SAXSdb — 9zcs

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

Small conjugating protein ligase-like protein

Thermochaetoides thermophila DSM 1495

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Vacuolar protein sorting-associated protein 16 × 1 （G0S6M7） Nyv1 SNARE motif × 1 （G0S5G3） SNAP receptor-like protein × 1 （G0S236）	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 29–696； UniProt 139–806

Vacuolar protein sorting-associated protein 16

Thermochaetoides thermophila DSM 1495

UniProt G0S6M7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Small conjugating protein ligase-like protein × 1 （G0SCM5） Nyv1 SNARE motif × 1 （G0S5G3） SNAP receptor-like protein × 1 （G0S236）	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 4–274； UniProt 521–773

Nyv1 SNARE motif

Thermochaetoides thermophila DSM 1495

UniProt G0S5G3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Small conjugating protein ligase-like protein × 1 （G0SCM5） Vacuolar protein sorting-associated protein 16 × 1 （G0S6M7） SNAP receptor-like protein × 1 （G0S236）	Consistent with protein count

Other States of the Same Protein in the Database

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

SNAP receptor-like protein

Thermochaetoides thermophila DSM 1495

UniProt G0S236

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Small conjugating protein ligase-like protein × 1 （G0SCM5） Vacuolar protein sorting-associated protein 16 × 1 （G0S6M7） Nyv1 SNARE motif × 1 （G0S5G3）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	G0S236_CHATD
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 3–51； UniProt 181–229

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	9zcs
Deposition date deposition_date	2025-11-24
Last revision last_revision	2026-06-03
Structure title title	Crystal structure of HOPS subunits Vps33 and Vps16 in complex with the Nyv1 and Vam3 SNARE motifs
Keywords keywords	MEMBRANE TRAFFICKING, SM PROTEIN, HOPS COMPLEX, THERMOPHILE, SNARE DOMAIN, 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.

9zcs__assembly_1__model_1

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

Download this curve (.dat)

9zcs__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9zcs__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.81 Å
Rg (electron density)	30.62 Å
Total Rg	31.39 Å
Atom count	7455
Residues	944
Excluded volume	132850 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9zcs__assembly_1__model_1`	tetrameric （4）	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 (4)

Entity 1 Entity 1 polymer

Description description	Small conjugating protein ligase-like protein
Molecular weight formula_weight	77119.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	7455

MKHHHHHHHGAAGTSLYKKAGENLYFQGSMAPRAGFDAEQVRDKARKDLLHLLEGVRGKKNLVIEKDLAGPLGVIVKASTLRDYGVDNFFFLENKNTGTSQRNIVFIARGESVRNAHAIAAQIKRIQRESQTSHDFHIFWVPRRTLFSDKVLEEAGVLGDANISELPLYFFPLERDVLSLELNDSFRDLYLAKDPTPVFLLSRALMGIQKKHGLFPRIIGKGENAKRVADLLSRMRQELLAGEEAGESDRAGLSPSTTIESVIIIDREVDFVTPLLTQLTYEGLIDEYFGIQNNQTDVDAVIVGAPAQSAASTSTAVPTNSSQSRKRKIQLDGSDSLYSQLRDANFAIVGSLLNTVARRLKSDYESRHNTKTTAELKEFVKKLPGYQAEQQSLKIHSNIAEEIINYTRTEIFNKLLEVQQNLAAGADPSSQFDSIEELVARDTPLPQVLRLLCLYSCISGGIKTKELDHFRRLVLQGYGHQHLLTLHNLERLQMFLSKSSPLASMITMSGSSGGPDQKTNYTYLRKQLRLIVDEVNEQDPNDIAYVYSGYAPLSIRLVQCVLQKQYLLSITKGSGTVIAAGPVAGGGAQGWKGFEEIVKHARGPTFDEIQKGEDKAVKARALLSGSSGDKKTVFVVFVGGITFTEIAALRFIAKQEEARRNIVICTTSIINGNRMMNAAIETATFEKTTVTTAAAQ

Source Source

Source organism organism	Thermochaetoides thermophila DSM 1495
NCBI taxonomy ID ncbi_taxonomy_id	759272
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Vacuolar protein sorting-associated protein 16
Molecular weight formula_weight	31252.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MGSLATELLNHEPRAGRQVPLLLSMEEDELALDKAIESGDTDLIYFVIHQLRRKLPLASFFRVVSSRPTASAMVEALARNSDGDGNEDTALLKDLYYQDDRRLDGASVFIREALQQPETRTASDKLDLAANLLQGNQKEHVFELGALKEAKMLLRMQETFERDLTDSFVGLSVNQTMFKLIKLGYHGRAKKIQSEFKVPERVAWWIRLQALVAKRDWNEIEEISRQRKSPIGWEPFFNQVLQAGNPRLAATFIPKCTNLEPGQTITMYEKCGMR

Source Source

Source organism organism	Thermochaetoides thermophila DSM 1495
NCBI taxonomy ID ncbi_taxonomy_id	759272
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Nyv1 SNARE motif
Molecular weight formula_weight	7570.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

GSVENNGGDSINSVQREIEDVRGIMSRNIEGLLERGERIDLLVDKTDRLGGSAREFRLRSRGLKRKM

Source Source

Source organism organism	Thermochaetoides thermophila DSM 1495
NCBI taxonomy ID ncbi_taxonomy_id	759272
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	SNAP receptor-like protein
Molecular weight formula_weight	5669.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

GSLILEREEEIRNIEQGVSDLNVLFQQVAQLVAEQGEVLDTIERNVEAVGD

Source Source

Source organism organism	Thermochaetoides thermophila DSM 1495
NCBI taxonomy ID ncbi_taxonomy_id	759272
Host organism host_organism	Escherichia coli

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Unit-cell length a length_a	100.844 Å
Unit-cell length b length_b	100.844 Å
Unit-cell length c length_c	312.412 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	3.190 Å
Low-resolution limit resolution_low	29.600 Å
R factor r_factor	0.1798
R_work r_work	0.1774
R_free r_free	0.2245

Crystal structure of HOPS subunits Vps33 and Vps16 in complex with the Nyv1 and Vam3 SNARE motifs

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

Small conjugating protein ligase-like protein

State in the Current Structure

Other States of the Same Protein in the Database

Vacuolar protein sorting-associated protein 16

State in the Current Structure

Other States of the Same Protein in the Database

Nyv1 SNARE motif

State in the Current Structure

Other States of the Same Protein in the Database

SNAP receptor-like 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

9zcs__assembly_1__model_1

9zcs__assembly_1__model_1 | I(q)

9zcs__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

7. Citations (2)

Crystal structure of HOPS subunits Vps33 and Vps16 in complex with the Nyv1 and Vam3 SNARE motifs

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

Small conjugating protein ligase-like 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

Vacuolar protein sorting-associated protein 16

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Nyv1 SNARE motif

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

SNAP receptor-like 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

9zcs__assembly_1__model_1

9zcs__assembly_1__model_1 | I(q)

9zcs__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

7. Citations (2)