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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Putative vacuolar protein sorting-associated protein × 1 （G0S6M7） D-MALATE × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Putative vacuolar protein sorting-associated protein × 1 （G0S6M7） D-MALATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	VPS33 × 1 （G0SCM5） D-MALATE × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	VPS33 × 1 （G0SCM5） D-MALATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

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. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

5bv1__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5bv1__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5bv1__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	32.33 Å
Rg (electron density)	31.22 Å
Total Rg	31.89 Å
Atom count	7126
Residues	898
Excluded volume	126900 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5bv1__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5bv1__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. 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

Source Source

Source organism organism	Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
NCBI taxonomy ID ncbi_taxonomy_id	759272
Host organism 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

Source Source

Source organism organism	Chaetomium thermophilum
NCBI taxonomy ID ncbi_taxonomy_id	759272
Host organism 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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6. 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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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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5bv1__assembly_1__model_1

5bv1__assembly_1__model_1 | I(q)

5bv1__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (2)

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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Putative vacuolar protein sorting-associated protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5bv1__assembly_1__model_1

5bv1__assembly_1__model_1 | I(q)

5bv1__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (2)