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9u6m

Cryo-EM structure of the Vo domain of V/A-ATPase under pmf condition, state3D

Method: ELECTRON MICROSCOPY D_max: 98.4 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9u6m
deposition_date	2025-03-23
last_revision	2025-10-29
title	Cryo-EM structure of the Vo domain of V/A-ATPase under pmf condition, state3D
keywords	ATP synthase, V ATPase, V1 ATPase, MOTOR PROTEIN; MOTOR PROTEIN
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	32.79 Å
rg_electron	31.57 Å
i0	186883000.00
molecular_weight	121310.0 kDa
excluded_volume	157650 Å³
envelope_volume	208260 Å³
shell_volume	52673 Å³
envelope_diameter	104.0 Å
shell_rg	40.42 Å
envelope_rg	31.19 Å
shape_rg	31.59 Å
total_rg	32.33 Å
total_atoms	8575
n_residues	1189
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	98.4 Å
rg_real	32.52 Å
rg_real_error	0.34 Å
i0_real	1.8690e+08
i0_real_error	2.6120e+06
rg_reciprocal	32.64 Å
i0_reciprocal	186900000.0000
total_estimate	0.7015
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	41.0 Å
skewness	0.081
kurtosis	-0.487
angular_range	— – 0.2400 Å⁻¹
current_alpha	0.0001
highest_alpha	17700000.0000
n_real_points	49
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.931; Stabil: 1.000; Sysdev: 0.145; Positv: 1.000; Valcen: 0.967; Smooth: 0.921

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	V-type ATP synthase subunit I
formula_weight	34679.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	N
atom_count	8575

AKPFELLVSFLNTPKYGTFDPTPVVPVFFPFWFGMIVGDIGYALLFYLVGRWLSGYVKRNEPLVIDLFALKLKPQVIGKLVHILNWMVFWTVVWGVIYGEFFGTFLEHLGVFGTPEHPGLIPILIHRIDTAKTANLLILLSVAFGVVLVFFGLALRAYLGLKHRHMAHFWEGVGYLGGLVGVLALAASYLGNLQAGWLQGLMYLGFGVFLLAVLMSRIWLMIPEIFTQAGHILSHIRIYAVGAAGGILAGLLTDVGFALAERLGLLGVLLGLLVAGVLHLLILLLTTLGHMLQPIRLLWVEFFTKFGFYEENG

Source

organism	Thermus thermophilus HB8
ncbi_taxonomy_id	300852
host_organism	Thermus thermophilus HB8

Entity 2 polymer

description	V-type ATP synthase, subunit K
formula_weight	7309.6 kDa
src_method	man
entity_count	12

Polymer

type	polypeptide(L)
strand_id	O,P,Q,R,S,T,U,V,W,X,Y,Z

SGGLDRGLIAVGMGLAVGLAALGTGVAQARIGAAGVGAIAEDRSNFGTALIFLLLPETLVIFGLLIAFILNGRL

Source

organism	Thermus thermophilus HB8
ncbi_taxonomy_id	300852
host_organism	Thermus thermophilus HB8

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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	triclinic

resolution	4.64 Å
resolution_method	—
num_particles	29932

fit	/app/data/saxs_computation/u6/9u6m/9u6m.fit
pddf	/app/data/pr_computation/u6/9u6m/9u6m.pr.out
profile	/app/data/saxs_computation/u6/9u6m/9u6m.dat

Cryo-EM structure of the Vo domain of V/A-ATPase under pmf condition, state3D

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

EM 3D

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)