2e7s

Crystal structure of the yeast Sec2p GEF domain

Method: X-RAY DIFFRACTION

▼

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

Rab guanine nucleotide exchange factor SEC2

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
10	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
7	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
8	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
9	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SEC2_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–135； UniProt 31–160 Author chain B； PDBConstruct 6–135； UniProt 31–160 Author chain C； PDBConstruct 6–135； UniProt 31–160 Author chain D； PDBConstruct 6–135； UniProt 31–160 Author chain E； PDBConstruct 6–135； UniProt 31–160 Author chain F； PDBConstruct 6–135； UniProt 31–160 Author chain G； PDBConstruct 6–135； UniProt 31–160 Author chain H； PDBConstruct 6–135； UniProt 31–160 Author chain I； PDBConstruct 6–135； UniProt 31–160 Author chain J； PDBConstruct 6–135； UniProt 31–160 Author chain K； PDBConstruct 6–135； UniProt 31–160 Author chain L； PDBConstruct 6–135； UniProt 31–160 Author chain M； PDBConstruct 6–135； UniProt 31–160 Author chain N； PDBConstruct 6–135； UniProt 31–160 Author chain O； PDBConstruct 6–135； UniProt 31–160 Author chain P； PDBConstruct 6–135； UniProt 31–160 Author chain Q； PDBConstruct 6–135； UniProt 31–160 Author chain R； PDBConstruct 6–135； UniProt 31–160 Author chain S； PDBConstruct 6–135； UniProt 31–160 Author chain T； PDBConstruct 6–135； UniProt 31–160

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	2e7s
Deposition date deposition_date	2007-01-12
Structure title title	Crystal structure of the yeast Sec2p GEF domain
Keywords keywords	COILED COIL, ENDOCYTOSIS-EXOCYTOSIS COMPLEX; ENDOCYTOSIS/EXOCYTOSIS
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.

2e7s__assembly_1__model_1

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

Download this curve (.dat)

2e7s__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2e7s__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	46.64 Å
Rg (electron density)	50.65 Å
Total Rg	50.06 Å
Atom count	1931
Residues	231
Excluded volume	34233 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2e7s__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2e7s__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2e7s__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2e7s__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2e7s__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`2e7s__assembly_6__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`2e7s__assembly_7__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`2e7s__assembly_8__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`2e7s__assembly_9__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
10	1	`2e7s__assembly_10__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 (2)

▼

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (20 domains)

Domain ID domain_id	d2e7sa1
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.33 — Sec2 N-terminal region
Family Family family	h.1.33.1 — Sec2 N-terminal region

Domain ID domain_id	d2e7sb_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.33 — Sec2 N-terminal region
Family Family family	h.1.33.1 — Sec2 N-terminal region

Domain ID domain_id	d2e7sc_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.33 — Sec2 N-terminal region
Family Family family	h.1.33.1 — Sec2 N-terminal region

Domain ID domain_id	d2e7sd_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.33 — Sec2 N-terminal region
Family Family family	h.1.33.1 — Sec2 N-terminal region

Domain ID domain_id	d2e7se_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.33 — Sec2 N-terminal region
Family Family family	h.1.33.1 — Sec2 N-terminal region

Domain ID domain_id	d2e7sf_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.33 — Sec2 N-terminal region
Family Family family	h.1.33.1 — Sec2 N-terminal region

Domain ID domain_id	d2e7sg_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.33 — Sec2 N-terminal region
Family Family family	h.1.33.1 — Sec2 N-terminal region

Domain ID domain_id	d2e7sh_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.33 — Sec2 N-terminal region
Family Family family	h.1.33.1 — Sec2 N-terminal region

Domain ID domain_id	d2e7si_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.33 — Sec2 N-terminal region
Family Family family	h.1.33.1 — Sec2 N-terminal region

Domain ID domain_id	d2e7sj_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.33 — Sec2 N-terminal region
Family Family family	h.1.33.1 — Sec2 N-terminal region

Domain ID domain_id	d2e7sk_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.33 — Sec2 N-terminal region
Family Family family	h.1.33.1 — Sec2 N-terminal region

Domain ID domain_id	d2e7sl_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.33 — Sec2 N-terminal region
Family Family family	h.1.33.1 — Sec2 N-terminal region

Domain ID domain_id	d2e7sm_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.33 — Sec2 N-terminal region
Family Family family	h.1.33.1 — Sec2 N-terminal region

Domain ID domain_id	d2e7sn_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.33 — Sec2 N-terminal region
Family Family family	h.1.33.1 — Sec2 N-terminal region

Domain ID domain_id	d2e7so_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.33 — Sec2 N-terminal region
Family Family family	h.1.33.1 — Sec2 N-terminal region

Domain ID domain_id	d2e7sp_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.33 — Sec2 N-terminal region
Family Family family	h.1.33.1 — Sec2 N-terminal region

Domain ID domain_id	d2e7sq_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.33 — Sec2 N-terminal region
Family Family family	h.1.33.1 — Sec2 N-terminal region

Domain ID domain_id	d2e7sr_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.33 — Sec2 N-terminal region
Family Family family	h.1.33.1 — Sec2 N-terminal region

Domain ID domain_id	d2e7ss_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.33 — Sec2 N-terminal region
Family Family family	h.1.33.1 — Sec2 N-terminal region

Domain ID domain_id	d2e7st_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.33 — Sec2 N-terminal region
Family Family family	h.1.33.1 — Sec2 N-terminal region

▶

Unit-cell length a length_a	101.937 Å
Unit-cell length b length_b	176.569 Å
Unit-cell length c length_c	181.453 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	40

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

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	—
R_work r_work	0.2290
R_free r_free	0.2850

Description description	Rab guanine nucleotide exchange factor SEC2
Molecular weight formula_weight	15780.5 kDa
Mutation mutation	M115L/K121M/T142M
Source method src_method	man
Copy count entity_count	20

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T
Atom count atom_count	19270

Crystal structure of the yeast Sec2p GEF domain

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

Rab guanine nucleotide exchange factor SEC2

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

2e7s__assembly_1__model_1

2e7s__assembly_1__model_1 | I(q)

2e7s__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) 20 domains

SCOP 2.08 (20 domains)

7. Citations (1)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	262

Crystal structure of the yeast Sec2p GEF domain

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

Rab guanine nucleotide exchange factor SEC2

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

2e7s__assembly_1__model_1

2e7s__assembly_1__model_1 | I(q)

2e7s__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) 20 domains

SCOP 2.08 (20 domains)

7. Citations (1)