SAXSdb — 1l4a

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

SYNAPTOBREVIN

Loligo pealei

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	S-SYNTAXIN × 1 （O46345） S-SNAP25 fusion protein × 1 （Q8T3S4） S-SNAP25 fusion protein × 1 （Q8T3S4） SYNAPHIN A × 1 （Q95PA1） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SYB_LOLPE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–80； UniProt 25–104

S-SYNTAXIN

Loligo pealei

UniProt O46345

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	SYNAPTOBREVIN × 1 （P47194） S-SNAP25 fusion protein × 1 （Q8T3S4） S-SNAP25 fusion protein × 1 （Q8T3S4） SYNAPHIN A × 1 （Q95PA1） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O46345_LOLPE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–88； UniProt 183–265

S-SNAP25 fusion protein

Loligo pealei

UniProt Q8T3S4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	SYNAPTOBREVIN × 1 （P47194） S-SYNTAXIN × 1 （O46345） SYNAPHIN A × 1 （Q95PA1） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8T3S4_LOLPE
Isoform	—
PDB entities	3, 4
Chains and sequence ranges	Author chain C； PDBConstruct 1–83； UniProt 4–86 Author chain D； PDBConstruct 1–87； UniProt 126–212

SYNAPHIN A

Loligo pealei

UniProt Q95PA1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	SYNAPTOBREVIN × 1 （P47194） S-SYNTAXIN × 1 （O46345） S-SNAP25 fusion protein × 1 （Q8T3S4） S-SNAP25 fusion protein × 1 （Q8T3S4） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q95PA1_LOLPE
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–79； UniProt 25–98

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	1l4a
Deposition date deposition_date	2002-03-04
Structure title title	X-RAY STRUCTURE OF THE NEURONAL COMPLEXIN/SNARE COMPLEX FROM THE SQUID LOLIGO PEALEI
Keywords keywords	SNARE, SNARE complex, membrane fusion, neurotransmission, ENDOCYTOSIS-EXOCYTOSIS COMPLEX; ENDOCYTOSIS/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.

1l4a__assembly_1__model_1

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

Download this curve (.dat)

1l4a__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1l4a__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.39 Å
Rg (electron density)	29.93 Å
Total Rg	29.77 Å
Atom count	2358
Residues	324
Excluded volume	40832 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1l4a__assembly_1__model_1`	pentameric （5）	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	SYNAPTOBREVIN
Molecular weight formula_weight	9046.3 kDa
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	2381

PGPPQGPPQPVQQSKRLQQTQAQVEEVVDIMRVNVDKVLERDSKISELDDRADALQAGASQFEASAGKLKRKFWWKNCKM

Source Source

Source organism organism	Loligo pealei
NCBI taxonomy ID ncbi_taxonomy_id	6621
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	S-SYNTAXIN
Molecular weight formula_weight	9981.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GKSASGIIMETQQAKQTLADIEARHADIMKLETSIRELHDMFMDMAMLVESQGEMIDRIEYNVEAAVDYIETAKVDTKKAVKYQSKAR

Source Source

Source organism organism	Loligo pealei
NCBI taxonomy ID ncbi_taxonomy_id	6621
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	S-SNAP25 fusion protein
Molecular weight formula_weight	9566.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

NGEVEVPKTELEEIQQQCNQVTDDSLESTRRMLNMCEESKEAGIRTLVMLDEQGEQLDRIEEGLDQINQDMKDAEKNLEGMEK

Source Source

Source organism organism	Loligo pealei
NCBI taxonomy ID ncbi_taxonomy_id	6621
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	S-SNAP25 fusion protein
Molecular weight formula_weight	9671.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

VTVGDQNGMGPSSGYVTRITNDAREDDMENNMKEVSSMIGNLRNMAIDMGNEIGSQNRQVDRIQQKAESNESRIDEANKKATKLLKN

Source Source

Source organism organism	Loligo pealei
NCBI taxonomy ID ncbi_taxonomy_id	6621
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	SYNAPHIN A
Molecular weight formula_weight	9251.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

GKSASGEKEGNENAEEEAAAIEEARREAEERRKEKHRKMEEEREEMRQTIRDKYGLKKKVKEEPEAEADLDEGRVGRKK

Source Source

Source organism organism	Loligo pealei
NCBI taxonomy ID ncbi_taxonomy_id	6621
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	23

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1l4aa_
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	d1l4ab1
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	d1l4ab2
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	d1l4ac_
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	d1l4ad_
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	d1l4ae_
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 (4 domains)

Domain ID domain_id	1l4aA00
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	1l4aB00
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	1l4aC00
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	1l4aD00
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	26.072 Å
Unit-cell length b length_b	75.430 Å
Unit-cell length c length_c	243.109 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.950 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.3004
R_work r_work	0.2970
R_free r_free	0.3445

X-RAY STRUCTURE OF THE NEURONAL COMPLEXIN/SNARE COMPLEX FROM THE SQUID LOLIGO PEALEI

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

SYNAPTOBREVIN

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

S-SYNTAXIN

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

S-SNAP25 fusion protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

SYNAPHIN A

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

1l4a__assembly_1__model_1

1l4a__assembly_1__model_1 | I(q)

1l4a__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 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

CATH v4.4 (4 domains)

7. Citations (1)