3cpi

Crystal structure of yeast Rab-GDI

Method: X-RAY DIFFRACTION

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

Rab GDP-dissociation inhibitor

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GDI1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain G； PDBConstruct 1–451； UniProt 1–451 Author chain H； PDBConstruct 1–451； UniProt 1–451

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	3cpi
Deposition date deposition_date	2008-03-31
Structure title title	Crystal structure of yeast Rab-GDI
Keywords keywords	Rab, GDI, vesicular transport, Cytoplasm, GTPase activation, Phosphoprotein, Protein transport; PROTEIN TRANSPORT
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.

3cpi__assembly_1__model_1

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

Download this curve (.dat)

3cpi__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3cpi__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.07 Å
Rg (electron density)	23.02 Å
Total Rg	23.94 Å
Atom count	3480
Residues	437
Excluded volume	62323 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3cpi__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3cpi__assembly_2__model_1`	monomeric （1）	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 (2)

Entity 1 Entity 1 polymer

Description description	Rab GDP-dissociation inhibitor
Molecular weight formula_weight	51271.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H
Atom count atom_count	7776

MDQETIDTDYDVIVLGTGITECILSGLLSVDGKKVLHIDKQDHYGGEAASVTLSQLYEKFKQNPISKEERESKFGKDRDWNVDLIPKFLMANGELTNILIHTDVTRYVDFKQVSGSYVFKQGKIYKVPANEIEAISSPLMGIFEKRRMKKFLEWISSYKEDDLSTHQGLDLDKNTMDEVYYKFGLGNSTKEFIGHAMALWTNDDYLQQPARPSFERILLYCQSVARYGKSPYLYPMYGLGELPQGFARLSAIYGGTYMLDTPIDEVLYKKDTGKFEGVKTKLGTFKAPLVIADPTYFPEKCKSTGQRVIRAICILNHPVPNTSNADSLQIIIPQSQLGRKSDIYVAIVSDAHNVCSKGHYLAIISTIIETDKPHIELEPAFKLLGPIEEKFMGIAELFEPREDGSKDNIYLSRSYDASSHFESMTDDVKDIYFRVTGHPLVLKQRQEQEKQ

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	797

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d3cpig1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
Family Family family	c.3.1.3 — GDI-like N domain

Domain ID domain_id	d3cpig2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
Family Family family	c.3.1.0 — automated matches

Domain ID domain_id	d3cpig3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.16 — FAD-linked reductases, C-terminal domain
Superfamily Superfamily superfamily	d.16.1 — FAD-linked reductases, C-terminal domain
Family Family family	d.16.1.0 — automated matches

Domain ID domain_id	d3cpih1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
Family Family family	c.3.1.3 — GDI-like N domain

Domain ID domain_id	d3cpih2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
Family Family family	c.3.1.0 — automated matches

Domain ID domain_id	d3cpih3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.16 — FAD-linked reductases, C-terminal domain
Superfamily Superfamily superfamily	d.16.1 — FAD-linked reductases, C-terminal domain
Family Family family	d.16.1.0 — automated matches

CATH v4.4 (6 domains)

Domain ID domain_id	3cpiG01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	3cpiG02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	519 — Guanine Nucleotide Dissociation Inhibitor; domain 2
Homologous superfamily homologous superfamily	10 — Guanine Nucleotide Dissociation Inhibitor, domain 2

Domain ID domain_id	3cpiG03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	405 — Guanine Nucleotide Dissociation Inhibitor; domain 1
Homologous superfamily homologous superfamily	10 — Guanine Nucleotide Dissociation Inhibitor, domain 1

Domain ID domain_id	3cpiH01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	3cpiH02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	519 — Guanine Nucleotide Dissociation Inhibitor; domain 2
Homologous superfamily homologous superfamily	10 — Guanine Nucleotide Dissociation Inhibitor, domain 2

Domain ID domain_id	3cpiH03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	405 — Guanine Nucleotide Dissociation Inhibitor; domain 1
Homologous superfamily homologous superfamily	10 — Guanine Nucleotide Dissociation Inhibitor, domain 1

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Unit-cell length a length_a	56.460 Å
Unit-cell length b length_b	159.780 Å
Unit-cell length c length_c	77.093 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.25 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	19.970 Å
R factor r_factor	0.1992
R_work r_work	0.1969
R_free r_free	0.2426

Crystal structure of yeast Rab-GDI

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

Rab GDP-dissociation inhibitor

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

3cpi__assembly_1__model_1

3cpi__assembly_1__model_1 | I(q)

3cpi__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of yeast Rab-GDI

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

Rab GDP-dissociation inhibitor

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

3cpi__assembly_1__model_1

3cpi__assembly_1__model_1 | I(q)

3cpi__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)