SAXSdb — 4q9u

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

Rab5 GDP/GTP exchange factor

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Ras-related protein Rab-5A × 2 （P20339） Rab GTPase-binding effector protein 1 × 4 （Q15276）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RABX5_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–317； UniProt 132–455 Author chain E； PDBConstruct 9–317； UniProt 132–455

Ras-related protein Rab-5A

Homo sapiens

UniProt P20339

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Rab5 GDP/GTP exchange factor × 2 （Q9UJ41） Rab GTPase-binding effector protein 1 × 4 （Q15276）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RAB5A_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–171； UniProt 15–184 Author chain F； PDBConstruct 2–171； UniProt 15–184

Rab GTPase-binding effector protein 1

Homo sapiens

UniProt Q15276

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Rab5 GDP/GTP exchange factor × 2 （Q9UJ41） Ras-related protein Rab-5A × 2 （P20339）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RABE1_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 2–92； UniProt 552–642 Author chain D； PDBConstruct 2–92； UniProt 552–642 Author chain G； PDBConstruct 2–92； UniProt 552–642 Author chain H； 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4q9u
Deposition date deposition_date	2014-05-01
Structure title title	Crystal structure of the Rab5, Rabex-5delta and Rabaptin-5C21 complex
Keywords keywords	Rab5, Rabex-5, Rabaptin-5, GEF activity, endocytosis, early endosomes, VPS9, coiled-coil, GEF, effector, small GTPases; ENDOCYTOSIS
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

4q9u__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4q9u__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4q9u__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	41.36 Å
Rg (electron density)	41.29 Å
Total Rg	41.60 Å
Atom count	9679
Residues	1196
Excluded volume	172720 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4q9u__assembly_1__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Rab5 GDP/GTP exchange factor
Molecular weight formula_weight	37320.9 kDa
Mutation mutation	393-407 deletion mutant
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E
Atom count atom_count	9679

MGHHHHHHSIETDRVSKEFIEFLKTFHKTGQEIYKQTKLFLEGMHYKRDLSIEEQSECAQDFYHNVAERMQTRGKVPPERVEKIMDQIEKYIMTRLYKYVFCPETTDDEKKDLAIQKRIRALRWVTPQMLCVPVNEDIPEVSDMVVKAITDIIEMDSKRVPRDKLACITKCSKHIFNAIKITKNEPASADDFLPTLIYIVLKGNPPRLQSNIQYITRFCNPSRLMTGEDGYYFTNLCCAVAFIEKLDAQSLNLSQEDFDRYMSGQTSPRKQMYKNLDLLSQLNERQERIMNEAKKLEKDLIDWTDGIAREVQDIVEK

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Ras-related protein Rab-5A
Molecular weight formula_weight	19074.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

SGNKICQFKLVLLGESAVGKSSLVLRFVKGQFHEFQESTIGAAFLTQTVCLDDTTVKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGNKADLANKRAVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKLPKN

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 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	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D,G,H

METRDQVKKLQLMLRQANDQLEKTMKDKQELEDFIKQSSEDSSHQISALVLRAQASEILLEELQQGLSQAKRDVQEQMAVLMQSREQVSEEL

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

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Unit-cell length a length_a	174.821 Å
Unit-cell length b length_b	174.821 Å
Unit-cell length c length_c	148.995 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	32

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	4.618 Å
Low-resolution limit resolution_low	40.781 Å
R factor r_factor	0.2561
R_work r_work	0.2513
R_free r_free	0.3427

Crystal structure of the Rab5, Rabex-5delta 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

Ras-related protein Rab-5A

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4q9u__assembly_1__model_1

4q9u__assembly_1__model_1 | I(q)

4q9u__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

7. Citations (1)

Crystal structure of the Rab5, Rabex-5delta 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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ras-related protein Rab-5A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Rab GTPase-binding effector protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4q9u__assembly_1__model_1

4q9u__assembly_1__model_1 | I(q)

4q9u__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

7. Citations (1)