5buz

Crystal Structure of a Complex Between the SNARE Vam3 and the HOPS Vps33-Vps16 subcomplex from Chaetomium thermophilum

Method: X-RAY DIFFRACTION Dmax: 190.0 Å Quality: GOOD

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

SM (Sec1/Munc18-like) protein

Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)

UniProt G0SCM5

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 139–806 Not recorded Putative vacuolar protein sorting-associated protein × 1 (G0S6M7) SNAP receptor-like protein × 1 (G0S236) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;293 K;HEPES buffer, 8-10% w/v PEG 5000 monomethyl ether Resolution 3.10 Å R-free 0.233
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain D; UniProt 139–806 Not recorded Putative vacuolar protein sorting-associated protein × 1 (G0S6M7) SNAP receptor-like protein × 1 (G0S236) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;293 K;HEPES buffer, 8-10% w/v PEG 5000 monomethyl ether Resolution 3.10 Å R-free 0.233

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.

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name G0SCM5_CHATD
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–669; UniProt 139–806 Author chain D; PDBConstruct 2–669; UniProt 139–806

Putative vacuolar protein sorting-associated protein

Chaetomium thermophilum

UniProt G0S6M7

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 505–816 Not recorded SM (Sec1/Munc18-like) protein × 1 (G0SCM5) SNAP receptor-like protein × 1 (G0S236) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;293 K;HEPES buffer, 8-10% w/v PEG 5000 monomethyl ether Resolution 3.10 Å R-free 0.233
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain E; UniProt 505–816 Not recorded SM (Sec1/Munc18-like) protein × 1 (G0SCM5) SNAP receptor-like protein × 1 (G0S236) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;293 K;HEPES buffer, 8-10% w/v PEG 5000 monomethyl ether Resolution 3.10 Å R-free 0.233

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.

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

View Construct and Data Evidence
UniProt name G0S6M7_CHATD
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 4–333; UniProt 505–816 Author chain E; PDBConstruct 4–333; UniProt 505–816

SNAP receptor-like protein

Chaetomium thermophilum

UniProt G0S236

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain C; UniProt 181–245 Fragment:SNARE domain SM (Sec1/Munc18-like) protein × 1 (G0SCM5) Putative vacuolar protein sorting-associated protein × 1 (G0S6M7) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;293 K;HEPES buffer, 8-10% w/v PEG 5000 monomethyl ether Resolution 3.10 Å R-free 0.233
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain F; UniProt 181–245 Fragment:SNARE domain SM (Sec1/Munc18-like) protein × 1 (G0SCM5) Putative vacuolar protein sorting-associated protein × 1 (G0S6M7) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;293 K;HEPES buffer, 8-10% w/v PEG 5000 monomethyl ether Resolution 3.10 Å R-free 0.233

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.

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name G0S236_CHATD
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 3–67; UniProt 181–245 Author chain F; PDBConstruct 3–67; UniProt 181–245

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 5buz

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5buz
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5buz
Deposition date deposition_date2015-06-04
Structure title titleCrystal Structure of a Complex Between the SNARE Vam3 and the HOPS Vps33-Vps16 subcomplex from Chaetomium thermophilum
Keywords keywordsMembrane trafficking, SM protein, HOPS complex, thermophile, SNARE domain, Transport Protein; TRANSPORT PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier51.89
Radius of gyration Rg (electron density) rg_electron52.03
Forward intensity I(0) i0679862000.00
Molecular weight molecular_weight216740.0 kDa
Excluded volume excluded_volume271850 ų
Envelope volume envelope_volume411650 ų
Hydration-shell volume shell_volume68311 ų
Envelope diameter envelope_diameter202.4
Shell Rg shell_rg51.65
Envelope Rg envelope_rg51.98
Shape Rg shape_rg52.02
Total Rg total_rg52.04
Total atoms total_atoms15276
Residues n_residues1936
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 dmax190.0
Rg (real space) rg_real52.23
Rg uncertainty (real space) rg_real_error3.04
I(0) (real space) i0_real6.7990e+08
I(0) uncertainty (real space) i0_real_error1.6120e+07
Rg (reciprocal space) rg_reciprocal51.60
I(0) (reciprocal space) i0_reciprocal679300000.0000
Solution quality estimate total_estimate0.8116
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary44.3
Skewness Skewness skewness0.501
Kurtosis Kurtosis kurtosis-0.422
Angular range angular_range— – 0.1500 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha96240000.0000
Real-space data points n_real_points31
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.581; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.900; Smooth: 0.903

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id5buzA01
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_id5buzA02
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_id5buzA03
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_id5buzA04
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily850 — Sec1/Munc18 (SM) protein, domain 3b
Domain ID domain_id5buzD01
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_id5buzD02
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_id5buzD03
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_id5buzD04
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily850 — Sec1/Munc18 (SM) protein, domain 3b

8. Citations (2)

9. Files and Curves (10)