6O9L

Human holo-PIC in the closed state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.2 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: 
    • Structure of promoter-bound TFIID and model of human pre-initiation complex assembly.
      Louder, R.K.,He, Y.,Lopez-Blanco, J.R.,Fang, J.,Chacon, P.,Nogales, E.
      (2016) Nature 531: 604


    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
DNA-directed RNA polymerase II subunit RPB1
A
1970Homo sapiensMutation(s): 0 
Gene Names: POLR2A (POLR2)
EC: 2.7.7.6
Find proteins for P24928 (Homo sapiens)
Go to Gene View: POLR2A
Go to UniProtKB:  P24928
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB2
B
1174Homo sapiensMutation(s): 0 
Gene Names: POLR2B
EC: 2.7.7.6
Find proteins for P30876 (Homo sapiens)
Go to Gene View: POLR2B
Go to UniProtKB:  P30876
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB3
C
275Homo sapiensMutation(s): 0 
Gene Names: POLR2C
Find proteins for P19387 (Homo sapiens)
Go to Gene View: POLR2C
Go to UniProtKB:  P19387
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB4
D
142Homo sapiensMutation(s): 0 
Gene Names: POLR2D
Find proteins for O15514 (Homo sapiens)
Go to Gene View: POLR2D
Go to UniProtKB:  O15514
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB5
E
210Homo sapiensMutation(s): 0 
Gene Names: POLR2E
Find proteins for P19388 (Homo sapiens)
Go to Gene View: POLR2E
Go to UniProtKB:  P19388
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC2
F
127Homo sapiensMutation(s): 0 
Gene Names: POLR2F (POLRF)
Find proteins for P61218 (Homo sapiens)
Go to Gene View: POLR2F
Go to UniProtKB:  P61218
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB7
G
172Homo sapiensMutation(s): 0 
Gene Names: POLR2G (RPB7)
Find proteins for P62487 (Homo sapiens)
Go to Gene View: POLR2G
Go to UniProtKB:  P62487
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC3
H
150Homo sapiensMutation(s): 0 
Gene Names: POLR2H
Find proteins for P52434 (Homo sapiens)
Go to Gene View: POLR2H
Go to UniProtKB:  P52434
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB9
I
125Homo sapiensMutation(s): 0 
Gene Names: POLR2I
Find proteins for P36954 (Homo sapiens)
Go to Gene View: POLR2I
Go to UniProtKB:  P36954
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC5
J
67Homo sapiensMutation(s): 0 
Gene Names: POLR2L
Find proteins for P62875 (Homo sapiens)
Go to Gene View: POLR2L
Go to UniProtKB:  P62875
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB11-a
K
117Homo sapiensMutation(s): 0 
Gene Names: POLR2J (POLR2J1)
Find proteins for P52435 (Homo sapiens)
Go to Gene View: POLR2J
Go to UniProtKB:  P52435
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC4
L
58Homo sapiensMutation(s): 0 
Gene Names: POLR2K
Find proteins for P53803 (Homo sapiens)
Go to Gene View: POLR2K
Go to UniProtKB:  P53803
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Transcription initiation factor IIB
M
316Homo sapiensMutation(s): 0 
Gene Names: GTF2B (TF2B, TFIIB)
EC: 2.3.1.48
Find proteins for Q00403 (Homo sapiens)
Go to Gene View: GTF2B
Go to UniProtKB:  Q00403
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Transcription initiation factor IIA subunit 1
N
376Homo sapiensMutation(s): 0 
Gene Names: GTF2A1 (TF2A1)
Find proteins for P52655 (Homo sapiens)
Go to Gene View: GTF2A1
Go to UniProtKB:  P52655
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Transcription initiation factor IIA subunit 2
O
109Homo sapiensMutation(s): 0 
Gene Names: GTF2A2 (TF2A2)
Find proteins for P52657 (Homo sapiens)
Go to Gene View: GTF2A2
Go to UniProtKB:  P52657
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
TATA-box-binding protein
P
339Homo sapiensMutation(s): 0 
Gene Names: TBP (GTF2D1, TF2D, TFIID)
Find proteins for P20226 (Homo sapiens)
Go to Gene View: TBP
Go to UniProtKB:  P20226
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
General transcription factor IIE subunit 1
Q
439Homo sapiensMutation(s): 0 
Gene Names: GTF2E1 (TF2E1)
Find proteins for P29083 (Homo sapiens)
Go to Gene View: GTF2E1
Go to UniProtKB:  P29083
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Transcription initiation factor IIE subunit beta
R
291Homo sapiensMutation(s): 0 
Gene Names: GTF2E2 (TF2E2)
Find proteins for P29084 (Homo sapiens)
Go to Gene View: GTF2E2
Go to UniProtKB:  P29084
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
General transcription factor IIF subunit 1
S
517Homo sapiensMutation(s): 0 
Gene Names: GTF2F1 (RAP74)
Find proteins for P35269 (Homo sapiens)
Go to Gene View: GTF2F1
Go to UniProtKB:  P35269
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
General transcription factor IIF subunit 2
T
249Homo sapiensMutation(s): 0 
Gene Names: GTF2F2 (RAP30)
EC: 3.6.4.12
Find proteins for P13984 (Homo sapiens)
Go to Gene View: GTF2F2
Go to UniProtKB:  P13984
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Transcription elongation factor A protein 1
U
301Homo sapiensMutation(s): 0 
Gene Names: TCEA1 (GTF2S, TFIIS)
Find proteins for P23193 (Homo sapiens)
Go to Gene View: TCEA1
Go to UniProtKB:  P23193
Entity ID: 22
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: 23
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: 24
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: 25
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: 26
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: 27
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: 28
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: 29
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
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
Cyclin-dependent kinase 7
8
346Homo sapiensMutation(s): 0 
Gene Names: CDK7 (CAK, CAK1, CDKN7, MO15, STK1)
EC: 2.7.11.22, 2.7.11.23
Find proteins for P50613 (Homo sapiens)
Go to Gene View: CDK7
Go to UniProtKB:  P50613
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
Cyclin-H
9
323Homo sapiensMutation(s): 0 
Gene Names: CCNH
Find proteins for P51946 (Homo sapiens)
Go to Gene View: CCNH
Go to UniProtKB:  P51946
Entity ID: 32
MoleculeChainsLengthOrganism
DNA (65-MER)X65synthetic construct
Entity ID: 33
MoleculeChainsLengthOrganism
DNA (65-MER)Y65synthetic construct
Small Molecules
Ligands 3 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, A, B, C, I, J, L, M, Q, U
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.2 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