3b5n

Structure of the yeast plasma membrane SNARE complex

Method: X-RAY DIFFRACTION

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

Synaptobrevin homolog 1

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Protein SSO1 × 1 （P32867） Protein transport protein SEC9 × 1 （P40357） Protein transport protein SEC9 × 1 （P40357） water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Protein SSO1 × 1 （P32867） Protein transport protein SEC9 × 1 （P40357） Protein transport protein SEC9 × 1 （P40357） water × 4	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Protein SSO1 × 1 （P32867） Protein transport protein SEC9 × 1 （P40357） Protein transport protein SEC9 × 1 （P40357） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SNC1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–61； UniProt 27–86 Author chain E； PDBConstruct 2–61； UniProt 27–86 Author chain I； PDBConstruct 2–61； UniProt 27–86

Protein SSO1

Saccharomyces cerevisiae

UniProt P32867

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Synaptobrevin homolog 1 × 1 （P31109） Protein transport protein SEC9 × 1 （P40357） Protein transport protein SEC9 × 1 （P40357） water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Synaptobrevin homolog 1 × 1 （P31109） Protein transport protein SEC9 × 1 （P40357） Protein transport protein SEC9 × 1 （P40357） water × 4	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Synaptobrevin homolog 1 × 1 （P31109） Protein transport protein SEC9 × 1 （P40357） Protein transport protein SEC9 × 1 （P40357） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SSO1_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–69； UniProt 189–257 Author chain F； PDBConstruct 1–69； UniProt 189–257 Author chain J； PDBConstruct 1–69； UniProt 189–257

Protein transport protein SEC9

Saccharomyces cerevisiae

UniProt P40357

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Synaptobrevin homolog 1 × 1 （P31109） Protein SSO1 × 1 （P32867） water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Synaptobrevin homolog 1 × 1 （P31109） Protein SSO1 × 1 （P32867） water × 4	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Synaptobrevin homolog 1 × 1 （P31109） Protein SSO1 × 1 （P32867） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SEC9_YEAST
Isoform	—
PDB entities	3, 4
Chains and sequence ranges	Author chain C； PDBConstruct 3–69； UniProt 433–499 Author chain G； PDBConstruct 3–69； UniProt 433–499 Author chain K； PDBConstruct 3–69； UniProt 433–499 Author chain D； PDBConstruct 3–64； UniProt 589–650 Author chain H； PDBConstruct 3–64； UniProt 589–650 Author chain L； PDBConstruct 3–64； UniProt 589–650

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	3b5n
Deposition date deposition_date	2007-10-26
Structure title title	Structure of the yeast plasma membrane SNARE complex
Keywords keywords	;SNARE complex, syntaxin, synaptobrevin, snap-25, Sso1p, Snc1p, Sec9p, Sec9, Sso1, Snc1, Coiled coil, Lipoprotein, Membrane, Palmitate, Transmembrane, Ubl conjugation, Phosphorylation, Protein transport, Transport, MEMBRANE PROTEIN ;; MEMBRANE PROTEIN
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.

3b5n__assembly_1__model_1

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

Download this curve (.dat)

3b5n__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3b5n__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.79 Å
Rg (electron density)	28.92 Å
Total Rg	29.05 Å
Atom count	2063
Residues	264
Excluded volume	36271 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3b5n__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3b5n__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3b5n__assembly_3__model_1`	tetrameric （4）	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 (5)

Entity 1 Entity 1 polymer

Description description	Synaptobrevin homolog 1
Molecular weight formula_weight	6771.6 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E,I
Atom count atom_count	6656

GSRTAELQAEIDDTVGIMRDNINKVAERGERLTSIEDKADNLAVSAQGFKRGANRVRKAMW

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	Protein SSO1
Molecular weight formula_weight	7797.7 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

ALAEVQARHQELLKLEKSMAELTQLFNDMEELVIEQQENVDVIDKNVEDAQLDVEQGVGHTDKAVKSAR

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 polymer

Description description	Protein transport protein SEC9
Molecular weight formula_weight	7685.8 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,G,K

GSIKFTKQSSVASTRNTLKMAQDAERAGMNTLGMLGHQSEQLNNVEGNLDLMKVQNKVADEKVAELKKLQ

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 4 Entity 4 polymer

Description description	Protein transport protein SEC9
Molecular weight formula_weight	7349.2 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,H,L

GSEMELEIDRNLDQIQQVSNRLKKMALTTGKELDSQQKRLNNIEESTDDLDINLHMNTNRLAGI

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 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	592

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6. Fold Classification (SCOP + CATH) 25 domains

SCOP 2.08 (13 domains)

Domain ID domain_id	d3b5na2
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.15 — SNARE fusion complex
Family Family family	h.1.15.1 — SNARE fusion complex

Domain ID domain_id	d3b5na3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3b5nb_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.15 — SNARE fusion complex
Family Family family	h.1.15.1 — SNARE fusion complex

Domain ID domain_id	d3b5nc2
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.15 — SNARE fusion complex
Family Family family	h.1.15.1 — SNARE fusion complex

Domain ID domain_id	d3b5nc3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3b5nc4
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3b5ne_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.15 — SNARE fusion complex
Family Family family	h.1.15.1 — SNARE fusion complex

Domain ID domain_id	d3b5nf_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.15 — SNARE fusion complex
Family Family family	h.1.15.1 — SNARE fusion complex

Domain ID domain_id	d3b5ng1
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.15 — SNARE fusion complex
Family Family family	h.1.15.1 — SNARE fusion complex

Domain ID domain_id	d3b5ng2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3b5ni_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.15 — SNARE fusion complex
Family Family family	h.1.15.1 — SNARE fusion complex

Domain ID domain_id	d3b5nj_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.15 — SNARE fusion complex
Family Family family	h.1.15.1 — SNARE fusion complex

Domain ID domain_id	d3b5nk_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.15 — SNARE fusion complex
Family Family family	h.1.15.1 — SNARE fusion complex

CATH v4.4 (12 domains)

Domain ID domain_id	3b5nA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	3b5nB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	3b5nC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	3b5nD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	3b5nE00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	3b5nF00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	3b5nG00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	3b5nH00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	3b5nI00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	3b5nJ00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	3b5nK00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	3b5nL00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	110 —

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Unit-cell length a length_a	76.956 Å
Unit-cell length b length_b	48.113 Å
Unit-cell length c length_c	110.265 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.77 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	6

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

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	34.571 Å
R factor r_factor	—
R_work r_work	0.2060
R_free r_free	0.2480

Structure of the yeast plasma membrane SNARE complex

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

Synaptobrevin homolog 1

State in the Current Structure

Other States of the Same Protein in the Database

Protein SSO1

State in the Current Structure

Other States of the Same Protein in the Database

Protein transport protein SEC9

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

3b5n__assembly_1__model_1

3b5n__assembly_1__model_1 | I(q)

3b5n__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 25 domains

SCOP 2.08 (13 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Structure of the yeast plasma membrane SNARE complex

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

Synaptobrevin homolog 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Protein SSO1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Protein transport protein SEC9

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

3b5n__assembly_1__model_1

3b5n__assembly_1__model_1 | I(q)

3b5n__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 25 domains

SCOP 2.08 (13 domains)

CATH v4.4 (12 domains)

7. Citations (1)