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
  • 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 ...

    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: 1
MoleculeChainsSequence LengthOrganismDetailsImage
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)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB2B1174Homo sapiensMutation(s): 0 
Gene Names: POLR2B
EC: 2.7.7.6
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3C275Homo sapiensMutation(s): 0 
Gene Names: POLR2CA-152E5.7
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB4D142Homo sapiensMutation(s): 0 
Gene Names: POLR2D
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB5E210Homo sapiensMutation(s): 0 
Gene Names: POLR2E
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2F127Homo sapiensMutation(s): 0 
Gene Names: POLR2FPOLRF
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7G172Homo sapiensMutation(s): 0 
Gene Names: POLR2GRPB7
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3H150Homo sapiensMutation(s): 0 
Gene Names: POLR2H
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9I125Homo sapiensMutation(s): 0 
Gene Names: POLR2I
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC5J67Homo sapiensMutation(s): 0 
Gene Names: POLR2L
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11-aK117Homo sapiensMutation(s): 0 
Gene Names: POLR2JPOLR2J1
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC4L58Homo sapiensMutation(s): 0 
Gene Names: POLR2K
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIBM316Homo sapiensMutation(s): 0 
Gene Names: GTF2BTF2BTFIIB
EC: 2.3.1.48
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIA subunit 1N376Homo sapiensMutation(s): 0 
Gene Names: GTF2A1TF2A1
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIA subunit 2O109Homo sapiensMutation(s): 0 
Gene Names: GTF2A2TF2A2
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
TATA-box-binding proteinP339Homo sapiensMutation(s): 0 
Gene Names: TBPGTF2D1TF2DTFIID
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIE subunit 1Q439Homo sapiensMutation(s): 0 
Gene Names: GTF2E1TF2E1
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIE subunit betaR291Homo sapiensMutation(s): 0 
Gene Names: GTF2E2TF2E2
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIF subunit 1S517Homo sapiensMutation(s): 0 
Gene Names: GTF2F1RAP74
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIF subunit 2T249Homo sapiensMutation(s): 0 
Gene Names: GTF2F2RAP30
EC: 3.6.4.12
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription elongation factor A protein 1U301Homo sapiensMutation(s): 0 
Gene Names: TCEA1GTF2STFIIS
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
TFIIH basal transcription factor complex helicase XPD subunitV [auth 0]760Homo sapiensMutation(s): 0 
Gene Names: ERCC2XPDXPDC
EC: 3.6.4.12
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIH subunit 1W [auth 1]548Homo sapiensMutation(s): 0 
Gene Names: GTF2H1BTF2
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIH subunit 4, p52X [auth 2]462Homo sapiensMutation(s): 0 
Gene Names: GTF2H4
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
CDK-activating kinase assembly factor MAT1Y [auth 3]309Homo sapiensMutation(s): 0 
Gene Names: MNAT1CAP35MAT1RNF66
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIH subunit 3Z [auth 4]308Homo sapiensMutation(s): 0 
Gene Names: GTF2H3
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIH subunit 5AA [auth 5]71Homo sapiensMutation(s): 0 
Gene Names: GTF2H5C6orf175TTDA
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIH subunit 2BA [auth 6]395Homo sapiensMutation(s): 0 
Gene Names: GTF2H2BTF2P44
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
TFIIH basal transcription factor complex helicase XPB subunitCA [auth 7]782Homo sapiensMutation(s): 0 
Gene Names: ERCC3XPBXPBC
EC: 3.6.4.12
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclin-dependent kinase 7DA [auth 8]346Homo sapiensMutation(s): 0 
Gene Names: CDK7CAKCAK1CDKN7MO15STK1
EC: 2.7.11.22 (PDB Primary Data), 2.7.11.23 (PDB Primary Data)
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclin-HEA [auth 9]323Homo sapiensMutation(s): 0 
Gene Names: CCNH
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Entity ID: 32
MoleculeChainsLengthOrganismImage
DNA (65-MER)FA [auth X]65synthetic construct
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Entity ID: 33
MoleculeChainsLengthOrganismImage
DNA (65-MER)GA [auth Y]65synthetic construct
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download Ideal Coordinates CCD File 
UA [auth 0]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
ZN
Query on ZN

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AB [auth 6] , IA [auth A] , JA [auth A] , LA [auth B] , MA [auth C] , NA [auth I] , OA [auth I] , PA [auth J] , 
AB [auth 6],  IA [auth A],  JA [auth A],  LA [auth B],  MA [auth C],  NA [auth I],  OA [auth I],  PA [auth J],  QA [auth L],  RA [auth M],  SA [auth Q],  TA [auth U],  VA [auth 3],  WA [auth 3],  XA [auth 4],  YA [auth 6],  ZA [auth 6]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
HA [auth A], KA [auth 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  (Full details and data files)

  • 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