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3p87

Structure of human PCNA bound to RNASEH2B PIP box peptide

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

Proliferating cell nuclear antigen

Homo sapiens

UniProt P12004

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 6 Ribonuclease H2 subunit B × 3 （Q5TBB1） Consistent with protein count
2 Protein heterocomplex Heteromer Protein 6 Ribonuclease H2 subunit B × 3 （Q5TBB1） Consistent with protein count
3 Protein heterocomplex Heteromer Protein 12 Ribonuclease H2 subunit B × 6 （Q5TBB1） Consistent with protein count

Other States of the Same Protein in the Database

Monomer
8e84 8e84 8e84

3 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers
1vym 1w60 1w60 3ja9 3vkx 3wgw 3wgw 5e0t 5e0t 5mlo 5mlw 5mom

21 assemblies; showing the first 12

Heteromeric or nucleic-acid complex
1axc 1u76 1u7b 1ul1 1vyj 1vyj 2zvk 2zvl 2zvl 2zvm 3p87 3p87

103 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name PCNA_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–261； UniProt 1–261 Author chain B； PDBConstruct 1–261； UniProt 1–261 Author chain C； PDBConstruct 1–261； UniProt 1–261 Author chain D； PDBConstruct 1–261； UniProt 1–261 Author chain E； PDBConstruct 1–261； UniProt 1–261 Author chain F； PDBConstruct 1–261； UniProt 1–261

Ribonuclease H2 subunit B

OrganismNot specified

UniProt Q5TBB1

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 6 Proliferating cell nuclear antigen × 3 （P12004） Consistent with protein count
2 Protein heterocomplex Heteromer Protein 6 Proliferating cell nuclear antigen × 3 （P12004） Consistent with protein count
3 Protein heterocomplex Heteromer Protein 12 Proliferating cell nuclear antigen × 6 （P12004） 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 G； PDBConstruct 1–23； UniProt 290–312 Author chain H； PDBConstruct 1–23； UniProt 290–312 Author chain I； PDBConstruct 1–23； UniProt 290–312 Author chain J； PDBConstruct 1–23； UniProt 290–312 Author chain K； PDBConstruct 1–23； UniProt 290–312 Author chain L； PDBConstruct 1–23； UniProt 290–312

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_id3p87
Deposition date deposition_date2010-10-13
Structure title titleStructure of human PCNA bound to RNASEH2B PIP box peptide
Keywords keywords;DNA binding, DNA replication, DNA repair, sliding clamp, PCNA Peptide Interacting Peptide (PIP) motif, PIP-box motif, DNA clamp, processivity factor, RNase H2, FEN-1, Ligase, polymerases, helicases, nucleases, nucleus, HYDROLASE-DNA BINDING PROTEIN complex ;; HYDROLASE/DNA BINDING PROTEIN
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.

3p87__assembly_1__model_1

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

Download this curve (.dat)

3p87__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.

3p87__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）33.05 Å
Rg (electron density)31.73 Å
Total Rg32.51 Å
Atom count5757
Residues770
Excluded volume103590 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3p87__assembly_1__model_1 hexameric （6） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3p87__assembly_2__model_1 hexameric （6） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 3p87__assembly_3__model_1 dodecameric （12） 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 (2)

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id3p87A00
Class class3 — Alpha Beta
Architecture architecture70 — Box
Topology topology10 — Proliferating Cell Nuclear Antigen
Homologous superfamily homologous superfamily10 —
Domain ID domain_id3p87B00
Class class3 — Alpha Beta
Architecture architecture70 — Box
Topology topology10 — Proliferating Cell Nuclear Antigen
Homologous superfamily homologous superfamily10 —
Domain ID domain_id3p87C00
Class class3 — Alpha Beta
Architecture architecture70 — Box
Topology topology10 — Proliferating Cell Nuclear Antigen
Homologous superfamily homologous superfamily10 —
Domain ID domain_id3p87D00
Class class3 — Alpha Beta
Architecture architecture70 — Box
Topology topology10 — Proliferating Cell Nuclear Antigen
Homologous superfamily homologous superfamily10 —
Domain ID domain_id3p87E00
Class class3 — Alpha Beta
Architecture architecture70 — Box
Topology topology10 — Proliferating Cell Nuclear Antigen
Homologous superfamily homologous superfamily10 —
Domain ID domain_id3p87F00
Class class3 — Alpha Beta
Architecture architecture70 — Box
Topology topology10 — Proliferating Cell Nuclear Antigen
Homologous superfamily homologous superfamily10 —
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7. Citations (1)