6O9M

Structure of the human apo TFIIH


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 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:  

  • 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

    Department of Chemistry, Georgia State University, Atlanta, GA, USA.,Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA.,Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.,Department of Molecular and Cellular Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA.,Department of Chemistry, Georgia State University, Atlanta, GA, USA. iivanov@gsu.edu.,Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA.,Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA. iivanov@gsu.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TFIIH basal transcription factor complex helicase XPD subunit
0
760Homo sapiensMutation(s): 0 
Gene Names: ERCC2 (XPD, XPDC)
EC: 3.6.4.12
Find proteins for P18074 (Homo sapiens)
Go to Gene View: ERCC2
Go to UniProtKB:  P18074
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
General transcription factor IIH subunit 1
1
548Homo sapiensMutation(s): 0 
Gene Names: GTF2H1 (BTF2)
Find proteins for P32780 (Homo sapiens)
Go to Gene View: GTF2H1
Go to UniProtKB:  P32780
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
General transcription factor IIH subunit 4, p52
2
462Homo sapiensMutation(s): 0 
Gene Names: GTF2H4
Find proteins for Q92759 (Homo sapiens)
Go to Gene View: GTF2H4
Go to UniProtKB:  Q92759
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
CDK-activating kinase assembly factor MAT1
3
309Homo sapiensMutation(s): 0 
Gene Names: MNAT1 (CAP35, MAT1, RNF66)
Find proteins for P51948 (Homo sapiens)
Go to Gene View: MNAT1
Go to UniProtKB:  P51948
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
General transcription factor IIH subunit 3
4
308Homo sapiensMutation(s): 0 
Gene Names: GTF2H3
Find proteins for Q13889 (Homo sapiens)
Go to Gene View: GTF2H3
Go to UniProtKB:  Q13889
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
General transcription factor IIH subunit 5
5
71Homo sapiensMutation(s): 0 
Gene Names: GTF2H5 (C6orf175, TTDA)
Find proteins for Q6ZYL4 (Homo sapiens)
Go to Gene View: GTF2H5
Go to UniProtKB:  Q6ZYL4
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
General transcription factor IIH subunit 2
6
395Homo sapiensMutation(s): 0 
Gene Names: GTF2H2 (BTF2P44)
Find proteins for Q13888 (Homo sapiens)
Go to Gene View: GTF2H2
Go to UniProtKB:  Q13888
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
TFIIH basal transcription factor complex helicase XPB subunit
7
782Homo sapiensMutation(s): 0 
Gene Names: ERCC3 (XPB, XPBC)
EC: 3.6.4.12
Find proteins for P19447 (Homo sapiens)
Go to Gene View: ERCC3
Go to UniProtKB:  P19447
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
0
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
3, 4, 6
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM110387

Revision History 

  • Version 1.0: 2019-05-29
    Type: Initial release
  • Version 1.1: 2019-06-05
    Type: Data collection, Database references
  • Version 1.2: 2019-06-19
    Type: Data collection, Database references