6O9L

Human holo-PIC in the closed state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.20 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
  • Structures With Same Primary Citation

  • 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

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



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB3C275Homo sapiensMutation(s): 0 
Gene Names: POLR2CA-152E5.7
Find proteins for P19387 (Homo sapiens)
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PHAROS  P19387
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB5E210Homo sapiensMutation(s): 0 
Gene Names: POLR2E
Find proteins for P19388 (Homo sapiens)
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PHAROS  P19388
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC2F127Homo sapiensMutation(s): 0 
Gene Names: POLR2FPOLRF
Find proteins for P61218 (Homo sapiens)
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PHAROS  P61218
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB7G172Homo sapiensMutation(s): 0 
Gene Names: POLR2GRPB7
Find proteins for P62487 (Homo sapiens)
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PHAROS  P62487
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC3H150Homo sapiensMutation(s): 0 
Gene Names: POLR2H
Find proteins for P52434 (Homo sapiens)
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PHAROS  P52434
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB9I125Homo sapiensMutation(s): 0 
Gene Names: POLR2I
Find proteins for P36954 (Homo sapiens)
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PHAROS  P36954
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Transcription initiation factor IIBM316Homo sapiensMutation(s): 0 
Gene Names: GTF2BTF2BTFIIB
EC: 2.3.1.48
Find proteins for Q00403 (Homo sapiens)
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PHAROS  Q00403
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
General transcription factor IIF subunit 1S517Homo sapiensMutation(s): 0 
Gene Names: GTF2F1RAP74
Find proteins for P35269 (Homo sapiens)
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PHAROS  P35269
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
General transcription factor IIF subunit 2T249Homo sapiensMutation(s): 0 
Gene Names: GTF2F2RAP30
EC: 3.6.4.12
Find proteins for P13984 (Homo sapiens)
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PHAROS  P13984
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Transcription elongation factor A protein 1U301Homo sapiensMutation(s): 0 
Gene Names: TCEA1GTF2STFIIS
Find proteins for P23193 (Homo sapiens)
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PHAROS  P23193
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
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: 30
MoleculeChainsSequence LengthOrganismDetails
Cyclin-dependent kinase 78346Homo sapiensMutation(s): 0 
Gene Names: CDK7CAKCAK1CDKN7MO15STK1
EC: 2.7.11.22 (PDB Primary Data), 2.7.11.23 (PDB Primary Data)
Find proteins for P50613 (Homo sapiens)
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PHAROS  P50613
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
Cyclin-H9323Homo sapiensMutation(s): 0 
Gene Names: CCNH
Find proteins for P51946 (Homo sapiens)
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PHAROS  P51946
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB1A1970Homo sapiensMutation(s): 0 
Gene Names: POLR2APOLR2
EC: 2.7.7.6 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
Find proteins for P24928 (Homo sapiens)
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PHAROS  P24928
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC5J67Homo sapiensMutation(s): 0 
Gene Names: POLR2L
Find proteins for P62875 (Homo sapiens)
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PHAROS  P62875
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB11-aK117Homo sapiensMutation(s): 0 
Gene Names: POLR2JPOLR2J1
Find proteins for P52435 (Homo sapiens)
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC4L58Homo sapiensMutation(s): 0 
Gene Names: POLR2K
Find proteins for P53803 (Homo sapiens)
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PHAROS  P53803
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Transcription initiation factor IIA subunit 1N376Homo sapiensMutation(s): 0 
Gene Names: GTF2A1TF2A1
Find proteins for P52655 (Homo sapiens)
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PHAROS  P52655
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Transcription initiation factor IIA subunit 2O109Homo sapiensMutation(s): 0 
Gene Names: GTF2A2TF2A2
Find proteins for P52657 (Homo sapiens)
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PHAROS  P52657
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
TATA-box-binding proteinP339Homo sapiensMutation(s): 0 
Gene Names: TBPGTF2D1TF2DTFIID
Find proteins for P20226 (Homo sapiens)
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PHAROS  P20226
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
General transcription factor IIE subunit 1Q439Homo sapiensMutation(s): 0 
Gene Names: GTF2E1TF2E1
Find proteins for P29083 (Homo sapiens)
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PHAROS  P29083
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Transcription initiation factor IIE subunit betaR291Homo sapiensMutation(s): 0 
Gene Names: GTF2E2TF2E2
Find proteins for P29084 (Homo sapiens)
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PHAROS  P29084
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB2B1174Homo sapiensMutation(s): 0 
Gene Names: POLR2B
EC: 2.7.7.6
Find proteins for P30876 (Homo sapiens)
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PHAROS  P30876
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
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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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
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: 24
MoleculeChainsSequence LengthOrganismDetails
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: 25
MoleculeChainsSequence LengthOrganismDetails
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: 27
MoleculeChainsSequence LengthOrganismDetails
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: 28
MoleculeChainsSequence LengthOrganismDetails
General transcription factor IIH subunit 26395Homo sapiensMutation(s): 0 
Gene Names: GTF2H2BTF2P44
Find proteins for Q13888 (Homo sapiens)
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PHAROS  Q13888
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
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)
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PHAROS  P19447
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB4D142Homo sapiensMutation(s): 0 
Gene Names: POLR2D
Find proteins for O15514 (Homo sapiens)
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PHAROS  O15514
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  • Reference Sequence

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Entity ID: 32
MoleculeChainsLengthOrganism
DNA (65-MER)X65synthetic construct

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

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

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.20 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