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9y08

Cryo-EM structure of human VCP/p97-G128D mutant bound to ADP

Method: ELECTRON MICROSCOPY D_max: 139.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9y08
deposition_date	2025-08-28
title	Cryo-EM structure of human VCP/p97-G128D mutant bound to ADP
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	45.81 Å
rg_electron	45.11 Å
i0	1989540000.00
molecular_weight	366380.0 kDa
excluded_volume	457130 Å³
envelope_volume	623080 Å³
shell_volume	107530 Å³
envelope_diameter	141.1 Å
shell_rg	55.19 Å
envelope_rg	44.36 Å
shape_rg	45.10 Å
total_rg	45.47 Å
total_atoms	25692
n_residues	3264
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	139.9 Å
rg_real	45.45 Å
rg_real_error	0.72 Å
i0_real	1.9900e+09
i0_real_error	3.4760e+07
rg_reciprocal	45.81 Å
i0_reciprocal	1990000000.0000
total_estimate	0.8902
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	61.7 Å
skewness	0.057
kurtosis	-0.538
angular_range	— – 0.1700 Å⁻¹
current_alpha	0.0000
highest_alpha	494500000.0000
n_real_points	35
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.953; Smooth: 0.876

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	Transitional endoplasmic reticulum ATPase
formula_weight	91303.8 kDa
ec_number	3.6.4.6
mutation	G128D
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F
atom_count	25692

HHHHHHSSGLVPRGSHMASGADSKGDDLSTAILKQKNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITDNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAALQAIRKKMDLIDLEDETIDAEVMNSLAVTMDDFRWALSQSNPSALRETVVEVPQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKLAIRESIESEIRRERERQTNPSAMEVEEDDPVPEIRRDHFEEAMRFARRSVSDNDIRKYEMFAQTLQQSRGFGSFRFPSGNQGGAGPSQGSGGGTGGSVYTEDNDDDLYG

Source

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

Entity 2 non-polymer

description	ADENOSINE-5'-DIPHOSPHATE
formula_weight	427.2 kDa
src_method	syn
entity_count	12

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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	2.780 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.78 Å
resolution_method	—
num_particles	99673

fit	/app/data/saxs_computation/y0/9y08/9y08.fit
pddf	/app/data/pr_computation/y0/9y08/9y08.pr.out
profile	/app/data/saxs_computation/y0/9y08/9y08.dat

Cryo-EM structure of human VCP/p97-G128D mutant bound to ADP

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

EM 3D

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)