1sfc

NEURONAL SYNAPTIC FUSION COMPLEX

Method: X-RAY DIFFRACTION

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

PROTEIN (SYNAPTOBREVIN 2)

Rattus norvegicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	PROTEIN (SYNTAXIN 1A) × 1 （P32851） PROTEIN (SNAP-25B) × 1 （P60881） PROTEIN (SNAP-25B) × 1 （P60881） STRONTIUM ION × 6 (4S)-2-METHYL-2,4-PENTANEDIOL × 2 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	PROTEIN (SYNTAXIN 1A) × 1 （P32851） PROTEIN (SNAP-25B) × 1 （P60881） PROTEIN (SNAP-25B) × 1 （P60881） STRONTIUM ION × 5 (4S)-2-METHYL-2,4-PENTANEDIOL × 2 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	PROTEIN (SYNTAXIN 1A) × 1 （P32851） PROTEIN (SNAP-25B) × 1 （P60881） PROTEIN (SNAP-25B) × 1 （P60881） STRONTIUM ION × 2 (4S)-2-METHYL-2,4-PENTANEDIOL × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VAMP2_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–96； UniProt 1–96 Author chain E； PDBConstruct 1–96； UniProt 1–96 Author chain I； PDBConstruct 1–96； UniProt 1–96

PROTEIN (SYNTAXIN 1A)

Rattus norvegicus

UniProt P32851

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	PROTEIN (SYNAPTOBREVIN 2) × 1 （P63045） PROTEIN (SNAP-25B) × 1 （P60881） PROTEIN (SNAP-25B) × 1 （P60881） STRONTIUM ION × 6 (4S)-2-METHYL-2,4-PENTANEDIOL × 2 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	PROTEIN (SYNAPTOBREVIN 2) × 1 （P63045） PROTEIN (SNAP-25B) × 1 （P60881） PROTEIN (SNAP-25B) × 1 （P60881） STRONTIUM ION × 5 (4S)-2-METHYL-2,4-PENTANEDIOL × 2 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	PROTEIN (SYNAPTOBREVIN 2) × 1 （P63045） PROTEIN (SNAP-25B) × 1 （P60881） PROTEIN (SNAP-25B) × 1 （P60881） STRONTIUM ION × 2 (4S)-2-METHYL-2,4-PENTANEDIOL × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	STX1A_RAT
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–83； UniProt 180–262 Author chain F； PDBConstruct 1–83； UniProt 180–262 Author chain J； PDBConstruct 1–83； UniProt 180–262

PROTEIN (SNAP-25B)

Rattus norvegicus

UniProt P60881

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	PROTEIN (SYNAPTOBREVIN 2) × 1 （P63045） PROTEIN (SYNTAXIN 1A) × 1 （P32851） STRONTIUM ION × 6 (4S)-2-METHYL-2,4-PENTANEDIOL × 2 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	PROTEIN (SYNAPTOBREVIN 2) × 1 （P63045） PROTEIN (SYNTAXIN 1A) × 1 （P32851） STRONTIUM ION × 5 (4S)-2-METHYL-2,4-PENTANEDIOL × 2 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	PROTEIN (SYNAPTOBREVIN 2) × 1 （P63045） PROTEIN (SYNTAXIN 1A) × 1 （P32851） STRONTIUM ION × 2 (4S)-2-METHYL-2,4-PENTANEDIOL × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SNP25_RAT
Isoform	—
PDB entities	3, 4
Chains and sequence ranges	Author chain C； PDBConstruct 1–83； UniProt 1–83 Author chain G； PDBConstruct 1–83； UniProt 1–83 Author chain K； PDBConstruct 1–83； UniProt 1–83 Author chain D； PDBConstruct 1–87； UniProt 120–206 Author chain H； PDBConstruct 1–87； UniProt 120–206 Author chain L； PDBConstruct 1–87； UniProt 120–206

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	1sfc
Deposition date deposition_date	1998-08-24
Structure title title	NEURONAL SYNAPTIC FUSION COMPLEX
Keywords keywords	MEMBRANE FUSION PROTEIN COMPLEX, TRANSPORT PROTEIN; TRANSPORT 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.

1sfc__assembly_1__model_1

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

Download this curve (.dat)

1sfc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1sfc__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.42 Å
Rg (electron density)	31.64 Å
Total Rg	31.37 Å
Atom count	2383
Residues	292
Excluded volume	42088 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1sfc__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1sfc__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1sfc__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 (7)

Entity 1 Entity 1 polymer

Description description	PROTEIN (SYNAPTOBREVIN 2)
Molecular weight formula_weight	10530.9 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	7105

MSATAATVPPAAPAGEGGPPAPPPNLTSNRRLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAKLKRKYWWKNLKMM

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Norway rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	PROTEIN (SYNTAXIN 1A)
Molecular weight formula_weight	9603.9 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

GIIMDSSISKQALSEIETRHSEIIKLENSIRELHDMFMDMAMLVESQGEMIDRIEYNVEHAVDYVERAVSDTKKAVKYQSKAR

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Norway rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	PROTEIN (SNAP-25B)
Molecular weight formula_weight	9662.8 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

MAEDADMRNELEEMQRRADQLADESLESTRRMLQLVEESKDAGIRTLVMLDEQGEQLDRVEEGMNHINQDMKEAEKNLKDLGK

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Norway rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	PROTEIN (SNAP-25B)
Molecular weight formula_weight	9862.0 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

VVDEREQMAISGGFIRRVTNDARENEMDENLEQVSGIIGNLRHMALDMGNEIDTQNRQIDRIMEKADSNKTRIDEANQRATKMLGSG

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Norway rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 non-polymer

Description description	STRONTIUM ION
Molecular weight formula_weight	87.6 kDa
Source method src_method	syn
Copy count entity_count	13

Entity 6 Entity 6 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	19

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d1sfca_
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	d1sfcb_
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	d1sfcc_
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	d1sfcd_
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	d1sfce_
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	d1sfcf_
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	d1sfcg_
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	d1sfch_
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	d1sfci_
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	d1sfcj_
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	d1sfck_
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	d1sfcl_
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	1sfcA00
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	1sfcB00
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	1sfcC00
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	1sfcD00
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	1sfcE00
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	1sfcF00
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	1sfcG00
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	1sfcH00
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	1sfcI00
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	1sfcJ00
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	1sfcK00
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	1sfcL00
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	98.715 Å
Unit-cell length b length_b	111.071 Å
Unit-cell length c length_c	198.844 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	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2650
R_work r_work	0.2650
R_free r_free	0.3030

NEURONAL SYNAPTIC FUSION COMPLEX

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

PROTEIN (SYNAPTOBREVIN 2)

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 (SYNTAXIN 1A)

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 (SNAP-25B)

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

1sfc__assembly_1__model_1

1sfc__assembly_1__model_1 | I(q)

1sfc__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 (7)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)