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2ot3

Crystal structure of rabex-5 VPS9 domain in complex with nucleotide free RAB21

Method: X-RAY DIFFRACTION Dmax: 76.6 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Rab5 GDP/GTP exchange factor

Homo sapiens

UniProt Q9UJ41

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 132–397 Fragment：residues 132-297 Ras-related protein Rab-21 × 1 （Q9UL25） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；10% PEG 6000, 0.2M MgCl2, 0.05 NaMES Microseeded, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.10 Å R-free 0.243

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 2OT3 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1TXU Crystal Structure of the Vps9 Domain of Rabex-5 Deposited 2004-07-06 Different construct Different mutation/modification 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 133–394（262 aa） Fragment：VPS9
Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；PEG 8000, MgCl, TRIS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 4K
Resolution 2.35 Å R-free 0.269
4N3X Crystal structure of Rabex-5 CC domain Deposited 2013-10-08 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 626–672（47 aa） Fragment：Rabex-5 CC domain, UNP residues 626-672
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；289 K；0.10M NaAc, 17.5% MPD, 2% PEG4000 , pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.00 Å R-free 0.234
4N3X Crystal structure of Rabex-5 CC domain Deposited 2013-10-08 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 626–672（47 aa） Fragment：Rabex-5 CC domain, UNP residues 626-672
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；289 K；0.10M NaAc, 17.5% MPD, 2% PEG4000 , pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.00 Å R-free 0.234
4N3X Crystal structure of Rabex-5 CC domain Deposited 2013-10-08 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 626–672（47 aa） Fragment：Rabex-5 CC domain, UNP residues 626-672
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；289 K；0.10M NaAc, 17.5% MPD, 2% PEG4000 , pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.00 Å R-free 0.234
4N3X Crystal structure of Rabex-5 CC domain Deposited 2013-10-08 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 626–672（47 aa） Fragment：Rabex-5 CC domain, UNP residues 626-672
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；289 K；0.10M NaAc, 17.5% MPD, 2% PEG4000 , pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.00 Å R-free 0.234
4N3Y Crystal structure of Rabex-5CC and Rabaptin-5C21 complex Deposited 2013-10-08 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 630–672（43 aa） Fragment：UNP residues 630-672
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.15M MgAc2, 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.20 Å R-free 0.234
4N3Z Crystal structure of Rabex-5delta and Rabaptin-5C21 complex Deposited 2013-10-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 132–455（324 aa） Fragment：UNP residues, isoform 2, 132-455
Mutation：residues 387-408 deletion mutant PO4 PHOSPHATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；2.0M NaH2PO4/K2HPO4, 0.05% n-octyl-beta-D-galactopyranoside, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 3.10 Å R-free 0.315
4Q9U Crystal structure of the Rab5, Rabex-5delta and Rabaptin-5C21 complex Deposited 2014-05-01 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 132–455（324 aa） Fragment：UNP residues 132-455
Chain E 132–455（324 aa） Fragment：UNP residues 132-455
Mutation：393-407 deletion mutant Mutation：393-407 deletion mutant No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 5；289 K；1.0M NaH2PO4/K2HPO4, pH 5.0, hanging drop, temperature 289K
Resolution 4.62 Å R-free 0.343

5 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RABX5_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 9–274； UniProt 132–397

Ras-related protein Rab-21

Homo sapiens

UniProt Q9UL25

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 16–183 Fragment：residues 16-183 Rab5 GDP/GTP exchange factor × 1 （Q9UJ41） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；10% PEG 6000, 0.2M MgCl2, 0.05 NaMES Microseeded, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.10 Å R-free 0.243

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 2OT3 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1YZT GppNHp-Bound Rab21 GTPase at 2.05 A Resolution Deposited 2005-02-28 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 16–183（168 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 8；277 K；18% PEG 6000, 200mM Lithium sufate, 50mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.05 Å R-free 0.286
1YZT GppNHp-Bound Rab21 GTPase at 2.05 A Resolution Deposited 2005-02-28 Different construct 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 16–183（168 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 8；277 K；18% PEG 6000, 200mM Lithium sufate, 50mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.05 Å R-free 0.286
1YZU GppNHp-Bound Rab21 GTPase at 2.50 A Resolution Deposited 2005-02-28 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 16–183（168 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 6.5；277 K；15% PEG 4000, 10% Glycerol, 200mM Na thiocyanate, 50mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.50 Å R-free 0.293
1YZU GppNHp-Bound Rab21 GTPase at 2.50 A Resolution Deposited 2005-02-28 Different construct 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 16–183（168 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 6.5；277 K；15% PEG 4000, 10% Glycerol, 200mM Na thiocyanate, 50mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.50 Å R-free 0.293
1Z08 GppNHp-Bound Rab21 Q53G mutant GTPase Deposited 2005-03-01 Different construct Different mutation/modification 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 16–183（168 aa） Fragment：GTPase domain
Mutation：Q53G MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；20% PEG 4000, 200mM Magnesium acetate, 50mM HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.80 Å R-free 0.225
1Z08 GppNHp-Bound Rab21 Q53G mutant GTPase Deposited 2005-03-01 Different construct Different mutation/modification 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 16–183（168 aa） Fragment：GTPase domain
Mutation：Q53G MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；20% PEG 4000, 200mM Magnesium acetate, 50mM HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.80 Å R-free 0.225
1Z08 GppNHp-Bound Rab21 Q53G mutant GTPase Deposited 2005-03-01 Different construct Different mutation/modification 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 16–183（168 aa） Fragment：GTPase domain
Mutation：Q53G MG MAGNESIUM ION × 2 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；20% PEG 4000, 200mM Magnesium acetate, 50mM HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.80 Å R-free 0.225
1Z08 GppNHp-Bound Rab21 Q53G mutant GTPase Deposited 2005-03-01 Different construct Different mutation/modification 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 16–183（168 aa） Fragment：GTPase domain
Mutation：Q53G MG MAGNESIUM ION × 4 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；20% PEG 4000, 200mM Magnesium acetate, 50mM HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.80 Å R-free 0.225
1Z08 GppNHp-Bound Rab21 Q53G mutant GTPase Deposited 2005-03-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 16–183（168 aa） Fragment：GTPase domain
Chain D 16–183（168 aa） Fragment：GTPase domain
Mutation：Q53G Mutation：Q53G MG MAGNESIUM ION × 6 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；20% PEG 4000, 200mM Magnesium acetate, 50mM HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.80 Å R-free 0.225
1Z0I GDP-Bound Rab21 GTPase Deposited 2005-03-01 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 16–183（168 aa）
Not recorded MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；277 K；20% PEG 6000, 10% Glycerol, 200mM Na acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.33 Å R-free 0.278

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

View Construct and Data Evidence
UniProt name RAB21_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 3–170； UniProt 16–183

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 2ot3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2ot3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2ot3
Deposition date deposition_date2007-02-07
Structure title titleCrystal structure of rabex-5 VPS9 domain in complex with nucleotide free RAB21
Keywords keywordsRabex-5, Vps9 Domain, Rab21, vesicular traffic, protein transport; 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_guinier24.09 Å
Radius of gyration Rg (electron density) rg_electron22.98 Å
Forward intensity I(0) i033803500.00
Molecular weight molecular_weight45304.0 kDa
Excluded volume excluded_volume56995 ų
Envelope volume envelope_volume68466 ų
Hydration-shell volume shell_volume25000 ų
Envelope diameter envelope_diameter78.1 Å
Shell Rg shell_rg30.09 Å
Envelope Rg envelope_rg23.25 Å
Shape Rg shape_rg22.99 Å
Total Rg total_rg23.80 Å
Total atoms total_atoms3179
Residues n_residues410
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 dmax76.6 Å
Rg (real space) rg_real24.01 Å
Rg uncertainty (real space) rg_real_error0.47 Å
I(0) (real space) i0_real3.3800e+07
I(0) uncertainty (real space) i0_real_error4.4360e+05
Rg (reciprocal space) rg_reciprocal24.03 Å
I(0) (reciprocal space) i0_reciprocal33800000.0000
Solution quality estimate total_estimate0.9067
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.7 Å
Skewness Skewness skewness0.233
Kurtosis Kurtosis kurtosis-0.457
Angular range angular_range— – 0.3300 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6245000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.929; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.997
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2ot3a_
Class classa — All alpha proteins
Fold Fold folda.222 — VPS9 domain
Superfamily Superfamily superfamilya.222.1 — VPS9 domain
Family Family familya.222.1.1 — VPS9 domain
Domain ID domain_idd2ot3b1
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 (3 domains)

Domain ID domain_id2ot3A01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily120 —
Domain ID domain_id2ot3A02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily80 — VPS9 domain
Domain ID domain_id2ot3B00
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)