6DRD

RNA Pol II(G)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.9 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Architecture of Pol II(G) and molecular mechanism of transcription regulation by Gdown1.

Jishage, M.Yu, X.Shi, Y.Ganesan, S.J.Chen, W.Y.Sali, A.Chait, B.T.Asturias, F.J.Roeder, R.G.

(2018) Nat. Struct. Mol. Biol. 25: 859-867

  • DOI: 10.1038/s41594-018-0118-5

  • PubMed Abstract: 
  • Tight binding of Gdown1 represses RNA polymerase II (Pol II) function in a manner that is reversed by Mediator, but the structural basis of these processes is unclear. Although Gdown1 is intrinsically disordered, its Pol II interacting domains were l ...

    Tight binding of Gdown1 represses RNA polymerase II (Pol II) function in a manner that is reversed by Mediator, but the structural basis of these processes is unclear. Although Gdown1 is intrinsically disordered, its Pol II interacting domains were localized and shown to occlude transcription factor IIF (TFIIF) and transcription factor IIB (TFIIB) binding by perfect positioning on their Pol II interaction sites. Robust binding of Gdown1 to Pol II is established by cooperative interactions of a strong Pol II binding region and two weaker binding modulatory regions, thus providing a mechanism both for tight Pol II binding and transcription inhibition and for its reversal. In support of a physiological function for Gdown1 in transcription repression, Gdown1 co-localizes with Pol II in transcriptionally silent nuclei of early Drosophila embryos but re-localizes to the cytoplasm during zygotic genome activation. Our study reveals a self-inactivation through Gdown1 binding as a unique mode of repression in Pol II function.


    Organizational Affiliation

    Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA.,Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA, USA.,Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, San Diego, CA, USA.,Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA. roeder@mail.rockefeller.edu.,Pfizer Inc., Groton, CT, USA.,Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA.,Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA.




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 polymerases I, II, and III subunit RPABC1
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
DNA-directed RNA polymerase II subunit GRINL1A
M
62Homo sapiensMutation(s): 0 
Gene Names: POLR2M (GRINL1A)
Find proteins for P0CAP2 (Homo sapiens)
Go to Gene View: POLR2M
Go to UniProtKB:  P0CAP2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
C, I, J, L
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
M
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.9 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer InstituteUnited StatesR01 CA202245

Revision History 

  • Version 1.0: 2019-06-12
    Type: Initial release