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4n3z

Crystal structure of Rabex-5delta and Rabaptin-5C21 complex

Method: X-RAY DIFFRACTION Dmax: 93.4 Å Quality: GOOD
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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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 132–455 Fragment：UNP residues, isoform 2, 132-455 Mutation：residues 387-408 deletion mutant Rab GTPase-binding effector protein 1 × 2 （Q15276） 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

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 4N3Z 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
2OT3 Crystal structure of rabex-5 VPS9 domain in complex with nucleotide free RAB21 Deposited 2007-02-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 132–397（266 aa） Fragment：residues 132-297
Not recorded No recorded non-water small molecule 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
4N3X Crystal structure of Rabex-5 CC domain 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 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 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 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 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 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 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 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 mutation/modification Different ligand/ion 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
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 ligand/ion 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 9–310； UniProt 132–455

Rab GTPase-binding effector protein 1

Homo sapiens

UniProt Q15276

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain B； UniProt 552–642 Chain C； UniProt 552–642 Fragment：UNP residues 552-642 Rab5 GDP/GTP exchange factor × 1 （Q9UJ41） 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

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 4N3Z Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1P4U CRYSTAL STRUCTURE OF GGA3 GAE DOMAIN IN COMPLEX WITH RABAPTIN-5 PEPTIDE Deposited 2003-04-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 435–447（13 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；1.6M sodium citrate, pH 6.5
Resolution 2.20 Å R-free 0.255
1P4U CRYSTAL STRUCTURE OF GGA3 GAE DOMAIN IN COMPLEX WITH RABAPTIN-5 PEPTIDE Deposited 2003-04-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 435–447（13 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；1.6M sodium citrate, pH 6.5
Resolution 2.20 Å R-free 0.255
1TU3 Crystal Structure of Rab5 complex with Rabaptin5 C-terminal Domain Deposited 2004-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 789–862（74 aa）
Chain G 789–862（74 aa）
Not recorded MG MAGNESIUM ION × 2 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；PEG3350, ammonium bromide, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.31 Å R-free 0.277
1TU3 Crystal Structure of Rab5 complex with Rabaptin5 C-terminal Domain Deposited 2004-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain H 789–862（74 aa）
Chain I 789–862（74 aa）
Not recorded MG MAGNESIUM ION × 2 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；PEG3350, ammonium bromide, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.31 Å R-free 0.277
1TU3 Crystal Structure of Rab5 complex with Rabaptin5 C-terminal Domain Deposited 2004-06-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain J 789–862（74 aa）
Not recorded MG MAGNESIUM ION × 2 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；PEG3350, ammonium bromide, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.31 Å R-free 0.277
1X79 Crystal structure of human GGA1 GAT domain complexed with the GAT-binding domain of Rabaptin5 Deposited 2004-08-13 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 551–661（111 aa）
Chain C 551–661（111 aa）
Not recorded SO4 SULFATE ION × 2 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；293 K；AMMONIUM SULFATE, TRIS, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.41 Å R-free 0.283
4N3Y Crystal structure of Rabex-5CC and Rabaptin-5C21 complex Deposited 2013-10-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 552–642（91 aa） Fragment：UNP residues 552-642
Chain C 552–642（91 aa） Fragment：UNP residues 552-642
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
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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain C 552–642（91 aa） Fragment：UNP residues 552-642
Chain D 552–642（91 aa） Fragment：UNP residues 552-642
Chain G 552–642（91 aa） Fragment：UNP residues 552-642
Chain H 552–642（91 aa） Fragment：UNP residues 552-642
Not recorded 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 RABE1_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 2–92； UniProt 552–642 Author chain C； PDBConstruct 2–92； UniProt 552–642

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 4n3z

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4n3z
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4n3z
Deposition date deposition_date2013-10-08
Structure title titleCrystal structure of Rabex-5delta and Rabaptin-5C21 complex
Keywords keywordsRab5, Rabex-5, Rabaptin-5, GEF activity, endocytosis, early endosome; ENDOCYTOSIS
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_guinier27.87 Å
Radius of gyration Rg (electron density) rg_electron27.34 Å
Forward intensity I(0) i035908300.00
Molecular weight molecular_weight44000.0 kDa
Excluded volume excluded_volume54266 ų
Envelope volume envelope_volume75816 ų
Hydration-shell volume shell_volume24785 ų
Envelope diameter envelope_diameter95.1 Å
Shell Rg shell_rg32.40 Å
Envelope Rg envelope_rg27.60 Å
Shape Rg shape_rg27.29 Å
Total Rg total_rg28.04 Å
Total atoms total_atoms3074
Residues n_residues403
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 dmax93.4 Å
Rg (real space) rg_real27.95 Å
Rg uncertainty (real space) rg_real_error0.91 Å
I(0) (real space) i0_real3.5910e+07
I(0) uncertainty (real space) i0_real_error5.3410e+05
Rg (reciprocal space) rg_reciprocal27.93 Å
I(0) (reciprocal space) i0_reciprocal35910000.0000
Solution quality estimate total_estimate0.8926
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary32.8 Å
Skewness Skewness skewness0.374
Kurtosis Kurtosis kurtosis-0.339
Angular range angular_range— – 0.2850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3358000.0000
Real-space data points n_real_points58
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.898; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.940; Smooth: 0.971
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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) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd4n3zb_
Class classh — Coiled coil proteins
Fold Fold foldh.1 — Parallel coiled-coil
Superfamily Superfamily superfamilyh.1.27 — G protein-binding domain
Family Family familyh.1.27.2 — Rabaptin-5
Domain ID domain_idd4n3zc_
Class classh — Coiled coil proteins
Fold Fold foldh.1 — Parallel coiled-coil
Superfamily Superfamily superfamilyh.1.27 — G protein-binding domain
Family Family familyh.1.27.2 — Rabaptin-5

CATH v4.4 (1 domains)

Domain ID domain_id4n3zA02
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
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8. Citations (1)

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9. Files and Curves (10)