SAXSdb — 4n3y

▼

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

Rab5 GDP/GTP exchange factor

Homo sapiens

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 630–672	Fragment：UNP residues 630-672	Rab GTPase-binding effector protein 1 × 2 （Q15276）	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

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 4N3Y	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 oligomeric state 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 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
4N3Z Crystal structure of Rabex-5delta 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 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 3–45； UniProt 630–672

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）	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

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 4N3Y	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 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 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
4N3Z Crystal structure of Rabex-5delta 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	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 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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4n3y
Deposition date deposition_date	2013-10-08
Structure title title	Crystal structure of Rabex-5CC and Rabaptin-5C21 complex
Keywords keywords	Rab5, Rabex-5, Rabaptin-5, GEF activity, endocytosis, early endosome; ENDOCYTOSIS
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	34.84 Å
Radius of gyration Rg (electron density) rg_electron	36.42 Å
Forward intensity I(0) i0	10043200.00
Molecular weight molecular_weight	23307.0 kDa
Excluded volume excluded_volume	28803 Å³
Envelope volume envelope_volume	40494 Å³
Hydration-shell volume shell_volume	12486 Å³
Envelope diameter envelope_diameter	130.2 Å
Shell Rg shell_rg	30.79 Å
Envelope Rg envelope_rg	37.31 Å
Shape Rg shape_rg	36.32 Å
Total Rg total_rg	36.21 Å
Total atoms total_atoms	1627
Residues n_residues	201
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

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

Maximum dimension Dmax dmax	129.8 Å
Rg (real space) rg_real	35.85 Å
Rg uncertainty (real space) rg_real_error	2.02 Å
I(0) (real space) i0_real	1.0040e+07
I(0) uncertainty (real space) i0_real_error	1.6640e+05
Rg (reciprocal space) rg_reciprocal	35.22 Å
I(0) (reciprocal space) i0_reciprocal	10040000.0000
Solution quality estimate total_estimate	0.5502
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	17.3 Å
Skewness Skewness skewness	0.687
Kurtosis Kurtosis kurtosis	-0.410
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	338500.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.050; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.006; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Rab5 GDP/GTP exchange factor
Molecular weight formula_weight	5261.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1814

GSNLDLLSQLNERQERIMNEAKKLEKDLIDWTDGIAREVQDIVEK

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Rab GTPase-binding effector protein 1
Molecular weight formula_weight	10701.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,C

METRDQVKKLQLMLRQANDQLEKTMKDKQELEDFIKQSSEDSSHQISALVLRAQASEILLEELQQGLSQAKRDVQEQMAVLMQSREQVSEEL

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	187

▼

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4n3yb_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.27 — G protein-binding domain
Family Family family	h.1.27.2 — Rabaptin-5

Domain ID domain_id	d4n3yc_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.27 — G protein-binding domain
Family Family family	h.1.27.2 — Rabaptin-5

CATH v4.4 (1 domains)

Domain ID domain_id	4n3yB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	340 —

▶

8. Citations (1)

▶

Unit-cell length a length_a	90.007 Å
Unit-cell length b length_b	28.857 Å
Unit-cell length c length_c	107.973 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.24 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	15.030 Å
R factor r_factor	0.1950
R_work r_work	0.1929
R_free r_free	0.2345

fit	/app/data/saxs_computation/n3/4n3y/4n3y.fit
pddf	/app/data/pr_computation/n3/4n3y/4n3y.pr.out
profile	/app/data/saxs_computation/n3/4n3y/4n3y.dat

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

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

Rab5 GDP/GTP exchange factor

State in the Current Structure

Other States of the Same Protein in the Database

Rab GTPase-binding effector protein 1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)