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3puj

Crystal structure of the MUNC18-1 and SYNTAXIN4 N-Peptide complex

Method: X-RAY DIFFRACTION Dmax: 128.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Syntaxin-binding protein 1

Rattus norvegicus

UniProt P61765

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 1–594 Not recorded Syntaxin-4 N-terminal peptide × 1 （P70452） 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
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 1–594 Not recorded Syntaxin-4 N-terminal peptide × 1 （P70452） 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

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 3PUJ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3C98 Revised structure of the munc18a-syntaxin1 complex Deposited 2008-02-15 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–594（594 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；294 K；PEG400, Ammonium Acetate, Sodium Acetate, EDTA, 2-mercaptoethanol, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 2.60 Å R-free 0.263
4JEH Crystal Structure of Munc18a and Syntaxin1 lacking N-peptide complex Deposited 2013-02-27 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–594（594 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；27% PEG 400, 10 mM EDTA, 10 mM DTT, 224 mM ammonium acetate, and 100 mM sodium acetate , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.50 Å R-free 0.223
4JEH Crystal Structure of Munc18a and Syntaxin1 lacking N-peptide complex Deposited 2013-02-27 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–594（594 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；27% PEG 400, 10 mM EDTA, 10 mM DTT, 224 mM ammonium acetate, and 100 mM sodium acetate , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.50 Å R-free 0.223
4JEU Crystal Structure of Munc18a and Syntaxin1 with native N-terminus complex Deposited 2013-02-27 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 3–592（590 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.2；298 K；27% PEG 400, 10 mM EDTA, 10 mM DTT, 224 mM ammonium acetate, and 100 mM sodium acetate , pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 3.20 Å R-free 0.263
6LPC Crystal Structure of rat Munc18-1 with K332E/K333E mutation Deposited 2020-01-09 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–594（594 aa）
Chain B 1–594（594 aa）
Mutation：K332E, K333E Mutation：K332E, K333E No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；289.15 K；4 M ammonium acetate, 0.1 M sodium acetate trihydrate
Resolution 3.40 Å R-free 0.331
7UDB Cryo-EM structure of a synaptobrevin-Munc18-1-syntaxin-1 complex class 2 Deposited 2022-03-18 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–594（594 aa）
Mutation：D326K No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7UDC cryo-EM structures of a synaptobrevin-Munc18-1-syntaxin-1 complex class1 Deposited 2022-03-18 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–594（594 aa）
Mutation：D326K No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
7XSJ The structure of the Mint1/Munc18-1/syntaxin-1 complex Deposited 2022-05-14 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–594（594 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；297 K；0.2M Sodium Malonate, pH 7.0, 20% (v/v) PEG 3350
Resolution 3.20 Å R-free 0.270

7 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name STXB1_RAT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–594； UniProt 1–594 Author chain B； PDBConstruct 1–594； UniProt 1–594

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 1 × 1 （P61765） 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
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 1 × 1 （P61765） 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

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 3PUJ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3PUK Re-refinement of the crystal structure of Munc18-3 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 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
3PUK Re-refinement of the crystal structure of Munc18-3 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 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
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.

SAXS scattering curve SAXS Profile

SAXS profile for 3puj

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3puj
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3puj
Deposition date deposition_date2010-12-05
Structure title titleCrystal structure of the MUNC18-1 and SYNTAXIN4 N-Peptide complex
Keywords keywordsMEMBRANE TRAFFICKING, SM PROTEIN, SYNTAXIN, SNARE PROTEINS, Syntaxin binding protein, ENDOCYTOSIS-EXOCYTOSIS complex; ENDOCYTOSIS/EXOCYTOSIS
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier40.54 Å
Radius of gyration Rg (electron density) rg_electron40.26 Å
Forward intensity I(0) i0219122000.00
Molecular weight molecular_weight122980.0 kDa
Excluded volume excluded_volume155100 ų
Envelope volume envelope_volume217130 ų
Hydration-shell volume shell_volume45760 ų
Envelope diameter envelope_diameter129.3 Å
Shell Rg shell_rg45.05 Å
Envelope Rg envelope_rg39.37 Å
Shape Rg shape_rg40.28 Å
Total Rg total_rg40.48 Å
Total atoms total_atoms8638
Residues n_residues1086
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax128.8 Å
Rg (real space) rg_real40.59 Å
Rg uncertainty (real space) rg_real_error1.33 Å
I(0) (real space) i0_real2.1910e+08
I(0) uncertainty (real space) i0_real_error3.8890e+06
Rg (reciprocal space) rg_reciprocal40.54 Å
I(0) (reciprocal space) i0_reciprocal219100000.0000
Solution quality estimate total_estimate0.8822
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary36.3 Å
Skewness Skewness skewness0.228
Kurtosis Kurtosis kurtosis-0.871
Angular range angular_range— – 0.1950 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha30850000.0000
Real-space data points n_real_points40
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.887; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.890; Smooth: 0.915
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id3pujA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2060 — Sec1/Munc18 (SM) protein, domain 1
Domain ID domain_id3pujA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1910 — Sec1/Munc18 (SM) protein, domain 2
Domain ID domain_id3pujA03
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology830 — Syntaxin Binding Protein 1; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Sec1/Munc18 (SM) protein, domain 3a
Domain ID domain_id3pujA04
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily60 —
Domain ID domain_id3pujB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2060 — Sec1/Munc18 (SM) protein, domain 1
Domain ID domain_id3pujB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1910 — Sec1/Munc18 (SM) protein, domain 2
Domain ID domain_id3pujB03
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology830 — Syntaxin Binding Protein 1; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Sec1/Munc18 (SM) protein, domain 3a
Domain ID domain_id3pujB04
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily60 —
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8. Citations (1)

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9. Files and Curves (10)