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Structure paper

TitlePrimer terminal ribonucleotide alters the active site dynamics of DNA polymerase eta and reduces DNA synthesis fidelity.
Journal, issue, pagesJ. Biol. Chem., Vol. 299, Page 102938-102938, Year 2023
Publish dateAug 25, 2022 (structure data deposition date)
AuthorsChang, C. / Lee Luo, C. / Eleraky, S. / Lin, A. / Zhou, G. / Gao, Y.
External linksJ. Biol. Chem. / PubMed:36702254
MethodsX-ray diffraction
Resolution1.72 - 2.4 Å
Structure data

PDB-8e85:
Human DNA polymerase eta-DNA-rG-ended primer-dGMPNPP ternary mismatch complex with Mn2+
Method: X-RAY DIFFRACTION / Resolution: 1.72 Å

PDB-8e86:
Human DNA polymerase eta-DNA-rC-ended primer-dGMPNPP ternary mismatch complex with Mn2+
Method: X-RAY DIFFRACTION / Resolution: 1.78 Å

PDB-8e87:
Human DNA polymerase eta-DNA-rA-ended primer-dGMPNPP ternary mismatch complex with Mg2+
Method: X-RAY DIFFRACTION / Resolution: 2.19 Å

PDB-8e88:
Human DNA polymerase eta-DNA-rU-ended primer-dGMPNPP ternary mismatch complex with Mg2+
Method: X-RAY DIFFRACTION / Resolution: 2.4 Å

PDB-8e89:
Human DNA polymerase eta-DNA-rU-ended primer-binary complex
Method: X-RAY DIFFRACTION / Resolution: 2.2 Å

PDB-8e8a:
Human DNA polymerase eta-DNA-dT-ended primer binary complex
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-8e8b:
Human DNA polymerase eta-DNA-rU-ended primer ternary mismatch complex:ground state at pH7.0 (K+ MES) with 1 Ca2+ ion
Method: X-RAY DIFFRACTION / Resolution: 2.2 Å

PDB-8e8c:
Human DNA polymerase eta-DNA-rU-ended primer ternary mismatch complex:reaction with 10 mM Mn2+ for 30s
Method: X-RAY DIFFRACTION / Resolution: 2.25 Å

PDB-8e8d:
Human DNA polymerase eta-DNA-rU-ended primer ternary mismatch complex:reaction with 10 mM Mn2+ for 60s
Method: X-RAY DIFFRACTION / Resolution: 2.09 Å

PDB-8e8e:
Human DNA polymerase eta-DNA-rU-ended primer ternary mismatch complex:reaction with 10 mM Mn2+ for 90s
Method: X-RAY DIFFRACTION / Resolution: 2.05 Å

PDB-8e8f:
Human DNA polymerase eta-DNA-rU-ended primer ternary mismatch complex:reaction with 10 mM Mn2+ for 120s
Method: X-RAY DIFFRACTION / Resolution: 2.14 Å

PDB-8e8g:
Human DNA polymerase eta-DNA-rU-ended primer ternary mismatch complex:reaction with 10 mM Mn2+ for 180s
Method: X-RAY DIFFRACTION / Resolution: 2.13 Å

PDB-8e8h:
Human DNA polymerase eta-DNA-rU-ended primer ternary mismatch complex:reaction with 10 mM Mn2+ for 300s
Method: X-RAY DIFFRACTION / Resolution: 2.13 Å

PDB-8e8j:
Human DNA polymerase eta-DNA-rG-ended primer-dGMPNPP ternary mismatch complex with Mg2+
Method: X-RAY DIFFRACTION / Resolution: 2.4 Å

PDB-8e8k:
Human DNA polymerase eta-DNA-rC-ended primer-dGMPNPP ternary mismatch complex with Mg2+
Method: X-RAY DIFFRACTION / Resolution: 2.4 Å

Chemicals

ChemComp-MN:
Unknown entry

ChemComp-XG4:
2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine

ChemComp-HOH:
WATER

ChemComp-MG:
Unknown entry

ChemComp-DGT:
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE

ChemComp-K:
Unknown entry

ChemComp-CA:
Unknown entry

ChemComp-DPO:
DIPHOSPHATE

Source
  • homo sapiens (human)
  • synthetic construct (others)
KeywordsTRANSFERASE/DNA / DNA polymerase / TRANSFERASE / TRANSFERASE-DNA complex

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