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4v3k

RNF38-UbcH5B-UB complex

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

UBIQUITIN-CONJUGATING ENZYME E2 D2

HOMO SAPIENS

UniProt P62837

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 POLYUBIQUITIN-C × 1 （P0CG48） E3 UBIQUITIN-PROTEIN LIGASE RNF38 × 1 （Q9H0F5） CHLORIDE ION × 3 1,2-ETHANEDIOL × 2 ZINC ION × 2 water × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 POLYUBIQUITIN-C × 1 （P0CG48） E3 UBIQUITIN-PROTEIN LIGASE RNF38 × 1 （Q9H0F5） CHLORIDE ION × 3 1,2-ETHANEDIOL × 3 ZINC ION × 2 water × 3 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2clw 2clw 2clw 2clw 2esk 2eso 2esp 2esq 3l1y 3tgd 5edv 7bol

13 assemblies; showing the first 12

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3a33 3jvz 3jvz 3jw0 3jw0 3zni 3zni 3zni 3zni 4a49 4a4b 4a4c

80 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name UB2D2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–146； UniProt 2–147 Author chain D； PDBConstruct 1–146； UniProt 2–147

POLYUBIQUITIN-C

HOMO SAPIENS

UniProt P0CG48

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 UBIQUITIN-CONJUGATING ENZYME E2 D2 × 1 （P62837） E3 UBIQUITIN-PROTEIN LIGASE RNF38 × 1 （Q9H0F5） CHLORIDE ION × 3 1,2-ETHANEDIOL × 2 ZINC ION × 2 water × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 UBIQUITIN-CONJUGATING ENZYME E2 D2 × 1 （P62837） E3 UBIQUITIN-PROTEIN LIGASE RNF38 × 1 （Q9H0F5） CHLORIDE ION × 3 1,2-ETHANEDIOL × 3 ZINC ION × 2 water × 3 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1ogw 2l3z 2ld9 2mi8 2mor 2rsu 2ru6 4boz 4dhj 4dhj 4dhz 4hk2

52 assemblies; showing the first 12

Homodimer
2mbo 2mbq 2n2k 3aul 4zqs

5 assemblies

Homotetramer
3alb 8e7o

2 assemblies

Other homooligomers

None

Heteromeric or nucleic-acid complex
11sy 2lvo 2lvp 2lvq 2lz6 2mcn 2mj5 2mre 2mws 2rr9 3b08 3b08

290 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name UBC_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 6–81； UniProt 77–152 Author chain E； PDBConstruct 6–81； UniProt 77–152

E3 UBIQUITIN-PROTEIN LIGASE RNF38

HOMO SAPIENS

UniProt Q9H0F5

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 UBIQUITIN-CONJUGATING ENZYME E2 D2 × 1 （P62837） POLYUBIQUITIN-C × 1 （P0CG48） CHLORIDE ION × 3 1,2-ETHANEDIOL × 2 ZINC ION × 2 water × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 UBIQUITIN-CONJUGATING ENZYME E2 D2 × 1 （P62837） POLYUBIQUITIN-C × 1 （P0CG48） CHLORIDE ION × 3 1,2-ETHANEDIOL × 3 ZINC ION × 2 water × 3 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1x4j 9q88

2 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
4v3k 4v3k 4v3l 7ojx 9q8y 9q8y

6 assemblies

View Construct and Data Evidence
UniProt name RNF38_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 3–79； UniProt 439–515 Author chain F； PDBConstruct 3–79； UniProt 439–515

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_id4v3k
Deposition date deposition_date2014-10-20
Structure title titleRNF38-UbcH5B-UB complex
Keywords keywordsRING E3, E2, UBIQUITIN, LIGASE; LIGASE
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.

4v3k__assembly_1__model_1

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

Download this curve (.dat)

4v3k__assembly_1__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

4v3k__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）20.79 Å
Rg (electron density)19.68 Å
Total Rg20.42 Å
Atom count2310
Residues293
Excluded volume41193 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 4v3k__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 4v3k__assembly_2__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 (7)

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd4v3ka_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.20 — UBC-like
Superfamily Superfamily superfamilyd.20.1 — UBC-like
Family Family familyd.20.1.1 — UBC-related
Domain ID domain_idd4v3kb1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.1 — Ubiquitin-related
Domain ID domain_idd4v3kb2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4v3kd_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.20 — UBC-like
Superfamily Superfamily superfamilyd.20.1 — UBC-like
Family Family familyd.20.1.1 — UBC-related
Domain ID domain_idd4v3ke1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.1 — Ubiquitin-related
Domain ID domain_idd4v3ke2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id4v3kA00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily10 — Ubiquitin Conjugating Enzyme
Domain ID domain_id4v3kC00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology40 — Herpes Virus-1
Homologous superfamily homologous superfamily10 — Zinc/RING finger domain, C3HC4 (zinc finger)
Domain ID domain_id4v3kD00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily10 — Ubiquitin Conjugating Enzyme
Domain ID domain_id4v3kF00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology40 — Herpes Virus-1
Homologous superfamily homologous superfamily10 — Zinc/RING finger domain, C3HC4 (zinc finger)
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7. Citations (1)