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3jvz

E2~Ubiquitin-HECT

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 E3 ubiquitin-protein ligase NEDD4-like × 1 （Q96PU5） Ubiquitin × 1 （P62988） Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 E3 ubiquitin-protein ligase NEDD4-like × 1 （Q96PU5） Ubiquitin × 1 （P62988） 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 B； PDBConstruct 1–146； UniProt 2–147

E3 ubiquitin-protein ligase NEDD4-like

Homo sapiens

UniProt Q96PU5

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） Ubiquitin × 1 （P62988） Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 Ubiquitin-conjugating enzyme E2 D2 × 1 （P62837） Ubiquitin × 1 （P62988） Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2nsq 2oni 7lp1 7lp4 9gik 9gim

6 assemblies

Homodimer
2mpt 2oni

2 assemblies

Homotetramer

None

Other homooligomers
2oni

1 assemblies

Heteromeric or nucleic-acid complex
2laj 2lb2 2lty 3jvz 3jvz 3jw0 3jw0 5hpk 6zbt 6zbt 6zc9 6zc9

17 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name NED4L_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 6–385； UniProt 596–975 Author chain D； PDBConstruct 6–385； UniProt 596–975

Ubiquitin

Homo sapiens

UniProt P62988

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 NEDD4-like × 1 （Q96PU5） Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 Ubiquitin-conjugating enzyme E2 D2 × 1 （P62837） E3 ubiquitin-protein ligase NEDD4-like × 1 （Q96PU5） Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1c3t 1d3z 1g6j 1sif 1ubi 1ubq 2gbj 2gbj 2gbk 2gbk 2gbk 2gbk

48 assemblies; showing the first 12

Homodimer
1tbe 2bgf 2gbk 2gbk 2gbr 2jf5 2pe9 2pea 2xk5 3h7p 3h7s 3nob

16 assemblies; showing the first 12

Homotetramer
1f9j 2o6v 2o6v 2o6v 2xew 2xew 2xew

7 assemblies

Other homooligomers
2gbr 2zcb 3eec 3eec

4 assemblies

Heteromeric or nucleic-acid complex
1fxt 1nbf 1nbf 1q5w 1s1q 1s1q 1xd3 1xd3 1yx5 1yx6 2ayo 2ayo

64 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name UBIQ_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain X； PDBConstruct 6–81； UniProt 1–76 Author chain Y； PDBConstruct 6–81； 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_id3jvz
Deposition date deposition_date2009-09-17
Structure title titleE2~Ubiquitin-HECT
Keywords keywords;Ubiquitin, HECT, E3, Ubiquitin ligase, UbcH5B, NEDD4L, NEDD4-2, Ligase, Ubl conjugation pathway, Host-virus interaction, LIGASE-SIGNALING PROTEIN COMPLEX ;; LIGASE/SIGNALING 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.

3jvz__assembly_1__model_1

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

Download this curve (.dat)

3jvz__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.

3jvz__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）28.45 Å
Rg (electron density)27.50 Å
Total Rg28.35 Å
Atom count4919
Residues599
Excluded volume87832 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3jvz__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3jvz__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 (3)

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6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id3jvzA00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily10 — Ubiquitin Conjugating Enzyme
Domain ID domain_id3jvzB00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily10 — Ubiquitin Conjugating Enzyme
Domain ID domain_id3jvzC01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1750 — Hect, E3 ligase catalytic domain fold
Homologous superfamily homologous superfamily10 — Hect, E3 ligase catalytic domains
Domain ID domain_id3jvzC02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology2160 — Hect, E3 ligase catalytic domain
Homologous superfamily homologous superfamily10 — Hect, E3 ligase catalytic domain
Domain ID domain_id3jvzC03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology2410 — Hect, E3 ligase catalytic fold
Homologous superfamily homologous superfamily10 — Hect, E3 ligase catalytic domain
Domain ID domain_id3jvzD01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1750 — Hect, E3 ligase catalytic domain fold
Homologous superfamily homologous superfamily10 — Hect, E3 ligase catalytic domains
Domain ID domain_id3jvzD02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology2160 — Hect, E3 ligase catalytic domain
Homologous superfamily homologous superfamily10 — Hect, E3 ligase catalytic domain
Domain ID domain_id3jvzD03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology2410 — Hect, E3 ligase catalytic fold
Homologous superfamily homologous superfamily10 — Hect, E3 ligase catalytic domain
Domain ID domain_id3jvzX00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id3jvzY00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
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7. Citations (1)