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3zni

Structure of phosphoTyr363-Cbl-b - UbcH5B-Ub - ZAP-70 peptide complex

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

E3 UBIQUITIN-PROTEIN LIGASE CBL-B

HOMO SAPIENS

UniProt Q13191

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 TYROSINE-PROTEIN KINASE ZAP-70 × 1 （P43403） UBIQUITIN-CONJUGATING ENZYME E2 D2 × 1 （P62837） POLYUBIQUITIN-C × 1 （P0CG48） ZINC ION × 2 CALCIUM ION × 1 1,2-ETHANEDIOL × 1 water × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 TYROSINE-PROTEIN KINASE ZAP-70 × 1 （P43403） UBIQUITIN-CONJUGATING ENZYME E2 D2 × 1 （P62837） POLYUBIQUITIN-C × 1 （P0CG48） ZINC ION × 2 CALCIUM ION × 1 1,2-ETHANEDIOL × 1 water × 4 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 4 TYROSINE-PROTEIN KINASE ZAP-70 × 1 （P43403） UBIQUITIN-CONJUGATING ENZYME E2 D2 × 1 （P62837） POLYUBIQUITIN-C × 1 （P0CG48） ZINC ION × 2 CALCIUM ION × 1 1,2-ETHANEDIOL × 1 water × 4 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 4 TYROSINE-PROTEIN KINASE ZAP-70 × 1 （P43403） UBIQUITIN-CONJUGATING ENZYME E2 D2 × 1 （P62837） POLYUBIQUITIN-C × 1 （P0CG48） ZINC ION × 2 CALCIUM ION × 1 1,2-ETHANEDIOL × 1 water × 3 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2jnh 2ldr 2ooa 2ooa 3vgo 3vgo 3vgo 8gcy 8qng 8qnh 8qni 8qtg

23 assemblies; showing the first 12

Homodimer
2do6

1 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2ak5 2bz8 2j6f 2oob 3pfv 3pfv 3zni 3zni 3zni 3zni

10 assemblies

View Construct and Data Evidence
UniProt name CBLB_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–394； UniProt 36–427 Author chain E； PDBConstruct 3–394； UniProt 36–427 Author chain I； PDBConstruct 3–394； UniProt 36–427 Author chain M； PDBConstruct 3–394； UniProt 36–427

TYROSINE-PROTEIN KINASE ZAP-70

OrganismNot specified

UniProt P43403

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 E3 UBIQUITIN-PROTEIN LIGASE CBL-B × 1 （Q13191） UBIQUITIN-CONJUGATING ENZYME E2 D2 × 1 （P62837） POLYUBIQUITIN-C × 1 （P0CG48） ZINC ION × 2 CALCIUM ION × 1 1,2-ETHANEDIOL × 1 water × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 E3 UBIQUITIN-PROTEIN LIGASE CBL-B × 1 （Q13191） UBIQUITIN-CONJUGATING ENZYME E2 D2 × 1 （P62837） POLYUBIQUITIN-C × 1 （P0CG48） ZINC ION × 2 CALCIUM ION × 1 1,2-ETHANEDIOL × 1 water × 4 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 4 E3 UBIQUITIN-PROTEIN LIGASE CBL-B × 1 （Q13191） UBIQUITIN-CONJUGATING ENZYME E2 D2 × 1 （P62837） POLYUBIQUITIN-C × 1 （P0CG48） ZINC ION × 2 CALCIUM ION × 1 1,2-ETHANEDIOL × 1 water × 4 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 4 E3 UBIQUITIN-PROTEIN LIGASE CBL-B × 1 （Q13191） UBIQUITIN-CONJUGATING ENZYME E2 D2 × 1 （P62837） POLYUBIQUITIN-C × 1 （P0CG48） ZINC ION × 2 CALCIUM ION × 1 1,2-ETHANEDIOL × 1 water × 3 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1m61 1u59 2ozo 4k2r 4xz0

5 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2oq1 2y1n 2y1n 3zni 3zni 3zni 3zni 4a4b 4a4c 4xz1 7siy

11 assemblies

View Construct and Data Evidence
UniProt name ZAP70_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–12； UniProt 286–297 Author chain F； PDBConstruct 1–12； UniProt 286–297 Author chain J； PDBConstruct 1–12； UniProt 286–297 Author chain N； PDBConstruct 1–12； UniProt 286–297

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 4 E3 UBIQUITIN-PROTEIN LIGASE CBL-B × 1 （Q13191） TYROSINE-PROTEIN KINASE ZAP-70 × 1 （P43403） POLYUBIQUITIN-C × 1 （P0CG48） ZINC ION × 2 CALCIUM ION × 1 1,2-ETHANEDIOL × 1 water × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 E3 UBIQUITIN-PROTEIN LIGASE CBL-B × 1 （Q13191） TYROSINE-PROTEIN KINASE ZAP-70 × 1 （P43403） POLYUBIQUITIN-C × 1 （P0CG48） ZINC ION × 2 CALCIUM ION × 1 1,2-ETHANEDIOL × 1 water × 4 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 4 E3 UBIQUITIN-PROTEIN LIGASE CBL-B × 1 （Q13191） TYROSINE-PROTEIN KINASE ZAP-70 × 1 （P43403） POLYUBIQUITIN-C × 1 （P0CG48） ZINC ION × 2 CALCIUM ION × 1 1,2-ETHANEDIOL × 1 water × 4 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 4 E3 UBIQUITIN-PROTEIN LIGASE CBL-B × 1 （Q13191） TYROSINE-PROTEIN KINASE ZAP-70 × 1 （P43403） POLYUBIQUITIN-C × 1 （P0CG48） ZINC ION × 2 CALCIUM ION × 1 1,2-ETHANEDIOL × 1 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 3
Chains and sequence ranges Author chain C； PDBConstruct 1–146； UniProt 2–147 Author chain G； PDBConstruct 1–146； UniProt 2–147 Author chain K； PDBConstruct 1–146； UniProt 2–147 Author chain O； 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 4 E3 UBIQUITIN-PROTEIN LIGASE CBL-B × 1 （Q13191） TYROSINE-PROTEIN KINASE ZAP-70 × 1 （P43403） UBIQUITIN-CONJUGATING ENZYME E2 D2 × 1 （P62837） ZINC ION × 2 CALCIUM ION × 1 1,2-ETHANEDIOL × 1 water × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 E3 UBIQUITIN-PROTEIN LIGASE CBL-B × 1 （Q13191） TYROSINE-PROTEIN KINASE ZAP-70 × 1 （P43403） UBIQUITIN-CONJUGATING ENZYME E2 D2 × 1 （P62837） ZINC ION × 2 CALCIUM ION × 1 1,2-ETHANEDIOL × 1 water × 4 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 4 E3 UBIQUITIN-PROTEIN LIGASE CBL-B × 1 （Q13191） TYROSINE-PROTEIN KINASE ZAP-70 × 1 （P43403） UBIQUITIN-CONJUGATING ENZYME E2 D2 × 1 （P62837） ZINC ION × 2 CALCIUM ION × 1 1,2-ETHANEDIOL × 1 water × 4 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 4 E3 UBIQUITIN-PROTEIN LIGASE CBL-B × 1 （Q13191） TYROSINE-PROTEIN KINASE ZAP-70 × 1 （P43403） UBIQUITIN-CONJUGATING ENZYME E2 D2 × 1 （P62837） ZINC ION × 2 CALCIUM ION × 1 1,2-ETHANEDIOL × 1 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 4
Chains and sequence ranges Author chain D； PDBConstruct 6–81； UniProt 77–152 Author chain H； PDBConstruct 6–81； UniProt 77–152 Author chain L； PDBConstruct 6–81； UniProt 77–152 Author chain P； PDBConstruct 6–81； UniProt 77–152

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_id3zni
Deposition date deposition_date2013-02-14
Structure title titleStructure of phosphoTyr363-Cbl-b - UbcH5B-Ub - ZAP-70 peptide complex
Keywords keywordsLIGASE, LIGASES, DEGRADATION; 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.

3zni__assembly_1__model_1

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

Download this curve (.dat)

3zni__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.

3zni__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）28.83 Å
Rg (electron density)27.91 Å
Total Rg28.63 Å
Atom count4924
Residues620
Excluded volume87812 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3zni__assembly_1__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3zni__assembly_2__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 3zni__assembly_3__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 3zni__assembly_4__model_1 tetrameric （4） 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 (8)

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6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

Domain ID domain_id3zniA01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology930 — Transcription Elongation Factor S-II; Chain A
Homologous superfamily homologous superfamily20 — Adaptor protein Cbl, N-terminal domain
Domain ID domain_id3zniA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id3zniA03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology505 — SHC Adaptor Protein
Homologous superfamily homologous superfamily10 — SH2 domain
Domain ID domain_id3zniA04
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_id3zniC00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily10 — Ubiquitin Conjugating Enzyme
Domain ID domain_id3zniD00
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_id3zniE01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology930 — Transcription Elongation Factor S-II; Chain A
Homologous superfamily homologous superfamily20 — Adaptor protein Cbl, N-terminal domain
Domain ID domain_id3zniE02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id3zniE03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology505 — SHC Adaptor Protein
Homologous superfamily homologous superfamily10 — SH2 domain
Domain ID domain_id3zniE04
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_id3zniG00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily10 — Ubiquitin Conjugating Enzyme
Domain ID domain_id3zniH00
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_id3zniI01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology930 — Transcription Elongation Factor S-II; Chain A
Homologous superfamily homologous superfamily20 — Adaptor protein Cbl, N-terminal domain
Domain ID domain_id3zniI02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id3zniI03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology505 — SHC Adaptor Protein
Homologous superfamily homologous superfamily10 — SH2 domain
Domain ID domain_id3zniI04
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_id3zniK00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily10 — Ubiquitin Conjugating Enzyme
Domain ID domain_id3zniL00
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_id3zniM01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology930 — Transcription Elongation Factor S-II; Chain A
Homologous superfamily homologous superfamily20 — Adaptor protein Cbl, N-terminal domain
Domain ID domain_id3zniM02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id3zniM03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology505 — SHC Adaptor Protein
Homologous superfamily homologous superfamily10 — SH2 domain
Domain ID domain_id3zniM04
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_id3zniO00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily10 — Ubiquitin Conjugating Enzyme
Domain ID domain_id3zniP00
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)