7B7U

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 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 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 ...

    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. patrick.cramer@mpibpc.mpg.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunitA1970Sus scrofa domesticusMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for I3LJR4 (Sus scrofa)
Explore I3LJR4 
Go to UniProtKB:  I3LJR4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI3LJR4
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaB1174Sus scrofa domesticusMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for I3LGP4 (Sus scrofa)
Explore I3LGP4 
Go to UniProtKB:  I3LGP4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI3LGP4
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3C271Sus scrofa domesticusMutation(s): 0 
UniProt
Find proteins for I3LCH3 (Sus scrofa)
Explore I3LCH3 
Go to UniProtKB:  I3LCH3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI3LCH3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit ED [auth E]210Sus scrofa domesticusMutation(s): 0 
UniProt
Find proteins for I3LSI7 (Sus scrofa)
Explore I3LSI7 
Go to UniProtKB:  I3LSI7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI3LSI7
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit FE [auth F]127Sus scrofa domesticusMutation(s): 0 
UniProt
Find proteins for F1SKN8 (Sus scrofa)
Explore F1SKN8 
Go to UniProtKB:  F1SKN8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF1SKN8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3F [auth H]150Sus scrofa domesticusMutation(s): 0 
UniProt
Find proteins for I3LCB2 (Sus scrofa)
Explore I3LCB2 
Go to UniProtKB:  I3LCB2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI3LCB2
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9G [auth I]125Sus scrofa domesticusMutation(s): 0 
UniProt
Find proteins for P60899 (Sus scrofa)
Explore P60899 
Go to UniProtKB:  P60899
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60899
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized ProteinH [auth J]67Sus scrofa domesticusMutation(s): 0 
UniProt
Find proteins for A0A4X1VYD0 (Sus scrofa)
Explore A0A4X1VYD0 
Go to UniProtKB:  A0A4X1VYD0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4X1VYD0
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
RNA_pol_L_2 domain-containing proteinI [auth K]117Sus scrofa domesticusMutation(s): 0 
UniProt
Find proteins for F1RKE4 (Sus scrofa)
Explore F1RKE4 
Go to UniProtKB:  F1RKE4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF1RKE4
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase II subunit KJ [auth L]58Sus scrofa domesticusMutation(s): 0 
UniProt
Find proteins for I3LN51 (Sus scrofa)
Explore I3LN51 
Go to UniProtKB:  I3LN51
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI3LN51
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Putative RNA polymerase II subunit B1 CTD phosphatase RPAP2K [auth M]612Homo sapiensMutation(s): 0 
Gene Names: RPAP2C1orf82
EC: 3.1.3.16
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IXW5 (Homo sapiens)
Explore Q8IXW5 
Go to UniProtKB:  Q8IXW5
PHAROS:  Q8IXW5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IXW5
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
UnknownL [auth N]30Homo sapiensMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report




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