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9zct

Crystal structure of HOPS subunits Vps33 and Vps16 in complex with the Nyv1 SNARE motif

Method: X-RAY DIFFRACTION Dmax: 97.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Small conjugating protein ligase-like protein

Thermochaetoides thermophila DSM 1495

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 Vacuolar protein sorting-associated protein 16 × 1 （G0S6M7） Nyv1 SNARE motif × 1 （G0S5G3） X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.90 Å R-free 0.250

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 9ZCT Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5BUZ Crystal Structure of a Complex Between the SNARE Vam3 and the HOPS Vps33-Vps16 subcomplex from Chaetomium thermophilum Deposited 2015-06-04 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 139–806（668 aa）
Not recorded No recorded non-water small molecule 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
5BUZ Crystal Structure of a Complex Between the SNARE Vam3 and the HOPS Vps33-Vps16 subcomplex from Chaetomium thermophilum Deposited 2015-06-04 Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 139–806（668 aa）
Not recorded No recorded non-water small molecule 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
5BV0 Crystal Structure of a Complex Between the SNARE Nyv1 and the HOPS Vps33-Vps16 subcomplex from Chaetomium thermophilum Deposited 2015-06-04 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 139–806（668 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；TRIS-HCl buffer, 0.8M Na Tartrate, 0.5% w/v PEG 5000 monomethyl ether
Resolution 3.10 Å R-free 0.246
5BV1 Crystal Structure of a Vps33-Vps16 Complex from Chaetomium thermophilum Deposited 2015-06-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 139–806（668 aa） Fragment：unp residues 139-806
Not recorded MLT D-MALATE × 1 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 2.90 Å R-free 0.276
5BV1 Crystal Structure of a Vps33-Vps16 Complex from Chaetomium thermophilum Deposited 2015-06-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 139–806（668 aa） Fragment：unp residues 139-806
Not recorded MLT D-MALATE × 1 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 2.90 Å R-free 0.276
9ZBE Revised structure of a complex between the SNARE Nyv1 and the HOPS Vps33-Vps16 subcomplex Deposited 2025-11-20 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 139–806（668 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.05 Å R-free 0.224
9ZCS Crystal structure of HOPS subunits Vps33 and Vps16 in complex with the Nyv1 and Vam3 SNARE motifs Deposited 2025-11-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 139–806（668 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.19 Å R-free 0.225

5 other PDB entries and 7 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 29–696； UniProt 139–806

Vacuolar protein sorting-associated protein 16

Thermochaetoides thermophila DSM 1495

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 521–773 Not recorded Small conjugating protein ligase-like protein × 1 （G0SCM5） Nyv1 SNARE motif × 1 （G0S5G3） X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.90 Å R-free 0.250

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 9ZCT Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5BUZ Crystal Structure of a Complex Between the SNARE Vam3 and the HOPS Vps33-Vps16 subcomplex from Chaetomium thermophilum Deposited 2015-06-04 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 505–816（312 aa）
Not recorded No recorded non-water small molecule 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
5BUZ Crystal Structure of a Complex Between the SNARE Vam3 and the HOPS Vps33-Vps16 subcomplex from Chaetomium thermophilum Deposited 2015-06-04 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 505–816（312 aa）
Not recorded No recorded non-water small molecule 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
5BV1 Crystal Structure of a Vps33-Vps16 Complex from Chaetomium thermophilum Deposited 2015-06-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 505–816（312 aa） Fragment：unp residues 503-816
Mutation：L672V MLT D-MALATE × 1 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 2.90 Å R-free 0.276
5BV1 Crystal Structure of a Vps33-Vps16 Complex from Chaetomium thermophilum Deposited 2015-06-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 505–816（312 aa） Fragment：unp residues 503-816
Mutation：L672V MLT D-MALATE × 1 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 2.90 Å R-free 0.276
9ZCS Crystal structure of HOPS subunits Vps33 and Vps16 in complex with the Nyv1 and Vam3 SNARE motifs Deposited 2025-11-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 521–773（253 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.19 Å R-free 0.225

3 other PDB entries and 5 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 4–274； UniProt 521–773

Nyv1 SNARE motif

Thermochaetoides thermophila DSM 1495

UniProt G0S5G3

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 148–212 Not recorded Small conjugating protein ligase-like protein × 1 （G0SCM5） Vacuolar protein sorting-associated protein 16 × 1 （G0S6M7） X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.90 Å R-free 0.250

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 9ZCT Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5BV0 Crystal Structure of a Complex Between the SNARE Nyv1 and the HOPS Vps33-Vps16 subcomplex from Chaetomium thermophilum Deposited 2015-06-04 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 183–212（30 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；TRIS-HCl buffer, 0.8M Na Tartrate, 0.5% w/v PEG 5000 monomethyl ether
Resolution 3.10 Å R-free 0.246
9ZBE Revised structure of a complex between the SNARE Nyv1 and the HOPS Vps33-Vps16 subcomplex Deposited 2025-11-20 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 148–212（65 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.05 Å R-free 0.224
9ZCS Crystal structure of HOPS subunits Vps33 and Vps16 in complex with the Nyv1 and Vam3 SNARE motifs Deposited 2025-11-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 148–212（65 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.19 Å R-free 0.225

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

View Construct and Data Evidence
UniProt name G0S5G3_CHATD
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 3–67； UniProt 148–212

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 9zct

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9zct
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9zct
Deposition date deposition_date2025-11-24
最后修订 last_revision2026-06-03
Structure title titleCrystal structure of HOPS subunits Vps33 and Vps16 in complex with the Nyv1 SNARE motif
Keywords keywordsMEMBRANE TRAFFICKING, SM PROTEIN, HOPS COMPLEX, THERMOPHILE, SNARE DOMAIN, TRANSPORT PROTEIN; TRANSPORT PROTEIN
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_guinier31.49 Å
Radius of gyration Rg (electron density) rg_electron30.26 Å
Forward intensity I(0) i0167163000.00
Molecular weight molecular_weight103020.0 kDa
Excluded volume excluded_volume129330 ų
Envelope volume envelope_volume165490 ų
Hydration-shell volume shell_volume44180 ų
Envelope diameter envelope_diameter101.3 Å
Shell Rg shell_rg38.42 Å
Envelope Rg envelope_rg30.46 Å
Shape Rg shape_rg30.24 Å
Total Rg total_rg31.05 Å
Total atoms total_atoms7257
Residues n_residues915
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 dmax97.7 Å
Rg (real space) rg_real31.31 Å
Rg uncertainty (real space) rg_real_error0.59 Å
I(0) (real space) i0_real1.6720e+08
I(0) uncertainty (real space) i0_real_error2.2710e+06
Rg (reciprocal space) rg_reciprocal31.39 Å
I(0) (reciprocal space) i0_reciprocal167200000.0000
Solution quality estimate total_estimate0.8980
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary41.0 Å
Skewness Skewness skewness0.166
Kurtosis Kurtosis kurtosis-0.436
Angular range angular_range— – 0.2500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha32330000.0000
Real-space data points n_real_points51
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.927; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.904
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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8. Citations (2)

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9. Files and Curves (10)