4jeu

Crystal Structure of Munc18a and Syntaxin1 with native N-terminus complex

Method: X-RAY DIFFRACTION Dmax: 101.8 Å Quality: EXCELLENT

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 3–592 Not recorded Syntaxin-1A × 1 (P32851) 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

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.

7 other PDB entries and 9 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 1–590; UniProt 3–592

Syntaxin-1A

Rattus norvegicus

UniProt P32851

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 B; UniProt 2–243 Not recorded Syntaxin-binding protein 1 × 1 (P61765) 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

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.

53 other PDB entries and 72 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name STX1A_RAT
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–242; UniProt 2–243

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 4jeu

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4jeu
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4jeu
Deposition date deposition_date2013-02-27
Structure title titleCrystal Structure of Munc18a and Syntaxin1 with native N-terminus complex
Keywords keywords;PROTEIN COMPLEX, MEMBRANE, PHOSPHOPROTEIN, PROTEIN TRANSPORT, TRANSPORT, NEUROTRANSMITTER TRANSPORT, TRANSMEMBRANE, ENDOCYTOSIS-EXOCYTOSIS complex ;; ENDOCYTOSIS/EXOCYTOSIS
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier31.54
Radius of gyration Rg (electron density) rg_electron30.65
Forward intensity I(0) i0130191000.00
Molecular weight molecular_weight89911.0 kDa
Excluded volume excluded_volume112560 ų
Envelope volume envelope_volume146230 ų
Hydration-shell volume shell_volume39642 ų
Envelope diameter envelope_diameter107.9
Shell Rg shell_rg37.76
Envelope Rg envelope_rg30.82
Shape Rg shape_rg30.64
Total Rg total_rg31.32
Total atoms total_atoms6303
Residues n_residues783
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax101.8
Rg (real space) rg_real31.48
Rg uncertainty (real space) rg_real_error0.82
I(0) (real space) i0_real1.3020e+08
I(0) uncertainty (real space) i0_real_error2.2840e+06
Rg (reciprocal space) rg_reciprocal31.51
I(0) (reciprocal space) i0_reciprocal130200000.0000
Solution quality estimate total_estimate0.9001
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary36.6
Skewness Skewness skewness0.270
Kurtosis Kurtosis kurtosis-0.451
Angular range angular_range— – 0.2500 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha39000000.0000
Real-space data points n_real_points51
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.922; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.931

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

Domain ID domain_id4jeuA01
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_id4jeuA02
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_id4jeuA03
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_id4jeuA04
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily60
Domain ID domain_id4jeuB00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily70

8. Citations (1)

9. Files and Curves (10)