SAXSdb — 3cpj

▼

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 heterocomplex	Heteromer	Protein 2	GTP-binding protein YPT31/YPT8 × 1 （P38555） CHLORIDE ION × 2 MAGNESIUM ION × 1 GUANOSINE-5'-DIPHOSPHATE × 1 water × 2	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

GTP-binding protein YPT31/YPT8

Saccharomyces cerevisiae

UniProt P38555

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Rab GDP-dissociation inhibitor × 1 （P39958） CHLORIDE ION × 2 MAGNESIUM ION × 1 GUANOSINE-5'-DIPHOSPHATE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YPT31_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–223； UniProt 1–223

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	3cpj
Deposition date deposition_date	2008-03-31
Structure title title	Crystal structure of Ypt31 in complex with yeast Rab-GDI
Keywords keywords	;Rab GTPase, prenylation, vesicular transport, Acetylation, Golgi apparatus, GTP-binding, Lipoprotein, Membrane, Nucleotide-binding, Protein transport, Cytoplasm, GTPase activation, Phosphoprotein ;; PROTEIN TRANSPORT
Experimental Method method	X-RAY DIFFRACTION

▼

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.

3cpj__assembly_1__model_1

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

Download this curve (.dat)

3cpj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3cpj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.74 Å
Rg (electron density)	26.82 Å
Total Rg	27.62 Å
Atom count	4780
Residues	602
Excluded volume	85320 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3cpj__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (6)

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	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G
Atom count atom_count	5232

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 polymer

Description description	GTP-binding protein YPT31/YPT8
Molecular weight formula_weight	24508.0 kDa
Mutation mutation	D58E
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MSSEDYGYDYDLLFKIVLIGDSGVGKSNLLSRFTKNEFNMDSKSTIGVEFATRTLEIEGKRIKAQIWDTAGQERYRAITSAYYRGAVGALIVYDISKSSSYENCNHWLSELRENADDNVAVGLIGNKSDLAHLRAVPTEESKTFAQENQLLFTETSALNSENVDKAFEELINTIYQKVSKHQMDLGDSSANGNANGASAPNGPTISLTPTPNENKKANGNNCC

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 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	GUANOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	443.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	452

▼

6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3cpjg1
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	d3cpjg2
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	d3cpjg3
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 (4 domains)

Domain ID domain_id	3cpjB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3cpjG01
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	3cpjG02
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	3cpjG03
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

▶

Unit-cell length a length_a	65.940 Å
Unit-cell length b length_b	61.430 Å
Unit-cell length c length_c	92.750 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.68 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.350 Å
Low-resolution limit resolution_low	19.790 Å
R factor r_factor	0.2016
R_work r_work	0.1988
R_free r_free	0.2552

Crystal structure of Ypt31 in complex with 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

GTP-binding protein YPT31/YPT8

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

3cpj__assembly_1__model_1

3cpj__assembly_1__model_1 | I(q)

3cpj__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of Ypt31 in complex with 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

GTP-binding protein YPT31/YPT8

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

3cpj__assembly_1__model_1

3cpj__assembly_1__model_1 | I(q)

3cpj__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

7. Citations (1)