7B7U | pdb_00007b7u

Cryo-EM structure of mammalian RNA polymerase II in complex with human RPAP2

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history. 


Literature

Cryo-EM structure of mammalian RNA polymerase II in complex with human RPAP2.

Fianu, I., Dienemann, C., Aibara, S., Schilbach, S., Cramer, P.

(2021) Commun Biol 4: 606-606

  • DOI: https://doi.org/10.1038/s42003-021-02088-z
  • Primary Citation of Related Structures:  
    7B7U

  • PubMed Abstract: 

    Nuclear import of RNA polymerase II (Pol II) involves the conserved factor RPAP2. Here we report the cryo-electron microscopy (cryo-EM) structure of mammalian Pol II in complex with human RPAP2 at 2.8 Å resolution. The structure shows that RPAP2 binds between the jaw domains of the polymerase subunits RPB1 and RPB5. RPAP2 is incompatible with binding of downstream DNA during transcription and is displaced upon formation of a transcription pre-initiation complex.

    • Organizational Affiliation: 

    Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit1,970Sus scrofa domesticusMutation(s): 0 
EC: 2.7.7.6
UniProt
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UniProt GroupI3LJR4
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta1,174Sus scrofa domesticusMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for I3LGP4 (Sus scrofa)
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UniProt GroupI3LGP4
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3271Sus scrofa domesticusMutation(s): 0 
UniProt
Find proteins for I3LCH3 (Sus scrofa)
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UniProt GroupI3LCH3
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit ED [auth E]210Sus scrofa domesticusMutation(s): 0 
UniProt
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UniProt GroupI3LSI7
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit FE [auth F]127Sus scrofa domesticusMutation(s): 0 
UniProt
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UniProt GroupA0A4X1VEK9
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3F [auth H]150Sus scrofa domesticusMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9G [auth I]125Sus scrofa domesticusMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized ProteinH [auth J]67Sus scrofa domesticusMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
RNA_pol_L_2 domain-containing proteinI [auth K]117Sus scrofa domesticusMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit KJ [auth L]58Sus scrofa domesticusMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Putative RNA polymerase II subunit B1 CTD phosphatase RPAP2K [auth M]612Homo sapiensMutation(s): 0 
Gene Names: RPAP2, C1orf82
EC: 3.1.3.16
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IXW5 (Homo sapiens)
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PHAROS:  Q8IXW5
GTEx:  ENSG00000122484 
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UniProt GroupQ8IXW5
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
UnknownL [auth N]30Homo sapiensMutation(s): 0 
Sequence Annotations
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.14
RECONSTRUCTIONRELION

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Research Council (ERC)Germany693023
German Research Foundation (DFG)GermanySFB860, SPP2191, EXC 2067/1-390729940
Marie Sklodowska-Curie Actions, FragNET ITNGermany894862

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-19
    Type: Initial release
  • Version 1.1: 2021-06-02
    Changes: Database references
  • Version 1.2: 2022-02-16
    Changes: Database references, Structure summary
  • Version 1.3: 2024-11-20
    Changes: Data collection, Refinement description, Structure summary