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3gqc

Structure of human Rev1-DNA-dNTP ternary complex

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA repair protein REV1

Homo sapiens

UniProt Q9UBZ9

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Monomer Protein 1 DNA 2 5'-D(*AP*TP*CP*CP*TP*CP*CP*CP*CP*TP*AP*(DOC))-3' × 1 5'-D(*TP*AP*AP*GP*GP*TP*AP*GP*GP*GP*GP*AP*GP*GP*AP*T)-3' × 1 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 4 water × 3 Consistent with all polymers
2 Protein–DNA Monomer Protein 1 DNA 2 5'-D(*AP*TP*CP*CP*TP*CP*CP*CP*CP*TP*AP*(DOC))-3' × 1 5'-D(*TP*AP*AP*GP*GP*TP*AP*GP*GP*GP*GP*AP*GP*GP*AP*T)-3' × 1 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 2 water × 3 Consistent with all polymers
3 Protein–DNA Monomer Protein 1 DNA 2 5'-D(*AP*TP*CP*CP*TP*CP*CP*CP*CP*TP*AP*(DOC))-3' × 1 5'-D(*TP*AP*AP*GP*GP*TP*AP*GP*GP*GP*GP*AP*GP*GP*AP*T)-3' × 1 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 3 water × 3 Consistent with all polymers
4 Protein–DNA Monomer Protein 1 DNA 2 5'-D(*AP*TP*CP*CP*TP*CP*CP*CP*CP*TP*AP*(DOC))-3' × 1 5'-D(*TP*AP*AP*GP*GP*TP*AP*GP*GP*GP*GP*AP*GP*GP*AP*T)-3' × 1 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 4 water × 3 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
2ebw 2lsy 6axd

3 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2lsi 2lsk 2n1g 3gqc 3gqc 3gqc 3gqc 3vu7 4ba9 4ba9 4ext 4ext

22 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name REV1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–504； UniProt 330–833 Author chain B； PDBConstruct 1–504； UniProt 330–833 Author chain C； PDBConstruct 1–504； UniProt 330–833 Author chain D； PDBConstruct 1–504； UniProt 330–833

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_id3gqc
Deposition date deposition_date2009-03-24
Structure title titleStructure of human Rev1-DNA-dNTP ternary complex
Keywords keywords;PROTEIN-DNA COMPLEX, DNA damage, DNA repair, DNA synthesis, DNA-binding, Magnesium, Metal-binding, Nucleotidyltransferase, Nucleus, Transferase, TRANSFERASE-DNA COMPLEX ;; TRANSFERASE/DNA
Experimental Method methodX-RAY DIFFRACTION
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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.

3gqc__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3gqc__assembly_4__model_1 | I(q)

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

3gqc__assembly_4__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）23.93 Å
Rg (electron density)23.36 Å
Total Rg24.09 Å
Atom count3807
Residues460
Excluded volume65663 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3gqc__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3gqc__assembly_2__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 3gqc__assembly_3__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 3gqc__assembly_4__model_1 trimeric （3） 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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6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

Domain ID domain_id3gqcA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily270 — Reverse transcriptase/Diguanylate cyclase domain
Domain ID domain_id3gqcA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1170 — MutS, DNA mismatch repair protein, domain I
Homologous superfamily homologous superfamily60 —
Domain ID domain_id3gqcA03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily20 — 5' to 3' exonuclease, C-terminal subdomain
Domain ID domain_id3gqcA04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily100 — DNA polymerase, Y-family, little finger domain
Domain ID domain_id3gqcB01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily270 — Reverse transcriptase/Diguanylate cyclase domain
Domain ID domain_id3gqcB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1170 — MutS, DNA mismatch repair protein, domain I
Homologous superfamily homologous superfamily60 —
Domain ID domain_id3gqcB03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily20 — 5' to 3' exonuclease, C-terminal subdomain
Domain ID domain_id3gqcB04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily100 — DNA polymerase, Y-family, little finger domain
Domain ID domain_id3gqcC01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily270 — Reverse transcriptase/Diguanylate cyclase domain
Domain ID domain_id3gqcC02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1170 — MutS, DNA mismatch repair protein, domain I
Homologous superfamily homologous superfamily60 —
Domain ID domain_id3gqcC03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily20 — 5' to 3' exonuclease, C-terminal subdomain
Domain ID domain_id3gqcC04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily100 — DNA polymerase, Y-family, little finger domain
Domain ID domain_id3gqcD01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily270 — Reverse transcriptase/Diguanylate cyclase domain
Domain ID domain_id3gqcD02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1170 — MutS, DNA mismatch repair protein, domain I
Homologous superfamily homologous superfamily60 —
Domain ID domain_id3gqcD03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily20 — 5' to 3' exonuclease, C-terminal subdomain
Domain ID domain_id3gqcD04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily100 — DNA polymerase, Y-family, little finger domain
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7. Citations (1)