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9zcs

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

Method: X-RAY DIFFRACTION D_max: 98.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zcs
deposition_date	2025-11-24
last_revision	2026-06-03
title	Crystal structure of HOPS subunits Vps33 and Vps16 in complex with the Nyv1 and Vam3 SNARE motifs
keywords	MEMBRANE TRAFFICKING, SM PROTEIN, HOPS COMPLEX, THERMOPHILE, SNARE DOMAIN, TRANSPORT PROTEIN; TRANSPORT PROTEIN
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	31.81 Å
rg_electron	30.62 Å
i0	175390000.00
molecular_weight	105810.0 kDa
excluded_volume	132850 Å³
envelope_volume	171050 Å³
shell_volume	45126 Å³
envelope_diameter	102.3 Å
shell_rg	38.83 Å
envelope_rg	30.79 Å
shape_rg	30.60 Å
total_rg	31.39 Å
total_atoms	7455
n_residues	944
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	98.7 Å
rg_real	31.63 Å
rg_real_error	0.55 Å
i0_real	1.7540e+08
i0_real_error	2.5060e+06
rg_reciprocal	31.71 Å
i0_reciprocal	175400000.0000
total_estimate	0.8987
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	41.4 Å
skewness	0.155
kurtosis	-0.448
angular_range	— – 0.2500 Å⁻¹
current_alpha	0.0000
highest_alpha	42930000.0000
n_real_points	51
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.926; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.917

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Small conjugating protein ligase-like protein
formula_weight	77119.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	7455

MKHHHHHHHGAAGTSLYKKAGENLYFQGSMAPRAGFDAEQVRDKARKDLLHLLEGVRGKKNLVIEKDLAGPLGVIVKASTLRDYGVDNFFFLENKNTGTSQRNIVFIARGESVRNAHAIAAQIKRIQRESQTSHDFHIFWVPRRTLFSDKVLEEAGVLGDANISELPLYFFPLERDVLSLELNDSFRDLYLAKDPTPVFLLSRALMGIQKKHGLFPRIIGKGENAKRVADLLSRMRQELLAGEEAGESDRAGLSPSTTIESVIIIDREVDFVTPLLTQLTYEGLIDEYFGIQNNQTDVDAVIVGAPAQSAASTSTAVPTNSSQSRKRKIQLDGSDSLYSQLRDANFAIVGSLLNTVARRLKSDYESRHNTKTTAELKEFVKKLPGYQAEQQSLKIHSNIAEEIINYTRTEIFNKLLEVQQNLAAGADPSSQFDSIEELVARDTPLPQVLRLLCLYSCISGGIKTKELDHFRRLVLQGYGHQHLLTLHNLERLQMFLSKSSPLASMITMSGSSGGPDQKTNYTYLRKQLRLIVDEVNEQDPNDIAYVYSGYAPLSIRLVQCVLQKQYLLSITKGSGTVIAAGPVAGGGAQGWKGFEEIVKHARGPTFDEIQKGEDKAVKARALLSGSSGDKKTVFVVFVGGITFTEIAALRFIAKQEEARRNIVICTTSIINGNRMMNAAIETATFEKTTVTTAAAQ

Source

organism	Thermochaetoides thermophila DSM 1495
ncbi_taxonomy_id	759272
host_organism	Escherichia coli

Entity 2 polymer

description	Vacuolar protein sorting-associated protein 16
formula_weight	31252.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MGSLATELLNHEPRAGRQVPLLLSMEEDELALDKAIESGDTDLIYFVIHQLRRKLPLASFFRVVSSRPTASAMVEALARNSDGDGNEDTALLKDLYYQDDRRLDGASVFIREALQQPETRTASDKLDLAANLLQGNQKEHVFELGALKEAKMLLRMQETFERDLTDSFVGLSVNQTMFKLIKLGYHGRAKKIQSEFKVPERVAWWIRLQALVAKRDWNEIEEISRQRKSPIGWEPFFNQVLQAGNPRLAATFIPKCTNLEPGQTITMYEKCGMR

Source

organism	Thermochaetoides thermophila DSM 1495
ncbi_taxonomy_id	759272
host_organism	Escherichia coli

Entity 3 polymer

description	Nyv1 SNARE motif
formula_weight	7570.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

GSVENNGGDSINSVQREIEDVRGIMSRNIEGLLERGERIDLLVDKTDRLGGSAREFRLRSRGLKRKM

Source

organism	Thermochaetoides thermophila DSM 1495
ncbi_taxonomy_id	759272
host_organism	Escherichia coli

Entity 4 polymer

description	SNAP receptor-like protein
formula_weight	5669.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

GSLILEREEEIRNIEQGVSDLNVLFQQVAQLVAEQGEVLDTIERNVEAVGD

Source

organism	Thermochaetoides thermophila DSM 1495
ncbi_taxonomy_id	759272
host_organism	Escherichia coli

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6. Citations (2)

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length_a	100.844 Å
length_b	100.844 Å
length_c	312.412 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 41 21 2
int_tables_number	92
crystal_system	—

resolution	3.190 Å
resolution_low	29.600 Å
r_factor	0.1798
r_work	0.1774
r_free	0.2245

fit	/app/data/saxs_computation/zc/9zcs/9zcs.fit
pddf	/app/data/pr_computation/zc/9zcs/9zcs.pr.out
profile	/app/data/saxs_computation/zc/9zcs/9zcs.dat

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

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

6. Citations (2)

7. Files & Curves (10)

Files (7)

Curves (3)