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9zbe

Revised structure of a complex between the SNARE Nyv1 and the HOPS Vps33-Vps16 subcomplex

Method: X-RAY DIFFRACTION D_max: 101.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zbe
deposition_date	2025-11-20
last_revision	2026-06-03
title	Revised structure of a complex between the SNARE Nyv1 and the HOPS Vps33-Vps16 subcomplex
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	30.65 Å
rg_electron	29.47 Å
i0	144609000.00
molecular_weight	95766.0 kDa
excluded_volume	120360 Å³
envelope_volume	153870 Å³
shell_volume	42401 Å³
envelope_diameter	108.6 Å
shell_rg	37.44 Å
envelope_rg	29.75 Å
shape_rg	29.45 Å
total_rg	30.28 Å
total_atoms	6749
n_residues	854
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	101.8 Å
rg_real	30.52 Å
rg_real_error	0.52 Å
i0_real	1.4460e+08
i0_real_error	2.1600e+06
rg_reciprocal	30.58 Å
i0_reciprocal	144600000.0000
total_estimate	0.8825
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	39.2 Å
skewness	0.231
kurtosis	-0.271
angular_range	— – 0.2600 Å⁻¹
current_alpha	0.0002
highest_alpha	36690000.0000
n_real_points	53
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.824; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.995

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	SM Protein Vps33
formula_weight	73990.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6758

GSMAPRAGFDAEQVRDKARKDLLHLLEGVRGKKNLVIEKDLAGPLGVIVKASTLRDYGVDNFFFLENKNTGTSQRNIVFIARGESVRNAHAIAAQIKRIQRESQTSHDFHIFWVPRRTLFSDKVLEEAGVLGDANISELPLYFFPLERDVLSLELNDSFRDLYLAKDPTPVFLLSRALMGIQKKHGLFPRIIGKGENAKRVADLLSRMRQELLAGEEAGESDRAGLSPSTTIESVIIIDREVDFVTPLLTQLTYEGLIDEYFGIQNNQTDVDAVIVGAPAQSAASTSTAVPTNSSQSRKRKIQLDGSDSLYSQLRDANFAIVGSLLNTVARRLKSDYESRHNTKTTAELKEFVKKLPGYQAEQQSLKIHSNIAEEIINYTRTEIFNKLLEVQQNLAAGADPSSQFDSIEELVARDTPLPQVLRLLCLYSCISGGIKTKELDHFRRLVLQGYGHQHLLTLHNLERLQMFLSKSSPLASMITMSGSSGGPDQKTNYTYLRKQLRLIVDEVNEQDPNDIAYVYSGYAPLSIRLVQCVLQKQYLLSITKGSGTVIAAGPVAGGGAQGWKGFEEIVKHARGPTFDEIQKGEDKAVKARALLSGSSGDKKTVFVVFVGGITFTEIAALRFIAKQEEARRNIVICTTSIINGNRMMNAAIETATFEKTTVTTAAAQ

Source

organism	Thermochaetoides thermophila DSM 1495
ncbi_taxonomy_id	759272
host_organism	Escherichia coli

Entity 2 polymer

description	Vps16
formula_weight	26005.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MGSSFEVIARTAYEEGRTRLATELLNHEPRAGRQVPLLLSMEEDELALDKAIESGDTDLIYFVIHQLRRKLPLASFFRVVSSRPTASAMVEALARNSDGDGNEDTALLKDLYYQDDRRLDGASVFIREALQQPETRTASDKLDLAANLLQGNQKEHVFELGALKEAKMLLRMQETFERDLTDSFVGLSVNQTMFKLIKLGYHGRAKKIQSEFKVPERVAWWIRLQALVA

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 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	9

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6. Citations (2)

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length_a	101.030 Å
length_b	258.936 Å
length_c	75.274 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 2
int_tables_number	18
crystal_system	orthorhombic

resolution	3.050 Å
resolution_low	49.470 Å
r_factor	0.1860
r_work	0.1840
r_free	0.2238

fit	/app/data/saxs_computation/zb/9zbe/9zbe.fit
pddf	/app/data/pr_computation/zb/9zbe/9zbe.pr.out
profile	/app/data/saxs_computation/zb/9zbe/9zbe.dat

Revised structure of a complex between the SNARE Nyv1 and the HOPS Vps33-Vps16 subcomplex

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 water

6. Citations (2)

7. Files & Curves (10)

Files (7)

Curves (3)