SAXSdb — 3a58

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

Exocyst complex component SEC3

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 RHO1 × 1 （P06780） PHOSPHATE ION × 3 PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MAGNESIUM ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	GTP-binding protein RHO1 × 1 （P06780） PHOSPHATE ION × 3 PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MAGNESIUM ION × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	GTP-binding protein RHO1 × 1 （P06780） PHOSPHATE ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MAGNESIUM ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SEC3_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–320； UniProt 1–320 Author chain C； PDBConstruct 1–320； UniProt 1–320 Author chain E； PDBConstruct 1–320； UniProt 1–320

GTP-binding protein RHO1

Saccharomyces cerevisiae

UniProt P06780

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Exocyst complex component SEC3 × 1 （P33332） PHOSPHATE ION × 3 PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MAGNESIUM ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Exocyst complex component SEC3 × 1 （P33332） PHOSPHATE ION × 3 PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MAGNESIUM ION × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Exocyst complex component SEC3 × 1 （P33332） PHOSPHATE ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MAGNESIUM ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RHO1_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–188； UniProt 1–188 Author chain D； PDBConstruct 1–188； UniProt 1–188 Author chain F； PDBConstruct 1–188； UniProt 1–188

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	3a58
Deposition date deposition_date	2009-08-03
Structure title title	Crystal structure of Sec3p - Rho1p complex from Saccharomyces cerevisiae
Keywords keywords	;protein complex, PH domain, GTPase, membrane traffic, Exocytosis, Phosphoprotein, Protein transport, Transport, Cell membrane, Endosome, GTP-binding, Lipoprotein, Membrane, Methylation, Nucleotide-binding, Peroxisome, Prenylation, PROTEIN TRANSPORT-EXOCYTOSIS COMPLEX ;; PROTEIN TRANSPORT/EXOCYTOSIS
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.

3a58__assembly_1__model_1

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

Download this curve (.dat)

3a58__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3a58__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.73 Å
Rg (electron density)	23.98 Å
Total Rg	24.72 Å
Atom count	2955
Residues	362
Excluded volume	52286 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3a58__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3a58__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3a58__assembly_3__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	Exocyst complex component SEC3
Molecular weight formula_weight	36267.0 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E
Atom count atom_count	8792

MRSSKSPFKRKSHSRETSHDENTSFFHKRTISGSSAHHSRNVSQGAVPSSAPPVSGGNYSHKRNVSRASNSSQTSNFLAEQYERDRKAIINCCFSRPDHKTGEPPNNYITHVRIIEDSKFPSSRPPPDSKLENKKKRLLILSAKPNNAKLIQIHKARENSDGSFQIGRTWQLTELVRVEKDLEISEGFILTMSKKYYWETNSAKERTVFIKSLITLYIQTFEGHVPELVNWDLSLFYLDERSYQRAVITNRPGSVSPIKSPTSNFTTNTTQSVGSVPFSAPTERTRRSETESVNPVSTPASVEYHAGMKSLNKAPYSSNS

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	GTP-binding protein RHO1
Molecular weight formula_weight	20766.4 kDa
Mutation mutation	F30N
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

MSQQVGNSIRRKLVIVGDGACGKTCLLIVNSKGQFPEVYVPTVFENYVADVEVDGRRVELALWDTAGQEDYDRLRPLSYPDSNVVLICFSIDLPDSLENVQEKWIAEVLHFCQGVPIILVGCKVDLRNDPQTIEQLRQEGQQPVTSQEGQSVADQIGATGYYECSAKTGYGVREVFEAATRASLMGKS

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 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 4 Entity 4 non-polymer

Description description	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
Molecular weight formula_weight	522.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	98

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6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3a58b_
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

Domain ID domain_id	d3a58d_
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

Domain ID domain_id	d3a58f_
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 (6 domains)

Domain ID domain_id	3a58A01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	90 —

Domain ID domain_id	3a58B00
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	3a58C01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	90 —

Domain ID domain_id	3a58D00
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	3a58E00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	90 —

Domain ID domain_id	3a58F00
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	116.000 Å
Unit-cell length b length_b	116.054 Å
Unit-cell length c length_c	247.675 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	24

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

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	47.850 Å
R factor r_factor	0.2350
R_work r_work	0.2340
R_free r_free	0.2650

Crystal structure of Sec3p - Rho1p complex from Saccharomyces cerevisiae

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

Exocyst complex component SEC3

State in the Current Structure

Other States of the Same Protein in the Database

GTP-binding protein RHO1

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

3a58__assembly_1__model_1

3a58__assembly_1__model_1 | I(q)

3a58__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) 9 domains

SCOP 2.08 (3 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of Sec3p - Rho1p complex from Saccharomyces cerevisiae

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

Exocyst complex component SEC3

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 RHO1

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

3a58__assembly_1__model_1

3a58__assembly_1__model_1 | I(q)

3a58__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) 9 domains

SCOP 2.08 (3 domains)

CATH v4.4 (6 domains)

7. Citations (1)