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9y05

Cryo-EM structure of human VCP/p97-R89W mutant bound to CB-5083

Method: ELECTRON MICROSCOPY D_max: 185.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9y05
deposition_date	2025-08-28
title	Cryo-EM structure of human VCP/p97-R89W mutant bound to CB-5083
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	59.34 Å
rg_electron	58.88 Å
i0	7710770000.00
molecular_weight	743750.0 kDa
excluded_volume	932280 Å³
envelope_volume	1325200 Å³
shell_volume	176210 Å³
envelope_diameter	190.3 Å
shell_rg	69.41 Å
envelope_rg	57.37 Å
shape_rg	58.85 Å
total_rg	59.15 Å
total_atoms	52272
n_residues	6672
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	185.2 Å
rg_real	59.00 Å
rg_real_error	1.25 Å
i0_real	7.7110e+09
i0_real_error	1.4620e+08
rg_reciprocal	59.61 Å
i0_reciprocal	7718000000.0000
total_estimate	0.8543
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	78.3 Å
skewness	0.167
kurtosis	-0.445
angular_range	— – 0.1300 Å⁻¹
current_alpha	0.0000
highest_alpha	4378000000.0000
n_real_points	27
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.894; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.948; Smooth: 0.471

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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	91274.8 kDa
ec_number	3.6.4.6
mutation	R89W
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	52272

HHHHHHSSGLVPRGSHMASGADSKGDDLSTAILKQKNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVWNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAALQAIRKKMDLIDLEDETIDAEVMNSLAVTMDDFRWALSQSNPSALRETVVEVPQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKLAIRESIESEIRRERERQTNPSAMEVEEDDPVPEIRRDHFEEAMRFARRSVSDNDIRKYEMFAQTLQQSRGFGSFRFPSGNQGGAGPSQGSGGGTGGSVYTEDNDDDLYG

Source

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

Entity 2 non-polymer

description	1-[4-(benzylamino)-7,8-dihydro-5H-pyrano[4,3-d]pyrimidin-2-yl]-2-methyl-1H-indole-4-carboxamide
formula_weight	413.5 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	2.580 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.58 Å
resolution_method	—
num_particles	169779

fit	/app/data/saxs_computation/y0/9y05/9y05.fit
pddf	/app/data/pr_computation/y0/9y05/9y05.pr.out
profile	/app/data/saxs_computation/y0/9y05/9y05.dat

Cryo-EM structure of human VCP/p97-R89W mutant bound to CB-5083

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)