SAXSdb — 2g77

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

GTPase-activating protein GYP1

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	Ras-related protein Rab-33B × 1 （O35963） MAGNESIUM ION × 1 GUANOSINE-5'-DIPHOSPHATE × 1 ALUMINUM FLUORIDE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GYP1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 17–410； UniProt 244–637

Ras-related protein Rab-33B

Mus musculus

UniProt O35963

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	GTPase-activating protein GYP1 × 1 （Q08484） MAGNESIUM ION × 1 GUANOSINE-5'-DIPHOSPHATE × 1 ALUMINUM FLUORIDE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RB33B_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 10–198； UniProt 14–202

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	2g77
Deposition date deposition_date	2006-02-27
Structure title title	Crystal Structure of Gyp1 TBC domain in complex with Rab33 GTPase bound to GDP and AlF3
Keywords keywords	Protein transport, Gyp1 TBC domain, Rab33, vesicular trafficking, HYDROLASE ACTIVATOR-PROTEIN TRANSPORT COMPLEX; HYDROLASE ACTIVATOR/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.

2g77__assembly_1__model_1

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

Download this curve (.dat)

2g77__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2g77__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.34 Å
Rg (electron density)	24.34 Å
Total Rg	25.27 Å
Atom count	4174
Residues	500
Excluded volume	74235 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2g77__assembly_1__model_1`	dimeric （2）	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 (6)

Entity 1 Entity 1 polymer

Description description	GTPase-activating protein GYP1
Molecular weight formula_weight	48158.5 kDa
Mutation mutation	E405K
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	4590

MGHHHHHHGSLVPRGSDVQELNSIIQRISKFDNILKDKTIINQQDLRQISWNGIPKIHRPVVWKLLIGYLPVNTKRQEGFLQRKRKEYRDSLKHTFSDQHSRDIPTWHQIEIDIPRTNPHIPLYQFKSVQNSLQRILYLWAIRHPASGYVQGINDLVTPFFETFLTEYLPPSQIDDVKIKDPSTYMVDEQITDLEADTFWCLTKLLEQITDNYIHGQPGILRQVKNLSQLVKRIDADLYNHFQNEHVEFIQFAFRWMNCLLMREFQMGTVIRMWDTYLSETSQEVTSSYSMSSNDIKPPVTPTEPRVASFVTPTKDFQSPTTALSNMTPNNAVEDSGKMRQSSLNEFHVFVCAAFLIKWSDQLMEMDFQETITFLQNPPTKDWTETDIEMLLSEAFIWQSLYKDATSHWL

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

Entity 2 Entity 2 polymer

Description description	Ras-related protein Rab-33B
Molecular weight formula_weight	22549.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MGHHHHHHGSSSCAVSGASGCLPPARSRIFKIIVIGDSNVGKTCLTYRFCAGRFPDRTEATIGVDFRERAVDIDGERIKIQLWDTAGQERFRKSMVQHYYRNVHAVVFVYDMTNMASFHSLPAWIEECKQHLLANDIPRILVGNKCDLRSAIQVPTDLAQKFADTHSMPLFETSAKNPNDNDHVEAIFMTLAHKLKSH

Source Source

Source organism organism	Mus musculus
Common name common_name	house mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

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

Entity 4 Entity 4 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 5 Entity 5 non-polymer

Description description	ALUMINUM FLUORIDE
Molecular weight formula_weight	84.0 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	416

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d2g77a1
Class class	a — All alpha proteins
Fold Fold fold	a.69 — Left-handed superhelix
Superfamily Superfamily superfamily	a.69.2 — Ypt/Rab-GAP domain of gyp1p
Family Family family	a.69.2.1 — Ypt/Rab-GAP domain of gyp1p

Domain ID domain_id	d2g77a2
Class class	a — All alpha proteins
Fold Fold fold	a.69 — Left-handed superhelix
Superfamily Superfamily superfamily	a.69.2 — Ypt/Rab-GAP domain of gyp1p
Family Family family	a.69.2.1 — Ypt/Rab-GAP domain of gyp1p

Domain ID domain_id	d2g77b1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.8 — G proteins

CATH v4.4 (2 domains)

Domain ID domain_id	2g77A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily	80 — Ypt/Rab-GAP domain of gyp1p, domain 3

Domain ID domain_id	2g77B00
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

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Unit-cell length a length_a	72.200 Å
Unit-cell length b length_b	94.526 Å
Unit-cell length c length_c	102.561 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.260 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.2073
R_work r_work	0.2052
R_free r_free	0.2436

Crystal Structure of Gyp1 TBC domain in complex with Rab33 GTPase bound to GDP and AlF3

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

GTPase-activating protein GYP1

State in the Current Structure

Other States of the Same Protein in the Database

Ras-related protein Rab-33B

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

2g77__assembly_1__model_1

2g77__assembly_1__model_1 | I(q)

2g77__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal Structure of Gyp1 TBC domain in complex with Rab33 GTPase bound to GDP and AlF3

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

GTPase-activating protein GYP1

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-33B

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

2g77__assembly_1__model_1

2g77__assembly_1__model_1 | I(q)

2g77__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (1)