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1jpl

GGA3 VHS domain complexed with C-terminal peptide from cation-independent mannose 6-phosphate receptor

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

ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3

Homo sapiens

UniProt Q9NZ52

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 Cation-Independent Mannose 6-phosphate receptor × 1 （P11717） water × 2 Consistent with protein count
10 Protein heterocomplex Heteromer Protein 4 Cation-Independent Mannose 6-phosphate receptor × 2 （P11717） water × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 Cation-Independent Mannose 6-phosphate receptor × 1 （P11717） water × 2 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 2 Cation-Independent Mannose 6-phosphate receptor × 1 （P11717） water × 2 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 2 Cation-Independent Mannose 6-phosphate receptor × 1 （P11717） water × 2 Consistent with protein count
5 Protein heterocomplex Heteromer Protein 8 Cation-Independent Mannose 6-phosphate receptor × 4 （P11717） water × 8 Consistent with protein count
6 Protein heterocomplex Heteromer Protein 8 Cation-Independent Mannose 6-phosphate receptor × 4 （P11717） water × 8 Consistent with protein count
7 Protein heterocomplex Heteromer Protein 8 Cation-Independent Mannose 6-phosphate receptor × 4 （P11717） water × 8 Consistent with protein count
8 Protein heterocomplex Heteromer Protein 8 Cation-Independent Mannose 6-phosphate receptor × 4 （P11717） water × 8 Consistent with protein count
9 Protein heterocomplex Heteromer Protein 4 Cation-Independent Mannose 6-phosphate receptor × 2 （P11717） water × 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
1jpl 1jpl 1jpl 1jpl 1jpl 1jpl 1jpl 1jpl 1jpl 1jpl 1juq 1juq

28 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name GGA3_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 6–171； UniProt 1–166 Author chain B； PDBConstruct 6–171； UniProt 1–166 Author chain C； PDBConstruct 6–171； UniProt 1–166 Author chain D； PDBConstruct 6–171； UniProt 1–166

Cation-Independent Mannose 6-phosphate receptor

OrganismNot specified

UniProt P11717

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3 × 1 （Q9NZ52） water × 2 Consistent with protein count
10 Protein heterocomplex Heteromer Protein 4 ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3 × 2 （Q9NZ52） water × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3 × 1 （Q9NZ52） water × 2 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 2 ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3 × 1 （Q9NZ52） water × 2 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 2 ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3 × 1 （Q9NZ52） water × 2 Consistent with protein count
5 Protein heterocomplex Heteromer Protein 8 ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3 × 4 （Q9NZ52） water × 8 Consistent with protein count
6 Protein heterocomplex Heteromer Protein 8 ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3 × 4 （Q9NZ52） water × 8 Consistent with protein count
7 Protein heterocomplex Heteromer Protein 8 ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3 × 4 （Q9NZ52） water × 8 Consistent with protein count
8 Protein heterocomplex Heteromer Protein 8 ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3 × 4 （Q9NZ52） water × 8 Consistent with protein count
9 Protein heterocomplex Heteromer Protein 4 ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3 × 2 （Q9NZ52） water × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1e6f 1e6f 1gp0 1gp3 1gqb 1gqb 2cnj 2v5n 2v5o 5iei 6v02 6z31

13 assemblies; showing the first 12

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1jpl 1jpl 1jpl 1jpl 1jpl 1jpl 1jpl 1jpl 1jpl 1jpl 1jwg 1jwg

25 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name MPRI_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain E； PDBConstruct 1–12； UniProt 2480–2491 Author chain F； PDBConstruct 1–12； UniProt 2480–2491 Author chain G； PDBConstruct 1–12； UniProt 2480–2491 Author chain H； PDBConstruct 1–12； UniProt 2480–2491

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_id1jpl
Deposition date deposition_date2001-08-02
Structure title titleGGA3 VHS domain complexed with C-terminal peptide from cation-independent mannose 6-phosphate receptor
Keywords keywordsProtein-peptide complex; VHS domain; DXXLL sorting signal, SIGNALING PROTEIN; 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.

1jpl__assembly_1__model_1

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

Download this curve (.dat)

1jpl__assembly_1__model_1 | I(q)

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

1jpl__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）16.95 Å
Rg (electron density)15.52 Å
Total Rg16.64 Å
Atom count1359
Residues164
Excluded volume24371 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1jpl__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 1jpl__assembly_2__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 1jpl__assembly_3__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 1jpl__assembly_4__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
5 1 1jpl__assembly_5__model_1 octameric （8） Success 4.1.3-1-20251215 (887e7ef) View Download
6 1 1jpl__assembly_6__model_1 octameric （8） Success 4.1.3-1-20251215 (887e7ef) View Download
7 1 1jpl__assembly_7__model_1 octameric （8） Success 4.1.3-1-20251215 (887e7ef) View Download
8 1 1jpl__assembly_8__model_1 octameric （8） Success 4.1.3-1-20251215 (887e7ef) View Download
9 1 1jpl__assembly_9__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
10 1 1jpl__assembly_10__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 (3)

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd1jpla1
Class classa — All alpha proteins
Fold Fold folda.118 — alpha-alpha superhelix
Superfamily Superfamily superfamilya.118.9 — ENTH/VHS domain
Family Family familya.118.9.2 — VHS domain
Domain ID domain_idd1jpla2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1jplb1
Class classa — All alpha proteins
Fold Fold folda.118 — alpha-alpha superhelix
Superfamily Superfamily superfamilya.118.9 — ENTH/VHS domain
Family Family familya.118.9.2 — VHS domain
Domain ID domain_idd1jplb2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1jplc1
Class classa — All alpha proteins
Fold Fold folda.118 — alpha-alpha superhelix
Superfamily Superfamily superfamilya.118.9 — ENTH/VHS domain
Family Family familya.118.9.2 — VHS domain
Domain ID domain_idd1jplc2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1jpld1
Class classa — All alpha proteins
Fold Fold folda.118 — alpha-alpha superhelix
Superfamily Superfamily superfamilya.118.9 — ENTH/VHS domain
Family Family familya.118.9.2 — VHS domain
Domain ID domain_idd1jpld2
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_id1jplA00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily90 —
Domain ID domain_id1jplB00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily90 —
Domain ID domain_id1jplC00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily90 —
Domain ID domain_id1jplD00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily90 —
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7. Citations (1)