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10qq

Structure of human VCP/p97 dodecamer bound to ADP (DMSO control)

Method: ELECTRON MICROSCOPY D_max: 269.9 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	10qq
deposition_date	2026-02-02
title	Structure of human VCP/p97 dodecamer bound to ADP (DMSO control)
keywords	VCP, p97, dodecamer, CHAPERONE; CHAPERONE
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	69.80 Å
rg_electron	69.75 Å
i0	14067700000.00
molecular_weight	994490.0 kDa
excluded_volume	1241100 Å³
envelope_volume	1950500 Å³
shell_volume	220020 Å³
envelope_diameter	227.1 Å
shell_rg	77.37 Å
envelope_rg	69.08 Å
shape_rg	69.74 Å
total_rg	69.87 Å
total_atoms	69744
n_residues	8820
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	269.9 Å
rg_real	73.94 Å
rg_real_error	2.03 Å
i0_real	1.4190e+10
i0_real_error	3.3500e+08
rg_reciprocal	70.34 Å
i0_reciprocal	14090000000.0000
total_estimate	0.6360
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	85.9 Å
skewness	0.645
kurtosis	0.617
angular_range	— – 0.1100 Å⁻¹
current_alpha	0.7986
highest_alpha	1868000000.0000
n_real_points	23
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.618; Stabil: 0.862; Sysdev: 0.006; Positv: 1.000; Valcen: 0.956; Smooth: 0.904

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Transitional endoplasmic reticulum ATPase
formula_weight	89436.8 kDa
ec_number	3.6.4.6
src_method	man
entity_count	12

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G,H,I,J,K,L
atom_count	69804

MASGADSKGDDLSTAILKQKNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAALQAIRKKMDLIDLEDETIDAEVMNSLAVTMDDFRWALSQSNPSALRETVVEVPQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKLAIRESIESEIRRERERQTNPSAMEVEEDDPVPEIRRDHFEEAMRFARRSVSDNDIRKYEMFAQTLQQSRGFGSFRFPSGNQGGAGPSQGSGGGTGGSVYTEDNDDDLYG

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	ADENOSINE-5'-DIPHOSPHATE
formula_weight	427.2 kDa
src_method	syn
entity_count	24

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	24

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	60

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.13 Å
resolution_method	—
num_particles	79312

fit	/app/data/saxs_computation/0q/10qq/10qq.fit
pddf	/app/data/pr_computation/0q/10qq/10qq.pr.out
profile	/app/data/saxs_computation/0q/10qq/10qq.dat