← Back to search

9y09

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

Method: ELECTRON MICROSCOPY D_max: 137.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9y09
deposition_date	2025-08-28
title	Cryo-EM structure of human VCP/p97-G128D mutant bound to ATPgS
keywords	AAA ATPase, Unfoldase, ERAD, HYDROLASE; HYDROLASE
method	ELECTRON MICROSCOPY

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	44.94 Å
rg_electron	44.31 Å
i0	2070390000.00
molecular_weight	371290.0 kDa
excluded_volume	462140 Å³
envelope_volume	613530 Å³
shell_volume	107090 Å³
envelope_diameter	143.2 Å
shell_rg	54.87 Å
envelope_rg	43.86 Å
shape_rg	44.32 Å
total_rg	44.65 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

▼

3. P(r) Analysis (GNOM)

dmax	137.5 Å
rg_real	44.59 Å
rg_real_error	0.63 Å
i0_real	2.0700e+09
i0_real_error	3.0360e+07
rg_reciprocal	44.94 Å
i0_reciprocal	2071000000.0000
total_estimate	0.8889
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	58.9 Å
skewness	0.068
kurtosis	-0.497
angular_range	— – 0.1750 Å⁻¹
current_alpha	0.0000
highest_alpha	537100000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.902; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.957; Smooth: 0.887

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (3)

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	25998

HHHHHHSSGLVPRGSHMASGADSKGDDLSTAILKQKNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITDNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAALQAIRKKMDLIDLEDETIDAEVMNSLAVTMDDFRWALSQSNPSALRETVVEVPQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKLAIRESIESEIRRERERQTNPSAMEVEEDDPVPEIRRDHFEEAMRFARRSVSDNDIRKYEMFAQTLQQSRGFGSFRFPSGNQGGAGPSQGSGGGTGGSVYTEDNDDDLYG

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

▶

6. Citations (1)

▶

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	2.400 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.40 Å
resolution_method	—
num_particles	264827

fit	/app/data/saxs_computation/y0/9y09/9y09.fit
pddf	/app/data/pr_computation/y0/9y09/9y09.pr.out
profile	/app/data/saxs_computation/y0/9y09/9y09.dat

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

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