1zbd

STRUCTURAL BASIS OF RAB EFFECTOR SPECIFICITY: CRYSTAL STRUCTURE OF THE SMALL G PROTEIN RAB3A COMPLEXED WITH THE EFFECTOR DOMAIN OF RABPHILIN-3A

Method: X-RAY DIFFRACTION Dmax: 83.9 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

RABPHILIN-3A

Rattus norvegicus

UniProt P63012

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 19–217 Fragment:19-217 Mutation:Q81L Non-standard monomer:Yes (specific site not provided by mmCIF) RABPHILIN-3A × 1 (P47709) MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:pH 8;pH 8.0 Resolution 2.60 Å R-free 0.263
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 19–217 Fragment:19-217 Mutation:Q81L Non-standard monomer:Yes (specific site not provided by mmCIF) RABPHILIN-3A × 2 (P47709) MG MAGNESIUM ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 ZN ZINC ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:pH 8;pH 8.0 Resolution 2.60 Å R-free 0.263

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RAB3A_RAT
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 5–203; UniProt 19–217

RABPHILIN-3A

Rattus norvegicus

UniProt P47709

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 41–170 Fragment:40-170, EFFECTOR DOMAIN Mutation:C108S Non-standard monomer:Yes (specific site not provided by mmCIF) RABPHILIN-3A × 1 (P63012) MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:pH 8;pH 8.0 Resolution 2.60 Å R-free 0.263
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 41–170 Fragment:40-170, EFFECTOR DOMAIN Mutation:C108S Non-standard monomer:Yes (specific site not provided by mmCIF) RABPHILIN-3A × 2 (P63012) MG MAGNESIUM ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 ZN ZINC ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:pH 8;pH 8.0 Resolution 2.60 Å R-free 0.263

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

10 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RP3A_RAT
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 5–134; UniProt 41–170

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.

SAXS scattering curve SAXS Profile

SAXS profile for 1zbd

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1zbd
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1zbd
Deposition date deposition_date1998-11-06
Structure title titleSTRUCTURAL BASIS OF RAB EFFECTOR SPECIFICITY: CRYSTAL STRUCTURE OF THE SMALL G PROTEIN RAB3A COMPLEXED WITH THE EFFECTOR DOMAIN OF RABPHILIN-3A
Keywords keywordsG PROTEIN, EFFECTOR, RABCDR, SYNAPTIC EXOCYTOSIS, RAB PROTEIN, RAB3A, RABPHILIN; G PROTEIN
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier24.06
Radius of gyration Rg (electron density) rg_electron23.19
Forward intensity I(0) i024768800.00
Molecular weight molecular_weight35888.0 kDa
Excluded volume excluded_volume43845 ų
Envelope volume envelope_volume53609 ų
Hydration-shell volume shell_volume21005 ų
Envelope diameter envelope_diameter87.5
Shell Rg shell_rg28.03
Envelope Rg envelope_rg23.47
Shape Rg shape_rg23.06
Total Rg total_rg24.17
Total atoms total_atoms2464
Residues n_residues290
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax83.9
Rg (real space) rg_real24.27
Rg uncertainty (real space) rg_real_error0.76
I(0) (real space) i0_real2.4770e+07
I(0) uncertainty (real space) i0_real_error3.6990e+05
Rg (reciprocal space) rg_reciprocal24.22
I(0) (reciprocal space) i0_reciprocal24770000.0000
Solution quality estimate total_estimate0.8393
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.9
Skewness Skewness skewness0.575
Kurtosis Kurtosis kurtosis-0.110
Angular range angular_range— – 0.3300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3267000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.735; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.783; Smooth: 0.921

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1zbda_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.8 — G proteins
Domain ID domain_idd1zbdb_
Class classg — Small proteins
Fold Fold foldg.50 — FYVE/PHD zinc finger
Superfamily Superfamily superfamilyg.50.1 — FYVE/PHD zinc finger
Family Family familyg.50.1.1 — FYVE, a phosphatidylinositol-3-phosphate binding domain

CATH v4.4 (2 domains)

Domain ID domain_id1zbdA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id1zbdB00
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)

8. Citations (1)

9. Files and Curves (10)