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9y04

Cryo-EM structure of human VCP/p97-R89W mutant bound to ATPgammaS

Method: ELECTRON MICROSCOPY D_max: 138.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9y04
deposition_date	2025-08-28
title	Cryo-EM structure of human VCP/p97-R89W mutant bound to ATPgammaS
keywords	AAA ATPase, Unfoldase, ERAD, HYDROLASE; HYDROLASE
method	ELECTRON MICROSCOPY

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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	45.15 Å
rg_electron	44.49 Å
i0	2070650000.00
molecular_weight	371290.0 kDa
excluded_volume	462140 Å³
envelope_volume	619670 Å³
shell_volume	107790 Å³
envelope_diameter	143.5 Å
shell_rg	55.01 Å
envelope_rg	43.99 Å
shape_rg	44.50 Å
total_rg	44.83 Å
total_atoms	25998
n_residues	3294
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	138.4 Å
rg_real	44.79 Å
rg_real_error	0.67 Å
i0_real	2.0710e+09
i0_real_error	3.4150e+07
rg_reciprocal	45.14 Å
i0_reciprocal	2071000000.0000
total_estimate	0.8893
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	59.3 Å
skewness	0.064
kurtosis	-0.502
angular_range	— – 0.1750 Å⁻¹
current_alpha	0.0000
highest_alpha	538600000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.899; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.958; Smooth: 0.901

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Transitional endoplasmic reticulum ATPase
formula_weight	91274.8 kDa
ec_number	3.6.4.6
mutation	R89W
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F
atom_count	25998

HHHHHHSSGLVPRGSHMASGADSKGDDLSTAILKQKNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVWNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAALQAIRKKMDLIDLEDETIDAEVMNSLAVTMDDFRWALSQSNPSALRETVVEVPQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKLAIRESIESEIRRERERQTNPSAMEVEEDDPVPEIRRDHFEEAMRFARRSVSDNDIRKYEMFAQTLQQSRGFGSFRFPSGNQGGAGPSQGSGGGTGGSVYTEDNDDDLYG

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
formula_weight	523.2 kDa
src_method	syn
entity_count	12

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	12

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6. Citations (1)

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resolution	2.550 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.55 Å
resolution_method	—
num_particles	244150

fit	/app/data/saxs_computation/y0/9y04/9y04.fit
pddf	/app/data/pr_computation/y0/9y04/9y04.pr.out
profile	/app/data/saxs_computation/y0/9y04/9y04.dat