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1vg0

The crystal structures of the REP-1 protein in complex with monoprenylated Rab7 protein

Method: X-RAY DIFFRACTION Dmax: 88.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Rab proteins geranylgeranyltransferase component A 1

Rattus norvegicus

UniProt P37727

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 1–650 Mutation：K231Q, K462R, T473A, A483G Ras-related protein Rab-7 × 1 （P09527） CL CHLORIDE ION × 1 GER GERAN-8-YL GERAN × 1 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 PG4 TETRAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；23% PEG 3350, 0.4M diAmmonium Tartrate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.20 Å R-free 0.233

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.

Other PDB Difference from Current Entry 1VG0 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1LTX Structure of Rab Escort Protein-1 in complex with Rab geranylgeranyl transferase and isoprenoid Deposited 2002-05-21 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain R 1–650（650 aa）
Mutation：A473T, G483A, Q231K ZN ZINC ION × 1 CL CHLORIDE ION × 1 FAR FARNESYL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；20% PEG 3350, 100mM KSCN, 100mM Namalonate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.70 Å R-free 0.272
1VG9 The crystal structures of the REP-1 protein in complex with C-terminally truncated Rab7 protein Deposited 2004-04-23 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–650（650 aa）
Mutation：K231Q, K462R, T473A, A483G MG MAGNESIUM ION × 1 K POTASSIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 P33 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；23% PEG 2000 MME, 0.4M Potassium Formate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.50 Å R-free 0.250
1VG9 The crystal structures of the REP-1 protein in complex with C-terminally truncated Rab7 protein Deposited 2004-04-23 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–650（650 aa）
Mutation：K231Q, K462R, T473A, A483G MG MAGNESIUM ION × 1 K POTASSIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 P33 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；23% PEG 2000 MME, 0.4M Potassium Formate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.50 Å R-free 0.250
1VG9 The crystal structures of the REP-1 protein in complex with C-terminally truncated Rab7 protein Deposited 2004-04-23 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 1–650（650 aa）
Mutation：K231Q, K462R, T473A, A483G MG MAGNESIUM ION × 1 K POTASSIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 P33 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；23% PEG 2000 MME, 0.4M Potassium Formate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.50 Å R-free 0.250
1VG9 The crystal structures of the REP-1 protein in complex with C-terminally truncated Rab7 protein Deposited 2004-04-23 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 1–650（650 aa）
Mutation：K231Q, K462R, T473A, A483G MG MAGNESIUM ION × 1 K POTASSIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 P33 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；23% PEG 2000 MME, 0.4M Potassium Formate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.50 Å R-free 0.250

2 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RAE1_RAT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–650； UniProt 1–650

Ras-related protein Rab-7

Rattus norvegicus

UniProt P09527

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 1–207 Not recorded Rab proteins geranylgeranyltransferase component A 1 × 1 （P37727） CL CHLORIDE ION × 1 GER GERAN-8-YL GERAN × 1 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 PG4 TETRAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；23% PEG 3350, 0.4M diAmmonium Tartrate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.20 Å R-free 0.233

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.

Other PDB Difference from Current Entry 1VG0 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1VG1 GDP-Bound Rab7 Deposited 2004-04-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–185（185 aa） Fragment：Gtpase Domain
Not recorded MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；25% PEG 3350, 0.25M Ammonium Phosphate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.90 Å R-free 0.247
1VG8 GPPNHP-Bound Rab7 Deposited 2004-04-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–207（207 aa）
Not recorded MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；24% PEG 3350, 0.25M Ammonium Phosphate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.70 Å R-free 0.224
1VG8 GPPNHP-Bound Rab7 Deposited 2004-04-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–207（207 aa）
Not recorded MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；24% PEG 3350, 0.25M Ammonium Phosphate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.70 Å R-free 0.224
1VG8 GPPNHP-Bound Rab7 Deposited 2004-04-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–207（207 aa）
Not recorded MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；24% PEG 3350, 0.25M Ammonium Phosphate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.70 Å R-free 0.224
1VG8 GPPNHP-Bound Rab7 Deposited 2004-04-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–207（207 aa）
Not recorded MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；24% PEG 3350, 0.25M Ammonium Phosphate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.70 Å R-free 0.224
1VG9 The crystal structures of the REP-1 protein in complex with C-terminally truncated Rab7 protein Deposited 2004-04-23 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–185（185 aa） Fragment：GTPase domain
Not recorded MG MAGNESIUM ION × 1 K POTASSIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 P33 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；23% PEG 2000 MME, 0.4M Potassium Formate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.50 Å R-free 0.250
1VG9 The crystal structures of the REP-1 protein in complex with C-terminally truncated Rab7 protein Deposited 2004-04-23 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–185（185 aa） Fragment：GTPase domain
Not recorded MG MAGNESIUM ION × 1 K POTASSIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 P33 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；23% PEG 2000 MME, 0.4M Potassium Formate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.50 Å R-free 0.250
1VG9 The crystal structures of the REP-1 protein in complex with C-terminally truncated Rab7 protein Deposited 2004-04-23 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–185（185 aa） Fragment：GTPase domain
Not recorded MG MAGNESIUM ION × 1 K POTASSIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 P33 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；23% PEG 2000 MME, 0.4M Potassium Formate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.50 Å R-free 0.250
1VG9 The crystal structures of the REP-1 protein in complex with C-terminally truncated Rab7 protein Deposited 2004-04-23 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1–185（185 aa） Fragment：GTPase domain
Not recorded MG MAGNESIUM ION × 1 K POTASSIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 P33 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；23% PEG 2000 MME, 0.4M Potassium Formate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.50 Å R-free 0.250

3 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RAB7_RAT
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–207； UniProt 1–207

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 1vg0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1vg0
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1vg0
Deposition date deposition_date2004-04-22
Structure title titleThe crystal structures of the REP-1 protein in complex with monoprenylated Rab7 protein
Keywords keywordsRAB PRENYLATION, POST-TRANSLATIONAL MODIFICATION, PROTEIN BINDING-PROTEIN TRANSPORT COMPLEX; PROTEIN BINDING/PROTEIN TRANSPORT
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier28.00 Å
Radius of gyration Rg (electron density) rg_electron27.07 Å
Forward intensity I(0) i092879000.00
Molecular weight molecular_weight76024.0 kDa
Excluded volume excluded_volume95210 ų
Envelope volume envelope_volume115980 ų
Hydration-shell volume shell_volume35450 ų
Envelope diameter envelope_diameter95.2 Å
Shell Rg shell_rg34.78 Å
Envelope Rg envelope_rg27.29 Å
Shape Rg shape_rg27.06 Å
Total Rg total_rg27.85 Å
Total atoms total_atoms5335
Residues n_residues663
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax88.3 Å
Rg (real space) rg_real27.92 Å
Rg uncertainty (real space) rg_real_error0.66 Å
I(0) (real space) i0_real9.2880e+07
I(0) uncertainty (real space) i0_real_error1.5320e+06
Rg (reciprocal space) rg_reciprocal27.95 Å
I(0) (reciprocal space) i0_reciprocal92880000.0000
Solution quality estimate total_estimate0.8266
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary32.5 Å
Skewness Skewness skewness0.270
Kurtosis Kurtosis kurtosis-0.392
Angular range angular_range— – 0.2850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha23730000.0000
Real-space data points n_real_points58
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.915; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

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7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1vg0a1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamilyc.3.1 — FAD/NAD(P)-binding domain
Family Family familyc.3.1.3 — GDI-like N domain
Domain ID domain_idd1vg0a2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.16 — FAD-linked reductases, C-terminal domain
Superfamily Superfamily superfamilyd.16.1 — FAD-linked reductases, C-terminal domain
Family Family familyd.16.1.6 — GDI-like
Domain ID domain_idd1vg0b_
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

CATH v4.4 (4 domains)

Domain ID domain_id1vg0A01
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily60 — FAD/NAD(P)-binding domain
Domain ID domain_id1vg0A02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology519 — Guanine Nucleotide Dissociation Inhibitor; domain 2
Homologous superfamily homologous superfamily10 — Guanine Nucleotide Dissociation Inhibitor, domain 2
Domain ID domain_id1vg0A03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology405 — Guanine Nucleotide Dissociation Inhibitor; domain 1
Homologous superfamily homologous superfamily10 — Guanine Nucleotide Dissociation Inhibitor, domain 1
Domain ID domain_id1vg0B00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
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8. Citations (1)

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9. Files and Curves (10)