChainsLengthOrganismImage
scp-XG [auth X]19Homo sapiens
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Entity ID: 8
MoleculeChainsLengthOrganismImage
scp-YH [auth Y]20Homo sapiens
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 10.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.4beta

Structure Validation

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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  (Full details and data files)

  • 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