3K7A | pdb_00003k7a

Crystal Structure of an RNA polymerase II-TFIIB complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 
    0.313 (Depositor), 0.311 (DCC) 
  • R-Value Work: 
    0.263 (Depositor), 0.261 (DCC) 
  • R-Value Observed: 
    0.268 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Structure of an RNA polymerase II-TFIIB complex and the transcription initiation mechanism.

Liu, X.Bushnell, D.A.Wang, D.Calero, G.Kornberg, R.D.

(2010) Science 327: 206-209

  • DOI: https://doi.org/10.1126/science.1182015
  • Primary Citation Related Structures: 
    3K7A

  • PubMed Abstract: 

    Previous x-ray crystal structures have given insight into the mechanism of transcription and the role of general transcription factors in the initiation of the process. A structure of an RNA polymerase II-general transcription factor TFIIB complex at 4.5 angstrom resolution revealed the amino-terminal region of TFIIB, including a loop termed the "B finger," reaching into the active center of the polymerase where it may interact with both DNA and RNA, but this structure showed little of the carboxyl-terminal region. A new crystal structure of the same complex at 3.8 angstrom resolution obtained under different solution conditions is complementary with the previous one, revealing the carboxyl-terminal region of TFIIB, located above the polymerase active center cleft, but showing none of the B finger. In the new structure, the linker between the amino- and carboxyl-terminal regions can also be seen, snaking down from above the cleft toward the active center. The two structures, taken together with others previously obtained, dispel long-standing mysteries of the transcription initiation process.


  • Organizational Affiliation
    • Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.

Macromolecule Content 

  • Total Structure Weight: 508.47 kDa 
  • Atom Count: 29,029 
  • Modeled Residue Count: 3,757 
  • Deposited Residue Count: 4,518 
  • Unique protein chains: 11

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11,733Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: D2150RPB1RPB220RPO21SUA8YDL140C
EC: 2.7.7.6
UniProt
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB21,224Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPB150RPB2RPO22YOR151C
EC: 2.7.7.6
UniProt
Find proteins for P08518 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3318Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPB3YIL021W
UniProt
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC1D [auth E]215Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPA7RPB5RPC9YBR1204YBR154C
UniProt
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2E [auth F]155Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: P9677.8RPB6RPO26YPR187W
UniProt
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3F [auth H]146Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPB8YOR224CYOR50-14
UniProt
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9G [auth I]122Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPB9YGL070C
UniProt
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC5H [auth J]70Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPB10YOR210W
UniProt
Find proteins for P22139 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11I [auth K]120Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPB11YOL005C
UniProt
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC4J [auth L]70Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPB12RPC10YHR143BWYHR143W-A
UniProt
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Transcription initiation factor IIBK [auth M]345Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: P9513.4SUA7YPR086W
UniProt
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN

Query on ZN



Download:Ideal Coordinates CCD File
L [auth A]
M [auth A]
N [auth B]
O [auth C]
P [auth I]
L [auth A],
M [auth A],
N [auth B],
O [auth C],
P [auth I],
Q [auth I],
R [auth J],
S [auth L],
T [auth M]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free:  0.313 (Depositor), 0.311 (DCC) 
  • R-Value Work:  0.263 (Depositor), 0.261 (DCC) 
  • R-Value Observed: 0.268 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 204.15α = 90
b = 216.21β = 90
c = 420.98γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-11-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-09-05
    Changes: Derived calculations
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-11-27
    Changes: Structure summary