6DRD

RNA Pol II(G)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 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
  • Primary Citation of Related Structures:  
    6DRD

  • 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 Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA. roeder@mail.rockefeller.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)
Find proteins for P24928 (Homo sapiens)
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PHAROS  P24928
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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
Find proteins for P30876 (Homo sapiens)
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PHAROS  P30876
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
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: 4
MoleculeChainsSequence LengthOrganismDetailsImage
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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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC1E210Homo sapiensMutation(s): 0 
Gene Names: POLR2E
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PHAROS  P19388
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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
Find proteins for P61218 (Homo sapiens)
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PHAROS  P61218
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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
Find proteins for P52434 (Homo sapiens)
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PHAROS  P52434
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
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: 10
MoleculeChainsSequence LengthOrganismDetailsImage
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 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
Find proteins for P53803 (Homo sapiens)
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PHAROS  P53803
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit GRINL1AM62Homo sapiensMutation(s): 0 
Gene Names: POLR2M
Find proteins for P0CAP2 (Homo sapiens)
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PHAROS  P0CAP2
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7G172Homo sapiensMutation(s): 0 
Gene Names: POLR2GRPB7
Find proteins for P62487 (Homo sapiens)
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
C, I, J, L
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01 CA202245

Revision History 

  • Version 1.0: 2019-06-12
    Type: Initial release
  • Version 1.1: 2019-12-04
    Changes: Author supporting evidence