6O9M

Structure of the human apo TFIIH


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Transcription preinitiation complex structure and dynamics provide insight into genetic diseases.

Yan, C.Dodd, T.He, Y.Tainer, J.A.Tsutakawa, S.E.Ivanov, I.

(2019) Nat Struct Mol Biol 26: 397-406

  • DOI: 10.1038/s41594-019-0220-3
  • Primary Citation of Related Structures:  
    6O9M, 6O9L

  • PubMed Abstract: 
  • Transcription preinitiation complexes (PICs) are vital assemblies whose function underlies the expression of protein-encoding genes. Cryo-EM advances have begun to uncover their structural organization. Nevertheless, functional analyses are hindered ...

    Transcription preinitiation complexes (PICs) are vital assemblies whose function underlies the expression of protein-encoding genes. Cryo-EM advances have begun to uncover their structural organization. Nevertheless, functional analyses are hindered by incompletely modeled regions. Here we integrate all available cryo-EM data to build a practically complete human PIC structural model. This enables simulations that reveal the assembly's global motions, define PIC partitioning into dynamic communities and delineate how structural modules function together to remodel DNA. We identify key TFIIE-p62 interactions that link core-PIC to TFIIH. p62 rigging interlaces p34, p44 and XPD while capping the DNA-binding and ATP-binding sites of XPD. PIC kinks and locks substrate DNA, creating negative supercoiling within the Pol II cleft to facilitate promoter opening. Mapping disease mutations associated with xeroderma pigmentosum, trichothiodystrophy and Cockayne syndrome onto defined communities reveals clustering into three mechanistic classes that affect TFIIH helicase functions, protein interactions and interface dynamics.


    Related Citations: 
    • The cryo-electron microscopy structure of human transcription factor IIH.
      Greber, B.J., Nguyen, T.H.D., Fang, J., Afonine, P.V., Adams, P.D., Nogales, E.
      (2017) Nature 549: 414

    Organizational Affiliation

    Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA. iivanov@gsu.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TFIIH basal transcription factor complex helicase XPD subunit0760Homo sapiensMutation(s): 0 
Gene Names: ERCC2XPDXPDC
EC: 3.6.4.12
Find proteins for P18074 (Homo sapiens)
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PHAROS  P18074
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIH subunit 11548Homo sapiensMutation(s): 0 
Gene Names: GTF2H1BTF2
Find proteins for P32780 (Homo sapiens)
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PHAROS  P32780
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIH subunit 4, p522462Homo sapiensMutation(s): 0 
Gene Names: GTF2H4
Find proteins for Q92759 (Homo sapiens)
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PHAROS  Q92759
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
CDK-activating kinase assembly factor MAT13309Homo sapiensMutation(s): 0 
Gene Names: MNAT1CAP35MAT1RNF66
Find proteins for P51948 (Homo sapiens)
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PHAROS  P51948
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIH subunit 34308Homo sapiensMutation(s): 0 
Gene Names: GTF2H3
Find proteins for Q13889 (Homo sapiens)
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PHAROS  Q13889
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIH subunit 5571Homo sapiensMutation(s): 0 
Gene Names: GTF2H5C6orf175TTDA
Find proteins for Q6ZYL4 (Homo sapiens)
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PHAROS  Q6ZYL4
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIH subunit 26395Homo sapiensMutation(s): 0 
Gene Names: GTF2H2BTF2P44
Find proteins for Q13888 (Homo sapiens)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
TFIIH basal transcription factor complex helicase XPB subunit7782Homo sapiensMutation(s): 0 
Gene Names: ERCC3XPBXPBC
EC: 3.6.4.12
Find proteins for P19447 (Homo sapiens)
Explore P19447 
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PHAROS  P19447
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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 StatesGM110387

Revision History 

  • Version 1.0: 2019-05-29
    Type: Initial release
  • Version 1.1: 2019-06-05
    Changes: Data collection, Database references
  • Version 1.2: 2019-06-19
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence