4GK5

Crystal structure of human Rev3-Rev7-Rev1-Polkappa complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report


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Literature

Structural insights into the assembly of human translesion polymerase complexes

Xie, W.Yang, X.Xu, M.Jiang, T.

(2012) Protein Cell 3: 864-874

  • DOI: 10.1007/s13238-012-2102-x
  • Primary Citation of Related Structures:  
    4GK0, 4GK5

  • PubMed Abstract: 
  • In addition to DNA repair pathways, cells utilize translesion DNA synthesis (TLS) to bypass DNA lesions during replication. During TLS, Y-family DNA polymerase (Polη, Polκ, Polı and Rev1) inserts specific nucleotide opposite preferred DNA lesions, and then Polζ consisting of two subunits, Rev3 and Rev7, carries out primer extension ...

    In addition to DNA repair pathways, cells utilize translesion DNA synthesis (TLS) to bypass DNA lesions during replication. During TLS, Y-family DNA polymerase (Polη, Polκ, Polı and Rev1) inserts specific nucleotide opposite preferred DNA lesions, and then Polζ consisting of two subunits, Rev3 and Rev7, carries out primer extension. Here, we report the complex structures of Rev3-Rev7-Rev1(CTD) and Rev3-Rev7-Rev1(CTD)-Polκ(RIR). These two structures demonstrate that Rev1(CTD) contains separate binding sites for Polκ and Rev7. Our BIAcore experiments provide additional support for the notion that the interaction between Rev3 and Rev7 increases the affinity of Rev7 and Rev1. We also verified through FRET experiment that Rev1, Rev3, Rev7 and Polκ form a stable quaternary complex in vivo, thereby suggesting an efficient switching mechanism where the "inserter" polymerase can be immediately replaced by an "extender" polymerase within the same quaternary complex.


    Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing, China.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mitotic spindle assembly checkpoint protein MAD2BA, B238Homo sapiensMutation(s): 1 
Gene Names: MAD2L2MAD2BREV7
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PHAROS:  Q9UI95
GTEx:  ENSG00000116670 
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UniProt GroupQ9UI95
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase zeta catalytic subunitC, D52Homo sapiensMutation(s): 0 
Gene Names: REV3LPOLZREV3
EC: 2.7.7.7
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PHAROS:  O60673
GTEx:  ENSG00000009413 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA repair protein REV1E, F136Homo sapiensMutation(s): 0 
Gene Names: REV1REV1L
EC: 2.7.7
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Find proteins for Q9UBZ9 (Homo sapiens)
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Go to UniProtKB:  Q9UBZ9
PHAROS:  Q9UBZ9
GTEx:  ENSG00000135945 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase kappaG10Homo sapiensMutation(s): 0 
Gene Names: POLKDINB1
EC: 2.7.7.7
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Find proteins for Q9UBT6 (Homo sapiens)
Explore Q9UBT6 
Go to UniProtKB:  Q9UBT6
PHAROS:  Q9UBT6
GTEx:  ENSG00000122008 
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.998α = 90
b = 72.762β = 90
c = 104.653γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2012-08-10 
  • Released Date: 2013-03-13 
  • Deposition Author(s): Tao, J., Min, X., Wei, X.

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-13
    Type: Initial release