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3puf

Crystal structure of human RNase H2 complex

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

Ribonuclease H2 subunit A

Homo sapiens

UniProt O75792

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 Ribonuclease H2 subunit B × 1 （Q5TBB1） Ribonuclease H2 subunit C × 1 （Q8TDP1） water × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 Ribonuclease H2 subunit B × 1 （Q5TBB1） Ribonuclease H2 subunit C × 1 （Q8TDP1） water × 3 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 Ribonuclease H2 subunit B × 1 （Q5TBB1） Ribonuclease H2 subunit C × 1 （Q8TDP1） water × 3 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 3 Ribonuclease H2 subunit B × 1 （Q5TBB1） Ribonuclease H2 subunit C × 1 （Q8TDP1） water × 3 Consistent with protein count
5 Protein heterocomplex Heteromer Protein 3 Ribonuclease H2 subunit B × 1 （Q5TBB1） Ribonuclease H2 subunit C × 1 （Q8TDP1） water × 3 Consistent with protein count
6 Protein heterocomplex Heteromer Protein 3 Ribonuclease H2 subunit B × 1 （Q5TBB1） Ribonuclease H2 subunit C × 1 （Q8TDP1） water × 3 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3p56 3p56 3puf 3puf 3puf 3puf 3puf 3puf 8yjz

9 assemblies

View Construct and Data Evidence
UniProt name RNH2A_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 4–302； UniProt 1–299 Author chain D； PDBConstruct 4–302； UniProt 1–299 Author chain G； PDBConstruct 4–302； UniProt 1–299 Author chain J； PDBConstruct 4–302； UniProt 1–299 Author chain M； PDBConstruct 4–302； UniProt 1–299 Author chain P； PDBConstruct 4–302； UniProt 1–299

Ribonuclease H2 subunit B

Homo sapiens

UniProt Q5TBB1

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 Ribonuclease H2 subunit A × 1 （O75792） Ribonuclease H2 subunit C × 1 （Q8TDP1） water × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 Ribonuclease H2 subunit A × 1 （O75792） Ribonuclease H2 subunit C × 1 （Q8TDP1） water × 3 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 Ribonuclease H2 subunit A × 1 （O75792） Ribonuclease H2 subunit C × 1 （Q8TDP1） water × 3 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 3 Ribonuclease H2 subunit A × 1 （O75792） Ribonuclease H2 subunit C × 1 （Q8TDP1） water × 3 Consistent with protein count
5 Protein heterocomplex Heteromer Protein 3 Ribonuclease H2 subunit A × 1 （O75792） Ribonuclease H2 subunit C × 1 （Q8TDP1） water × 3 Consistent with protein count
6 Protein heterocomplex Heteromer Protein 3 Ribonuclease H2 subunit A × 1 （O75792） Ribonuclease H2 subunit C × 1 （Q8TDP1） water × 3 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3p56 3p56 3p87 3p87 3p87 3puf 3puf 3puf 3puf 3puf 3puf 8yjz

12 assemblies

View Construct and Data Evidence
UniProt name RNH2B_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 5–224； UniProt 14–233 Author chain E； PDBConstruct 5–224； UniProt 14–233 Author chain H； PDBConstruct 5–224； UniProt 14–233 Author chain K； PDBConstruct 5–224； UniProt 14–233 Author chain N； PDBConstruct 5–224； UniProt 14–233 Author chain Q； PDBConstruct 5–224； UniProt 14–233

Ribonuclease H2 subunit C

Homo sapiens

UniProt Q8TDP1

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 Ribonuclease H2 subunit A × 1 （O75792） Ribonuclease H2 subunit B × 1 （Q5TBB1） water × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 Ribonuclease H2 subunit A × 1 （O75792） Ribonuclease H2 subunit B × 1 （Q5TBB1） water × 3 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 Ribonuclease H2 subunit A × 1 （O75792） Ribonuclease H2 subunit B × 1 （Q5TBB1） water × 3 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 3 Ribonuclease H2 subunit A × 1 （O75792） Ribonuclease H2 subunit B × 1 （Q5TBB1） water × 3 Consistent with protein count
5 Protein heterocomplex Heteromer Protein 3 Ribonuclease H2 subunit A × 1 （O75792） Ribonuclease H2 subunit B × 1 （Q5TBB1） water × 3 Consistent with protein count
6 Protein heterocomplex Heteromer Protein 3 Ribonuclease H2 subunit A × 1 （O75792） Ribonuclease H2 subunit B × 1 （Q5TBB1） water × 3 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3p56 3p56 3puf 3puf 3puf 3puf 3puf 3puf 8yjz

9 assemblies

View Construct and Data Evidence
UniProt name RNH2C_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 4–167； UniProt 1–164 Author chain F； PDBConstruct 4–167； UniProt 1–164 Author chain I； PDBConstruct 4–167； UniProt 1–164 Author chain L； PDBConstruct 4–167； UniProt 1–164 Author chain O； PDBConstruct 4–167； UniProt 1–164 Author chain R； PDBConstruct 4–167； UniProt 1–164

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_id3puf
Deposition date deposition_date2010-12-04
Structure title titleCrystal structure of human RNase H2 complex
Keywords keywordsRNase H fold, triple barrel fold, hydrolase, RNase H; HYDROLASE
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.

3puf__assembly_1__model_1

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

Download this curve (.dat)

3puf__assembly_1__model_1 | I(q)

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

3puf__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）33.77 Å
Rg (electron density)34.14 Å
Total Rg34.49 Å
Atom count4423
Residues582
Excluded volume79216 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3puf__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3puf__assembly_2__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 3puf__assembly_3__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 3puf__assembly_4__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
5 1 3puf__assembly_5__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
6 1 3puf__assembly_6__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 (4)

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6. Fold Classification (SCOP + CATH) 18 domains

CATH v4.4 (18 domains)

Domain ID domain_id3pufA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily10 — Ribonuclease H-like superfamily/Ribonuclease H
Domain ID domain_id3pufA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily460 — Ribonuclease hii. Domain 2
Domain ID domain_id3pufC00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily680 —
Domain ID domain_id3pufD01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily10 — Ribonuclease H-like superfamily/Ribonuclease H
Domain ID domain_id3pufD02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily460 — Ribonuclease hii. Domain 2
Domain ID domain_id3pufF00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily680 —
Domain ID domain_id3pufG01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily10 — Ribonuclease H-like superfamily/Ribonuclease H
Domain ID domain_id3pufG02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily460 — Ribonuclease hii. Domain 2
Domain ID domain_id3pufI00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily680 —
Domain ID domain_id3pufJ01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily10 — Ribonuclease H-like superfamily/Ribonuclease H
Domain ID domain_id3pufJ02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily460 — Ribonuclease hii. Domain 2
Domain ID domain_id3pufL00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily680 —
Domain ID domain_id3pufM01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily10 — Ribonuclease H-like superfamily/Ribonuclease H
Domain ID domain_id3pufM02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily460 — Ribonuclease hii. Domain 2
Domain ID domain_id3pufO00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily680 —
Domain ID domain_id3pufP01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily10 — Ribonuclease H-like superfamily/Ribonuclease H
Domain ID domain_id3pufP02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily460 — Ribonuclease hii. Domain 2
Domain ID domain_id3pufR00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily680 —
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7. Citations (1)