SAXSdb — 5bv1

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

VPS33

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

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 139–806	Fragment：unp residues 139-806	Putative vacuolar protein sorting-associated protein × 1 （G0S6M7） 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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 139–806	Fragment：unp residues 139-806	Putative vacuolar protein sorting-associated protein × 1 （G0S6M7） 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

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 5BV1	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 oligomeric state Different ligand/ion 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 construct Different oligomeric state Different ligand/ion 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 construct Different oligomeric state Different ligand/ion 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
9ZBE Revised structure of a complex between the SNARE Nyv1 and the HOPS Vps33-Vps16 subcomplex Deposited 2025-11-20	Different construct Different oligomeric state Different ligand/ion 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 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 construct Different oligomeric state Different ligand/ion Different experimental conditions 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
9ZCT Crystal structure of HOPS subunits Vps33 and Vps16 in complex with the Nyv1 SNARE motif Deposited 2025-11-24	Different construct Different oligomeric state Different ligand/ion 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 mmCIF provides none of the parsed conditions	Resolution 2.90 Å R-free 0.250

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 C； 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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 505–816	Fragment：unp residues 503-816 Mutation：L672V	VPS33 × 1 （G0SCM5） 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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 505–816	Fragment：unp residues 503-816 Mutation：L672V	VPS33 × 1 （G0SCM5） 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

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 5BV1	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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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
9ZCS Crystal structure of HOPS subunits Vps33 and Vps16 in complex with the Nyv1 and Vam3 SNARE motifs Deposited 2025-11-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions 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
9ZCT Crystal structure of HOPS subunits Vps33 and Vps16 in complex with the Nyv1 SNARE motif Deposited 2025-11-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	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 2.90 Å R-free 0.250

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 D； PDBConstruct 4–333； UniProt 505–816

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	5bv1
Deposition date deposition_date	2015-06-04
Structure title title	Crystal Structure of a Vps33-Vps16 Complex from Chaetomium thermophilum
Keywords keywords	Membrane trafficking, SM protein, HOPS complex, thermophile, TRANSPORT PROTEIN; TRANSPORT PROTEIN
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	44.43 Å
Radius of gyration Rg (electron density) rg_electron	43.82 Å
Forward intensity I(0) i0	601297000.00
Molecular weight molecular_weight	202360.0 kDa
Excluded volume excluded_volume	253940 Å³
Envelope volume envelope_volume	369450 Å³
Hydration-shell volume shell_volume	69831 Å³
Envelope diameter envelope_diameter	140.0 Å
Shell Rg shell_rg	49.48 Å
Envelope Rg envelope_rg	42.35 Å
Shape Rg shape_rg	43.81 Å
Total Rg total_rg	44.15 Å
Total atoms total_atoms	14259
Residues n_residues	1797
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	137.8 Å
Rg (real space) rg_real	44.33 Å
Rg uncertainty (real space) rg_real_error	0.83 Å
I(0) (real space) i0_real	6.0130e+08
I(0) uncertainty (real space) i0_real_error	1.0020e+07
Rg (reciprocal space) rg_reciprocal	44.43 Å
I(0) (reciprocal space) i0_reciprocal	601400000.0000
Solution quality estimate total_estimate	0.8827
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	49.8 Å
Skewness Skewness skewness	0.203
Kurtosis Kurtosis kurtosis	-0.607
Angular range angular_range	— – 0.1800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	50890000.0000
Real-space data points n_real_points	37
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.967; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.571

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	VPS33
Molecular weight formula_weight	73990.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	14259

GSMAPRAGFDAEQVRDKARKDLLHLLEGVRGKKNLVIEKDLAGPLGVIVKASTLRDYGVDNFFFLENKNTGTSQRNIVFIARGESVRNAHAIAAQIKRIQRESQTSHDFHIFWVPRRTLFSDKVLEEAGVLGDANISELPLYFFPLERDVLSLELNDSFRDLYLAKDPTPVFLLSRALMGIQKKHGLFPRIIGKGENAKRVADLLSRMRQELLAGEEAGESDRAGLSPSTTIESVIIIDREVDFVTPLLTQLTYEGLIDEYFGIQNNQTDVDAVIVGAPAQSAASTSTAVPTNSSQSRKRKIQLDGSDSLYSQLRDANFAIVGSLLNTVARRLKSDYESRHNTKTTAELKEFVKKLPGYQAEQQSLKIHSNIAEEIINYTRTEIFNKLLEVQQNLAAGADPSSQFDSIEELVARDTPLPQVLRLLCLYSCISGGIKTKELDHFRRLVLQGYGHQHLLTLHNLERLQMFLSKSSPLASMITMSGSSGGPDQKTNYTYLRKQLRLIVDEVNEQDPNDIAYVYSGYAPLSIRLVQCVLQKQYLLSITKGSGTVIAAGPVAGGGAQGWKGFEEIVKHARGPTFDEIQKGEDKAVKARALLSGSSGDKKTVFVVFVGGITFTEIAALRFIAKQEEARRNIVICTTSIINGNRMMNAAIETATFEKTTVTTAAAQ

来源 Source

来源生物 organism	Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
NCBI Class编号 ncbi_taxonomy_id	759272
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Putative vacuolar protein sorting-associated protein
Molecular weight formula_weight	37912.2 kDa
Mutation mutation	L672V
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MGSSFEVIARTAYEEGRTRLATELLNHEPRAGRQVPLLLSMEEDELALDKAIESGDTDLIYFVIHQLRRKLPLASFFRVVSSRPTASAMVEALARNSDGDGNEDTALLKDLYYQDDRRLDGASVFIREALQQPETRTASDKLDLAANLLQGNQKEHVFELGALKEAKMLLRMQETFERDLTDSFVGLSVNQTMFKLIKLGYHGRAKKIQSEFKVPERVAWWIRLQALVAKRDWNEIEEISRQRKSPIGWEPFFNQVLQAGNPRLAATFIPKCTNLEPGQTITMYEKCGMRVKAAEEAVRLKDTEAWNRLLEAAGRNTAEGREIERLGATVFKK

来源 Source

来源生物 organism	Chaetomium thermophilum
NCBI Class编号 ncbi_taxonomy_id	759272
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	D-MALATE
Molecular weight formula_weight	134.1 kDa
Source method src_method	syn
Copy count entity_count	2

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7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	5bv1A01
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	5bv1A02
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	5bv1A03
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	5bv1A04
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	850 — Sec1/Munc18 (SM) protein, domain 3b

Domain ID domain_id	5bv1C01
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	5bv1C02
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	5bv1C03
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	5bv1C04
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	850 — Sec1/Munc18 (SM) protein, domain 3b

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8. Citations (2)

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Unit-cell length a length_a	79.280 Å
Unit-cell length b length_b	159.902 Å
Unit-cell length c length_c	97.394 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.21 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.902 Å
Low-resolution limit resolution_low	61.592 Å
R factor r_factor	0.2148
R_work r_work	0.2115
R_free r_free	0.2759

fit	/app/data/saxs_computation/bv/5bv1/5bv1.fit
pddf	/app/data/pr_computation/bv/5bv1/5bv1.pr.out
profile	/app/data/saxs_computation/bv/5bv1/5bv1.dat

Crystal Structure of a Vps33-Vps16 Complex from Chaetomium thermophilum

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

VPS33

State in the Current Structure

Other States of the Same Protein in the Database

Putative vacuolar protein sorting-associated protein

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-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)