SAXSdb — 7udb

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

Syntaxin-binding protein 1

Rattus norvegicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Syntaxin-1A × 1 （P32851） Synaptobrevin-2 × 1 （P63045）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	STXB1_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 14–607； UniProt 1–594

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 3	Syntaxin-binding protein 1 × 1 （P61765） Synaptobrevin-2 × 1 （P63045）	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 3–254； UniProt 2–253

Synaptobrevin-2

Rattus norvegicus

UniProt P63045

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Syntaxin-binding protein 1 × 1 （P61765） Syntaxin-1A × 1 （P32851）	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	3
Chains and sequence ranges	Author chain C； PDBConstruct 5–59； UniProt 29–83

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	7udb
Deposition date deposition_date	2022-03-18
Structure title title	Cryo-EM structure of a synaptobrevin-Munc18-1-syntaxin-1 complex class 2
Keywords keywords	Munc18, syntaxin, synaptobrevin, SNARE, membrane fusion, neurotransmitter release, EXOCYTOSIS; EXOCYTOSIS
Experimental Method method	ELECTRON MICROSCOPY

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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.

7udb__assembly_1__model_1

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

Download this curve (.dat)

7udb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7udb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.82 Å
Rg (electron density)	30.92 Å
Total Rg	31.65 Å
Atom count	6472
Residues	807
Excluded volume	115560 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7udb__assembly_1__model_1`	trimeric （3）	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 (3)

Entity 1 Entity 1 polymer

Description description	Syntaxin-binding protein 1
Molecular weight formula_weight	68714.9 kDa
Mutation mutation	D326K
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	6472

GSPGISGGGGGIHMAPIGLKAVVGEKIMHDVIKKVKKKGEWKVLVVDQLSMRMLSSCCKMTDIMTEGITIVEDINKRREPLPSLEAVYLITPSEKSVHSLISDFKDPPTAKYRAAHVFFTDSCPDALFNELVKSRAAKVIKTLTEINIAFLPYESQVYSLDSADSFQSFYSPHKAQMKNPILERLAEQIATLCATLKEYPAVRYRGEYKDNALLAQLIQDKLDAYKADDPTMGEGPDKARSQLLILDRGFDPSSPVLHELTFQAMSYDLLPIENDVYKYETSGIGEARVKEVLLDEDDDLWIALRHKHIAEVSQEVTRSLKDFSSSKRMNTGEKTTMRKLSQMLKKMPQYQKELSKYSTHLHLAEDCMKHYQGTVDKLCRVEQDLAMGTDAEGEKIKDPMRAIVPILLDANVSTYDKIRIILLYIFLKNGITEENLNKLIQHAQIPPEDSEIITNMAHLGVPIVTDSTLRRRSKPERKERISEQTYQLSRWTPIIKDIMEDTIEDKLDTKHYPYISTRSSASFSTTAVSARYGHWHKNKAPGEYRSGPRLIIFILGGVSLNEMRCAYEVTQANGKWEVLIGSTHILTPQKLLDTLKKLNKTDEEISS

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Syntaxin-1A
Molecular weight formula_weight	29221.5 kDa
Mutation mutation	C145A,L165A,E166A,L205C
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GSKDRTQELRTAKDSDDDDDVTVTVDRDRFMDEFFEQVEEIRGFIDKIAENVEEVKRKHSAILASPNPDEKTKEELEELMSDIKKTANKVRSKLKSIEQSIEQEEGLNRSSADLRIRKTQHSTLSRKFVEVMSEYNATQSDYRERAKGRIQRQLEITGRTTTSEEAADMLESGNPAIFASGIIMDSSISKQALSEIETRHSEIIKCENSIRELHDMFMDMAMLVESQGEMIDRIEYNVEHAVDYVERAVSDTKK

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 BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Synaptobrevin-2
Molecular weight formula_weight	6645.4 kDa
Mutation mutation	Q36C
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

GSMWNRRLQQTCAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAK

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 BL21(DE3)

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	7udbA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2060 — Sec1/Munc18 (SM) protein, domain 1

Domain ID domain_id	7udbA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	830 — Syntaxin Binding Protein 1; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Sec1/Munc18 (SM) protein, domain 3a

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

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

Resolution resolution	3.50 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	345463

Cryo-EM structure of a synaptobrevin-Munc18-1-syntaxin-1 complex class 2

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

Syntaxin-binding protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Syntaxin-1A

State in the Current Structure

Other States of the Same Protein in the Database

Synaptobrevin-2

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

7udb__assembly_1__model_1

7udb__assembly_1__model_1 | I(q)

7udb__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (3)

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

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Cryo-EM structure of a synaptobrevin-Munc18-1-syntaxin-1 complex class 2

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

Syntaxin-binding protein 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

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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7udb__assembly_1__model_1

7udb__assembly_1__model_1 | I(q)

7udb__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (3)

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

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)