SAXSdb — 3puk

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

Syntaxin-binding protein 3

Mus musculus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–592	Not recorded	Syntaxin-4 N-terminal peptide × 1 （P70452）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；10-13% PEG 3350, 0.2M MGACETATE, 0.1M MES, PH6.5, 50MM MGCL2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.05 Å R-free 0.279
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–592	Not recorded	Syntaxin-4 N-terminal peptide × 1 （P70452）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；10-13% PEG 3350, 0.2M MGACETATE, 0.1M MES, PH6.5, 50MM MGCL2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.05 Å R-free 0.279

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	STXB3_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–592； UniProt 1–592 Author chain B； PDBConstruct 1–592； UniProt 1–592

Syntaxin-4 N-terminal peptide

OrganismNot specified

UniProt P70452

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–10	Fragment：UNP residues 1-10	Syntaxin-binding protein 3 × 1 （Q60770）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；10-13% PEG 3350, 0.2M MGACETATE, 0.1M MES, PH6.5, 50MM MGCL2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.05 Å R-free 0.279
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 1–10	Fragment：UNP residues 1-10	Syntaxin-binding protein 3 × 1 （Q60770）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；10-13% PEG 3350, 0.2M MGACETATE, 0.1M MES, PH6.5, 50MM MGCL2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.05 Å R-free 0.279

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 3PUK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3PUJ Crystal structure of the MUNC18-1 and SYNTAXIN4 N-Peptide complex Deposited 2010-12-05	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–10（10 aa） Fragment：UNP residues 1-10	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；60% Tascimate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.31 Å R-free 0.258
3PUJ Crystal structure of the MUNC18-1 and SYNTAXIN4 N-Peptide complex Deposited 2010-12-05	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–10（10 aa） Fragment：UNP residues 1-10	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；60% Tascimate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.31 Å R-free 0.258
8BBJ Secretagogin (mouse) in complex with its target peptide from Syntaxin-4 Deposited 2022-10-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 82–109（28 aa）	Mutation：F64L,Q80R,I167T Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 4 CAC CACODYLATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；277 K；0.1 M Na cacodylate pH 5.5, 0.2 M NH4SO4, 25% v/v PEGSM (PEG-smear)	Resolution 2.65 Å R-free 0.269
8BBJ Secretagogin (mouse) in complex with its target peptide from Syntaxin-4 Deposited 2022-10-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 82–109（28 aa）	Mutation：F64L,Q80R,I167T Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；277 K；0.1 M Na cacodylate pH 5.5, 0.2 M NH4SO4, 25% v/v PEGSM (PEG-smear)	Resolution 2.65 Å R-free 0.269

2 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	STX4_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–10； UniProt 1–10 Author chain D； PDBConstruct 1–10； UniProt 1–10

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	3puk
Deposition date deposition_date	2010-12-05
Structure title title	Re-refinement of the crystal structure of Munc18-3 and Syntaxin4 N-peptide complex
Keywords keywords	MEMBRANE TRAFFICKING, SM PROTEIN, SYNTAXIN, SNARE PROTEINS, Syntaxin binding protein, ENDOCYTOSIS-EXOCYTOSIS complex; ENDOCYTOSIS/EXOCYTOSIS
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	46.65 Å
Radius of gyration Rg (electron density) rg_electron	46.66 Å
Forward intensity I(0) i0	219720000.00
Molecular weight molecular_weight	121260.0 kDa
Excluded volume excluded_volume	151250 Å³
Envelope volume envelope_volume	231230 Å³
Hydration-shell volume shell_volume	41831 Å³
Envelope diameter envelope_diameter	137.5 Å
Shell Rg shell_rg	50.79 Å
Envelope Rg envelope_rg	44.76 Å
Shape Rg shape_rg	46.64 Å
Total Rg total_rg	46.88 Å
Total atoms total_atoms	8521
Residues n_residues	1116
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	128.7 Å
Rg (real space) rg_real	46.87 Å
Rg uncertainty (real space) rg_real_error	0.87 Å
I(0) (real space) i0_real	2.1970e+08
I(0) uncertainty (real space) i0_real_error	3.6870e+06
Rg (reciprocal space) rg_reciprocal	46.65 Å
I(0) (reciprocal space) i0_reciprocal	219700000.0000
Solution quality estimate total_estimate	0.7297
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.3 Å
Skewness Skewness skewness	0.161
Kurtosis Kurtosis kurtosis	-1.178
Angular range angular_range	— – 0.1700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	16250000.0000
Real-space data points n_real_points	35
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.694; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.399; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Syntaxin-binding protein 3
Molecular weight formula_weight	68044.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	8521

MAPPVSERGLKSVVWRKIKTAVFDDCRKEGEWKIMLLDEFTTKLLSSCCKMTDLLEEGITVIENIYKNREPVRQMKALYFISPTPKSVDCFLRDFGSKSEKKYKAAYIYFTDFCPDSLFNKIKASCSKSIRRCKEINISFIPQESQVYTLDVPDAFYYCYSPDPSNASRKEVVMEAMAEQIVTVCATLDENPGVRYKSKPLDNASKLAQLVEKKLEDYYKIDEKGLIKGKTQSQLLIIDRGFDPVSTVLHELTFQAMAYDLLPIENDTYKYKTDGKEKEAVLEEDDDLWVRVRHRHIAVVLEEIPKLMKEISSTKKATEGKTSLSALTQLMKKMPHFRKQISKQVVHLNLAEDCMNKFKLNIEKLCKTEQDLALGTDAEGQRVKDSMLVLLPVLLNKNHDNCDKIRAVLLYIFGINGTTEENLDRLIHNVKIEDDSDMIRNWSHLGVPIVPPSQQAKPLRKDRSAEETFQLSRWTPFIKDIMEDAIDNRLDSKEWPYCSRCPAVWNGSGAVSARQKPRTNYLELDRKNGSRLIIFVIGGITYSEMRCAYEVSQAHKSCEVIIGSTHILTPRKLLDDIKMLNKSKDKVSFKDE

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	Syntaxin-4 N-terminal peptide
Molecular weight formula_weight	1345.5 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

MRDRTHELRQ

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7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	3pukA01
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	3pukA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1910 — Sec1/Munc18 (SM) protein, domain 2

Domain ID domain_id	3pukA03
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

Domain ID domain_id	3pukA04
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	3pukB01
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	3pukB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1910 — Sec1/Munc18 (SM) protein, domain 2

Domain ID domain_id	3pukB03
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

Domain ID domain_id	3pukB04
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	60 —

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8. Citations (2)

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Unit-cell length a length_a	170.400 Å
Unit-cell length b length_b	170.400 Å
Unit-cell length c length_c	170.400 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	P 21 3
Space-group number int_tables_number	198
Crystal system crystal_system	—

Resolution resolution	3.054 Å
Low-resolution limit resolution_low	45.541 Å
R factor r_factor	0.2407
R_work r_work	0.2387
R_free r_free	0.2790

fit	/app/data/saxs_computation/pu/3puk/3puk.fit
pddf	/app/data/pr_computation/pu/3puk/3puk.pr.out
profile	/app/data/saxs_computation/pu/3puk/3puk.dat

Re-refinement of the crystal structure of Munc18-3 and Syntaxin4 N-peptide complex

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

Syntaxin-binding protein 3

State in the Current Structure

Other States of the Same Protein in the Database

Syntaxin-4 N-terminal peptide

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)