Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 8-mer - A1B1C1D1E1F1G1H1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: homology, homology

Macromolecule Content

• Total Structure Weight: 414.36 kDa 
• Atom Count: 25785 
• Residue Count: 3228 
• Unique protein chains: 8

6O9M

Structure of the human apo TFIIH

• DOI: 10.2210/pdb6O9M/pdb
• EMDataResource: EMD-3802

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2019-03-14 Released: 2019-05-29 
• Deposition Author(s): Yan, C.L., Dodd, T., He, Y., Tainer, J.A., Tsutakawa, S.E., Ivanov, I.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

---

Experimental Data Snapshot

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

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

• PubMed: 31110295 
• 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 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. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TFIIH basal transcription factor complex helicase XPD subunit	0	760	Homo sapiens	Mutation(s): 0  Gene Names: ERCC2, XPD, XPDC EC: 3.6.4.12
Find proteins for P18074 (Homo sapiens) Explore P18074  Go to UniProtKB:  P18074
NIH Common Fund Data Resources
PHAROS  P18074 GTEx  ENSG00000104884

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
General transcription factor IIH subunit 1	1	548	Homo sapiens	Mutation(s): 0  Gene Names: GTF2H1, BTF2
Find proteins for P32780 (Homo sapiens) Explore P32780  Go to UniProtKB:  P32780
NIH Common Fund Data Resources
PHAROS  P32780 GTEx  ENSG00000110768

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
General transcription factor IIH subunit 4, p52	2	462	Homo sapiens	Mutation(s): 0  Gene Names: GTF2H4
Find proteins for Q92759 (Homo sapiens) Explore Q92759  Go to UniProtKB:  Q92759
NIH Common Fund Data Resources
PHAROS  Q92759 GTEx  ENSG00000213780

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
CDK-activating kinase assembly factor MAT1	3	309	Homo sapiens	Mutation(s): 0  Gene Names: MNAT1, CAP35, MAT1, RNF66
Find proteins for P51948 (Homo sapiens) Explore P51948  Go to UniProtKB:  P51948
NIH Common Fund Data Resources
PHAROS  P51948 GTEx  ENSG00000020426

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
General transcription factor IIH subunit 3	4	308	Homo sapiens	Mutation(s): 0  Gene Names: GTF2H3
Find proteins for Q13889 (Homo sapiens) Explore Q13889  Go to UniProtKB:  Q13889
NIH Common Fund Data Resources
PHAROS  Q13889 GTEx  ENSG00000111358

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
General transcription factor IIH subunit 5	5	71	Homo sapiens	Mutation(s): 0  Gene Names: GTF2H5, C6orf175, TTDA
Find proteins for Q6ZYL4 (Homo sapiens) Explore Q6ZYL4  Go to UniProtKB:  Q6ZYL4
NIH Common Fund Data Resources
PHAROS  Q6ZYL4 GTEx  ENSG00000272047

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
General transcription factor IIH subunit 2	6	395	Homo sapiens	Mutation(s): 0  Gene Names: GTF2H2, BTF2P44
Find proteins for Q13888 (Homo sapiens) Explore Q13888  Go to UniProtKB:  Q13888
NIH Common Fund Data Resources
PHAROS  Q13888 GTEx  ENSG00000145736

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
TFIIH basal transcription factor complex helicase XPB subunit	7	782	Homo sapiens	Mutation(s): 0  Gene Names: ERCC3, XPB, XPBC EC: 3.6.4.12
Find proteins for P19447 (Homo sapiens) Explore P19447  Go to UniProtKB:  P19447
NIH Common Fund Data Resources
PHAROS  P19447 GTEx  ENSG00000163161

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4	0	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-VKOJMFJBAC
ZN	3, 4, 6	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-03-14 
• Released Date: 2019-05-29 
Deposition Author(s): Yan, C.L., Dodd, T., He, Y., Tainer, J.A., Tsutakawa, S.E., Ivanov, I.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM110387

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