← Back to search

9u6k

Cryo-EM structure of the Vo domain of V/A-ATPase under pmf condition, State3B

Method: ELECTRON MICROSCOPY D_max: 93.1 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9u6k
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, State3B
keywords	ATP synthase, V ATPase, V1 ATPase, MOTOR PROTEIN; MOTOR PROTEIN
method	ELECTRON MICROSCOPY

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	32.38 Å
rg_electron	31.18 Å
i0	183303000.00
molecular_weight	120620.0 kDa
excluded_volume	156890 Å³
envelope_volume	203890 Å³
shell_volume	51972 Å³
envelope_diameter	103.4 Å
shell_rg	40.26 Å
envelope_rg	30.96 Å
shape_rg	31.20 Å
total_rg	31.97 Å
total_atoms	8529
n_residues	1184
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	93.1 Å
rg_real	32.12 Å
rg_real_error	0.35 Å
i0_real	1.8330e+08
i0_real_error	2.2700e+06
rg_reciprocal	32.24 Å
i0_reciprocal	183300000.0000
total_estimate	0.9008
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	39.9 Å
skewness	0.091
kurtosis	-0.468
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0000
highest_alpha	15800000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.963; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.841

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (2)

Entity 1 polymer

description	V-type ATP synthase subunit I
formula_weight	34210.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	N
atom_count	8529

FELLVSFLNTPKYGTFDPTPVVPVFFPFWFGMIVGDIGYALLFYLVGRWLSGYVKRNEPLVIDLFALKLKPQVIGKLVHILNWMVFWTVVWGVIYGEFFGTFLEHLGVFGTPEHPGLIPILIHRIDTAKTANLLILLSVAFGVVLVFFGLALRAYLGLKHRHMAHFWEGVGYLGGLVGVLALAASYLGNLQAGWLQGLMYLGFGVFLLAVLMSRIWLMIPEIFTQAGHILSHIRIYAVGAAGGILAGLLTDVGFALAERLGLLGVLLGLLVAGVLHLLILLLTTLGHMLQPIRLLWVEFFTKFGFYEE

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

▶

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	triclinic

resolution	4.10 Å
resolution_method	—
num_particles	40093

fit	/app/data/saxs_computation/u6/9u6k/9u6k.fit
pddf	/app/data/pr_computation/u6/9u6k/9u6k.pr.out
profile	/app/data/saxs_computation/u6/9u6k/9u6k.dat

Cryo-EM structure of the Vo domain of V/A-ATPase under pmf condition, State3B

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)