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- PDB-11ss: Cryo-EM structure of DNA polymerase Zeta with RNA:DNA hybrid and ... -

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Basic information

Entry
Database: PDB / ID: 11ss
TitleCryo-EM structure of DNA polymerase Zeta with RNA:DNA hybrid and incoming dNTP
Components
  • (DNA polymerase delta ...) x 2
  • (DNA polymerase zeta ...) x 2
  • DNA (5'-D(P*AP*TP*TP*AP*CP*GP*AP*AP*TP*TP*GP*C)-3')
  • DNA repair protein REV1
  • RNA (5'-R(P*AP*AP*UP*GP*GP*CP*AP*AP*UP*UP*CP*GP*UP*AP*AP*U)-3')
KeywordsDNA BINDING PROTEIN/DNA/RNA / Protein complex / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA-RNA complex
Function / homology
Function and homology information


Translesion synthesis by REV1 / delta DNA polymerase complex / DNA amplification / deoxycytidyl transferase activity / H3-H4 histone complex chaperone activity / zeta DNA polymerase complex / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / RNA-templated DNA biosynthetic process / DNA replication, removal of RNA primer ...Translesion synthesis by REV1 / delta DNA polymerase complex / DNA amplification / deoxycytidyl transferase activity / H3-H4 histone complex chaperone activity / zeta DNA polymerase complex / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / RNA-templated DNA biosynthetic process / DNA replication, removal of RNA primer / lagging strand elongation / DNA damage tolerance / error-free translesion synthesis / double-strand break repair via break-induced replication / DNA metabolic process / DNA strand elongation involved in DNA replication / leading strand elongation / error-prone translesion synthesis / mismatch repair / translesion synthesis / replication fork / double-strand break repair via homologous recombination / nucleotide-excision repair / base-excision repair / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / site of double-strand break / DNA-directed DNA polymerase / damaged DNA binding / DNA-directed DNA polymerase activity / molecular adaptor activity / nucleotide binding / DNA repair / chromatin / mitochondrion / DNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
DNA polymerase delta subunit, OB-fold domain / DNA polymerase delta subunit 2, C-terminal domain / DNA polymerase delta subunit OB-fold domain / DNA polymerase zeta catalytic subunit / : / DNA polymerase zeta catalytic subunit, N-terminal / DNA repair protein Rev1 / DNA polymerase delta/II small subunit family / C4-type zinc-finger of DNA polymerase delta / : ...DNA polymerase delta subunit, OB-fold domain / DNA polymerase delta subunit 2, C-terminal domain / DNA polymerase delta subunit OB-fold domain / DNA polymerase zeta catalytic subunit / : / DNA polymerase zeta catalytic subunit, N-terminal / DNA repair protein Rev1 / DNA polymerase delta/II small subunit family / C4-type zinc-finger of DNA polymerase delta / : / C4-type zinc-finger of DNA polymerase delta / DNA polymerase delta catalytic subunit-like, N-terminal domain / Mad2-like / HORMA domain / HORMA domain / HORMA domain profile. / HORMA domain superfamily / : / DNA polymerase-iota, thumb domain / DNA polymerase alpha/delta/epsilon, subunit B / DNA polymerase alpha/epsilon subunit B / Ubiquitin-binding motif (UBM) domain profile. / BRCT domain / DNA polymerase family B, thumb domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B signature. / DNA polymerase family B / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / IRON/SULFUR CLUSTER / DNA / DNA (> 10) / RNA / RNA (> 10) / Translesion synthesis protein REV1 / DNA polymerase zeta catalytic subunit / DNA polymerase zeta processivity subunit / DNA polymerase delta small subunit / DNA polymerase delta subunit 3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsMalik, R. / Aggarwal, A.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Nat Commun / Year: 2026
Title: Molecular basis of DNA polymerase zeta's reverse transcriptase activity
Authors: Malik, R. / Johnson, R.E. / Prakash, L. / Prakash, S. / Aggarwal, A.K.
History
DepositionMar 11, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 7, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase zeta catalytic subunit
D: DNA polymerase zeta processivity subunit
E: DNA polymerase zeta processivity subunit
G: DNA polymerase delta subunit 3
B: DNA repair protein REV1
P: DNA (5'-D(P*AP*TP*TP*AP*CP*GP*AP*AP*TP*TP*GP*C)-3')
F: DNA polymerase delta small subunit
X: RNA (5'-R(P*AP*AP*UP*GP*GP*CP*AP*AP*UP*UP*CP*GP*UP*AP*AP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)458,37811
Polymers457,5198
Non-polymers8593
Water1267
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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DNA polymerase zeta ... , 2 types, 3 molecules ADE

#1: Protein DNA polymerase zeta catalytic subunit / Protein reversionless 3


Mass: 177068.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: REV3, PSO1, YPL167C, P2535 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P14284, DNA-directed DNA polymerase
#2: Protein DNA polymerase zeta processivity subunit / Revertibility protein 7


Mass: 28791.654 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: REV7, YIL139C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38927

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DNA polymerase delta ... , 2 types, 2 molecules GF

#3: Protein DNA polymerase delta subunit 3


Mass: 40377.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: POL32, YJR043C, J1626 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P47110
#6: Protein DNA polymerase delta small subunit / Hydroxyurea-sensitive protein 2


Mass: 55987.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: POL31, HUS2, HYS2, SDP5, YJR006W, J1427, YJR83.7 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P46957, DNA-directed DNA polymerase

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Protein / DNA chain / RNA chain , 3 types, 3 molecules BPX

#4: Protein DNA repair protein REV1 / Reversionless protein 1


Mass: 112384.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: REV1, YOR346W, O6339 / Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P12689, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#5: DNA chain DNA (5'-D(P*AP*TP*TP*AP*CP*GP*AP*AP*TP*TP*GP*C)-3')


Mass: 6132.991 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#7: RNA chain RNA (5'-R(P*AP*AP*UP*GP*GP*CP*AP*AP*UP*UP*CP*GP*UP*AP*AP*U)-3')


Mass: 7984.772 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 10 molecules

#8: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1protein complexCOMPLEX#1-#70MULTIPLE SOURCES
2protein complexCOMPLEX#1-#4, #61RECOMBINANT
3nucleic acidCOMPLEX#5, #71SYNTHETIC
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Saccharomyces cerevisiae (brewer's yeast)4932
33synthetic construct (others)32630
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 6.5
SpecimenEmbedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
EM embeddingMaterial: VITREOUS ICE
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 54.24 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv4.7particle selection
9PHENIXv1.21.2-5419-000model refinement
13cryoSPARCv4.73D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 544413 / Symmetry type: POINT
RefinementHighest resolution: 3.03 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00319557
ELECTRON MICROSCOPYf_angle_d0.50626680
ELECTRON MICROSCOPYf_dihedral_angle_d18.2797102
ELECTRON MICROSCOPYf_chiral_restr0.0453081
ELECTRON MICROSCOPYf_plane_restr0.0043244

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