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 11SS | pdb_000011ss

Cryo-EM structure of DNA polymerase Zeta with RNA:DNA hybrid and incoming dNTP

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.03 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history. 

Literature

Molecular basis of DNA polymerase zeta's reverse transcriptase activity

Malik, R., Johnson, R.E., Prakash, L., Prakash, S., Aggarwal, A.K.

(2026) Nat Commun 

Macromolecule Content 

  • Total Structure Weight: 458.38 kDa 
  • Atom Count: 19,069 
  • Modeled Residue Count: 2,409 
  • Deposited Residue Count: 3,902 
  • Unique protein chains: 5
  • Unique nucleic acid chains: 2

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA polymerase zeta catalytic subunit1,538Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: REV3, PSO1, YPL167C, P2535
EC: 2.7.7.7
UniProt
Find proteins for P14284 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P14284 
Go to UniProtKB:  P14284
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UniProt GroupP14284
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA polymerase zeta processivity subunitB [auth D],
C [auth E]		245Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: REV7, YIL139C
UniProt
Find proteins for P38927 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38927 
Go to UniProtKB:  P38927
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UniProt GroupP38927
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA polymerase delta subunit 3D [auth G]350Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: POL32, YJR043C, J1626
UniProt
Find proteins for P47110 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P47110
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UniProt GroupP47110
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Reference Sequence
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|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA repair protein REV1E [auth B]985Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: REV1, YOR346W, O6339
EC: 2.7.7
UniProt
Find proteins for P12689 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P12689 
Go to UniProtKB:  P12689
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UniProt GroupP12689
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA polymerase delta small subunitG [auth F]494Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: POL31, HUS2, HYS2, SDP5, YJR006W, J1427, YJR83.7
EC: 2.7.7.7
UniProt
Find proteins for P46957 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P46957 
Go to UniProtKB:  P46957
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UniProt GroupP46957
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Reference Sequence
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (5'-D(P*AP*TP*TP*AP*CP*GP*AP*AP*TP*TP*GP*C)-3')F [auth P]20synthetic construct
Sequence Annotations
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Reference Sequence
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Entity ID: 7
MoleculeChains LengthOrganismImage
RNA (5'-R(P*AP*AP*UP*GP*GP*CP*AP*AP*UP*UP*CP*GP*UP*AP*AP*U)-3')H [auth X]25synthetic construct
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.03 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIXv1.21.2-5419-000
RECONSTRUCTIONcryoSPARCv4.7

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 States--

Revision History  (Full details and data files)

  • Version 1.0: 2026-10-07
    Type: Initial release