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4whv

E3 ubiquitin-protein ligase RNF8 in complex with Ubiquitin-conjugating enzyme E2 N and Polyubiquitin-B

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

Ubiquitin-conjugating enzyme E2 N

Homo sapiens

UniProt P61088

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 6 E3 ubiquitin-protein ligase RNF8 × 2 （O76064） Polyubiquitin-B × 2 （P0CG47） ZINC ION × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 6 E3 ubiquitin-protein ligase RNF8 × 2 （O76064） Polyubiquitin-B × 2 （P0CG47） ZINC ION × 4 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
1j7d 2c2v 2c2v 3hct 3hcu 3hcu 3von 3von 3von 3von 3von 3von

74 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name UBE2N_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain B； PDBConstruct 9–160； UniProt 1–152 Author chain E； PDBConstruct 9–160； UniProt 1–152 Author chain H； PDBConstruct 9–160； UniProt 1–152 Author chain K； PDBConstruct 9–160； UniProt 1–152

E3 ubiquitin-protein ligase RNF8

Homo sapiens

UniProt O76064

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 6 Ubiquitin-conjugating enzyme E2 N × 2 （P61088） Polyubiquitin-B × 2 （P0CG47） ZINC ION × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 6 Ubiquitin-conjugating enzyme E2 N × 2 （P61088） Polyubiquitin-B × 2 （P0CG47） ZINC ION × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2csw

1 assemblies

Homodimer

None

Homotetramer
4ayc

1 assemblies

Other homooligomers

None

Heteromeric or nucleic-acid complex
2pie 4orh 4orh 4orh 4whv 4whv

6 assemblies

View Construct and Data Evidence
UniProt name RNF8_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 9–149； UniProt 345–485 Author chain D； PDBConstruct 9–149； UniProt 345–485 Author chain I； PDBConstruct 9–149； UniProt 345–485 Author chain J； PDBConstruct 9–149； UniProt 345–485

Polyubiquitin-B

Homo sapiens

UniProt P0CG47

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 6 Ubiquitin-conjugating enzyme E2 N × 2 （P61088） E3 ubiquitin-protein ligase RNF8 × 2 （O76064） ZINC ION × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 6 Ubiquitin-conjugating enzyme E2 N × 2 （P61088） E3 ubiquitin-protein ligase RNF8 × 2 （O76064） ZINC ION × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2msg 3ons 4wzp 4wzp 4wzp 4wzp 4wzp 4wzp 4wzp 4wzp 4xof 5dk8

32 assemblies; showing the first 12

Homodimer
4zpz 5emz 5emz 5emz 5gob 5goc 5god 5gog 5goh 5goi 5goj 5khy

25 assemblies; showing the first 12

Homotetramer
5go8 5xdp

2 assemblies

Other homooligomers
3zlz 3zlz 3zlz 5go7 5gok 6oq1 6oq1 6oq2 7cap

9 assemblies

Heteromeric or nucleic-acid complex
2mbb 2mro 2n13 2y5b 2y5b 3o65 3o65 3o65 3o65 3o65 3o65 3oj3

362 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name UBB_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain A； PDBConstruct 8–83； UniProt 1–76 Author chain F； PDBConstruct 8–83； UniProt 1–76 Author chain G； PDBConstruct 8–83； UniProt 1–76 Author chain L； PDBConstruct 8–83； UniProt 1–76

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_id4whv
Deposition date deposition_date2014-09-23
Structure title titleE3 ubiquitin-protein ligase RNF8 in complex with Ubiquitin-conjugating enzyme E2 N and Polyubiquitin-B
Keywords keywordsE3 ligase, E2 conjugating enzyme, ubiquitination, coiled coil, ligase-protein binding complex; ligase/protein binding
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.

4whv__assembly_1__model_1

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

Download this curve (.dat)

4whv__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.

4whv__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）35.44 Å
Rg (electron density)35.39 Å
Total Rg35.00 Å
Atom count4992
Residues711
Excluded volume88546 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 4whv__assembly_1__model_1 hexameric （6） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 4whv__assembly_2__model_1 hexameric （6） 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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7. Citations (1)