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6hms

Cryo-EM map of DNA polymerase D from Pyrococcus abyssi in complex with DNA

Method: ELECTRON MICROSCOPY
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA polymerase II small subunit

Pyrococcus abyssi

UniProt Q9V2F3

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 2 DNA 2 DNA polymerase II large subunit,DNA polymerase II large subunit × 1 （Q9V2F4） ;DNA (5'-D(*GP*AP*GP*AP*CP*GP*GP*GP*CP*CP*GP*CP*GP*TP*C)-3') ; × 1 ;DNA (5'-D(P*TP*GP*AP*CP*GP*CP*GP*GP*CP*CP*CP*GP*TP*CP*TP*C)-3') ; × 1 FE (III) ION × 1 ZINC ION × 4 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
5ihe 5ihe 6hmf 6hmf

4 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
6hms 6t8h 8ppt 8ppu 8ppv 9f29 9f2a

7 assemblies

View Construct and Data Evidence
UniProt name DP2S_PYRAB
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 6–400； UniProt 225–619

DNA polymerase II large subunit,DNA polymerase II large subunit

Pyrococcus abyssi

UniProt Q9V2F4

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 2 DNA 2 DNA polymerase II small subunit × 1 （Q9V2F3） ;DNA (5'-D(*GP*AP*GP*AP*CP*GP*GP*GP*CP*CP*GP*CP*GP*TP*C)-3') ; × 1 ;DNA (5'-D(P*TP*GP*AP*CP*GP*CP*GP*GP*CP*CP*CP*GP*TP*CP*TP*C)-3') ; × 1 FE (III) ION × 1 ZINC ION × 4 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
2lcj 5ijl

2 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
6hms

1 assemblies

View Construct and Data Evidence
UniProt name DP2L_PYRAB
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–955； UniProt 1–955 Author chain B； PDBConstruct 956–1270； UniProt 1141–1455

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id6hms
Deposition date deposition_date2018-09-12
Structure title titleCryo-EM map of DNA polymerase D from Pyrococcus abyssi in complex with DNA
Keywords keywordsDNA, polymerase D, Pyrococcus, REPLICATION; REPLICATION
Experimental Method methodELECTRON MICROSCOPY
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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

6hms__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6hms__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

6hms__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）40.46 Å
Rg (electron density)41.24 Å
Total Rg41.83 Å
Atom count640
Residues31
Excluded volume219340 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6hms__assembly_1__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (6)

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7. Citations (1)