SAXSdb — 9u6y

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1. Structure Basics

entry_id	9u6y
deposition_date	2025-03-23
last_revision	2025-10-29
title	Cryo-EM structure of the V1 domain of V/A-ATPase in liposomes under pmf condition, state3N
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	46.24 Å
rg_electron	45.68 Å
i0	2066480000.00
molecular_weight	383430.0 kDa
excluded_volume	482140 Å³
envelope_volume	654370 Å³
shell_volume	111850 Å³
envelope_diameter	152.9 Å
shell_rg	55.76 Å
envelope_rg	45.14 Å
shape_rg	45.69 Å
total_rg	46.01 Å
total_atoms	26989
n_residues	3453
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	143.4 Å
rg_real	45.92 Å
rg_real_error	0.64 Å
i0_real	2.0660e+09
i0_real_error	3.4380e+07
rg_reciprocal	46.24 Å
i0_reciprocal	2067000000.0000
total_estimate	0.8791
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	59.0 Å
skewness	0.139
kurtosis	-0.397
angular_range	— – 0.1700 Å⁻¹
current_alpha	0.0002
highest_alpha	661700000.0000
n_real_points	35
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.888; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.947; Smooth: 0.814

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	V-type ATP synthase alpha chain
formula_weight	63700.0 kDa
ec_number	7.1.2.2
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	26989

MIQGVIQKIAGPAVIAKGMLGARMYDICKVGEEGLVGEIIRLDGDTAFVQVYEDTSGLKVGEPVVSTGLPLAVELGPGMLNGIYDGIQRPLERIREKTGIYITRGVVVHALDREKKWAWTPMVKPGDEVRGGMVLGTVPEFGFTHKILVPPDVRGRVKEVKPAGEYTVEEPVVVLEDGTELKMYHTWPVRRARPVQRKLDPNTPFLTGMRILDVLFPVAMGGTAAIPGPFGSGKTVTQQSLAKWSNADVVVYVGCGERGNEMTDVLVEFPELTDPKTGGPLMHRTVLIANTSNMPVAAREASIYVGVTIAEYFRDQGFSVALMADSTSRWAEALREISSRLEEMPAEEGYPPYLAARLAAFYERAGKVITLGGEEGAVTIVGAVSPPGGDMSEPVTQSTLRIVGAFWRLDASLAFRRHFPAINWNGSYSLFTSALDPWYRENVAEDYPELRDAISELLQREAGLQEIVQLVGPDALQDAERLVIEVGRIIREDFLQQNAYHEVDAYCSMKKAYGIMKMILAFYKEAEAAIKRGVSIDEILQLPVLERIGRARYVSEEEFPAYFEEAMKEIQGAFKALA

Source

organism	Thermus thermophilus HB8
ncbi_taxonomy_id	300852
host_organism	Thermus thermophilus HB8

Entity 2 polymer

description	V-type ATP synthase beta chain
formula_weight	52660.9 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	D,E,F

DLLKKEYTGITYISGPLLFVENAKDLAYGAIVDIKDGTGRVRGGQVIEVSEEYAVIQVFEETTGLDLATTSVSLVEDVARLGVSKEMLGRRFNGIGKPIDGLPPITPEKRLPITGLPLNPVARRKPEQFIQTGISTIDVMNTLVRGQKLPIFSGSGLPANEIAAQIARQATVRPDLSGEGEKEEPFAVVFAAMGITQRELSYFIQEFERTGALSRSVLFLNKADDPTIERILTPRMALTVAEYLAFEHDYHVLVILTDMTNYCEALREIGAAREEIPGRRGYPGYMYTDLATIYERAGVVEGKKGSVTQIPILSMPDDDRTHPIPDLTGYITEGQIQLSRELHRKGIYPPIDPLPSLSRLMNNGVGKGKTREDHKQVSDQLYSAYANGVDIRKLVAIIGEDALTENDRRYLQFADAFERFFINQGQQNRSIEESLQIAWALLSMLPQGELKRISKDHIGKYYGQKLEEIWGAP

Source

organism	Thermus thermophilus HB8
ncbi_taxonomy_id	300852
host_organism	Thermus thermophilus HB8

Entity 3 polymer

description	V-type ATP synthase subunit D
formula_weight	23021.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	G

VSPTRMNLLQRRGQLRLAQKGVDLLKKKRDALVAEFFGLVREAMEARKALDQAAKEAYAALLLAQAFDGPEVVAGAALGVPPLEGVEAEVENVWGSKVPRLKATFPDGALLSPVGTPAYTLEASRAFRRYAEALIRVANTETRLKKIGEEIKKTTRRVNALEQVVIPGIRAQIRFIQQVLEQREREDTFRLKRIKGKIEAREAEEE

Source

organism	Thermus thermophilus HB8
ncbi_taxonomy_id	300852
host_organism	Thermus thermophilus HB8

Entity 4 polymer

description	V-type ATP synthase subunit F
formula_weight	11294.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

MAVIADPETAQGFRLAGLEGYGASSAEEAQSLLETLVERGGYALVAVDEALLPDPERAVERLMRGRDLPVLLPIAGLKEAFQGHDVEGYMRELVRKTIGFDIKL

Source

organism	Thermus thermophilus HB8
ncbi_taxonomy_id	300852
host_organism	Thermus thermophilus HB8

Entity 5 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	3

Entity 6 non-polymer

description	ADENOSINE-5'-TRIPHOSPHATE
formula_weight	507.2 kDa
src_method	syn
entity_count	2

Entity 7 non-polymer

description	ADENOSINE-5'-DIPHOSPHATE
formula_weight	427.2 kDa
src_method	syn
entity_count	1

Entity 8 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
entity_count	1

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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	2.90 Å
resolution_method	—
num_particles	67715

fit	/app/data/saxs_computation/u6/9u6y/9u6y.fit
pddf	/app/data/pr_computation/u6/9u6y/9u6y.pr.out
profile	/app/data/saxs_computation/u6/9u6y/9u6y.dat

Cryo-EM structure of the V1 domain of V/A-ATPase in liposomes under pmf condition, state3N

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 (8)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)