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9vkr

Cryo-EM structure of F-ATP synthase from Mycobacteroides abscessus (Rotational State 3)

Method: ELECTRON MICROSCOPY D_max: 167.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vkr
deposition_date	2025-06-23
title	Cryo-EM structure of F-ATP synthase from Mycobacteroides abscessus (Rotational State 3)
keywords	Hydrolase, ATP synthase, membrane protein, mycobacterium abscessus, mycobacterial, nontuberculous mycobacteria; 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	49.99 Å
rg_electron	49.43 Å
i0	2606800000.00
molecular_weight	420230.0 kDa
excluded_volume	523970 Å³
envelope_volume	758030 Å³
shell_volume	121330 Å³
envelope_diameter	176.0 Å
shell_rg	57.84 Å
envelope_rg	49.30 Å
shape_rg	49.45 Å
total_rg	49.61 Å
total_atoms	29560
n_residues	3872
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	167.5 Å
rg_real	49.86 Å
rg_real_error	1.53 Å
i0_real	2.6070e+09
i0_real_error	4.7170e+07
rg_reciprocal	50.09 Å
i0_reciprocal	2608000000.0000
total_estimate	0.8567
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	62.8 Å
skewness	0.314
kurtosis	-0.066
angular_range	— – 0.1600 Å⁻¹
current_alpha	0.0000
highest_alpha	547100000.0000
n_real_points	33
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.765; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.862

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4. Crystallography & Experiment

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5. Entities & Polymer Info (9)

Entity 1 polymer

description	ATP synthase subunit alpha
formula_weight	58915.2 kDa
ec_number	7.1.2.2
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	29560

MTELTISSADISGAIEQYVATFSADPTREEIGIVSDAGDGIAHVEGLPSVMTQELLEFPGGVLGVALNLDERSVGTVVLGDFQDIEEGQQVKRTGEVLSVPVGDAFLGRVINPLGQPIDGRGDIEAETRRALELQAPSVVQRQSVSEPLQTGIKAIDSQTPIGRGQRQLIIGDRKTGKTAVCIDTILNQKQAWETGDPAQQVRCIYVAVGQKGSTVAAVRRTLDEAGALEYTTIVAAPASDAAGFKWLAPYTGSALGQHWMYQGKHVLIVFDDLTKQAEAYRAISLLLRRPPGREAYPGDVFYLHSRLLERCAKLSDELGAGSLTGLPIIETKANDISAYIPTNVISITDGQCFLQTDLFNQGVRPAVNVGVSVSRVGGAAQIKAMKEVAGSLRLELSQYRELEAFAAFASDLDATSKAQLERGARLVELLKQPQNSPYPVEEQVVAIYLGTGGHLDSVPVEDVMRFEQEFLDHVRGSHADILADIRETKKFSEDTETKLTNAVNAFKKSFAATDGSSVEVKGVAAEALDESAVGQETVQVRKPAPKK

Source

organism	Mycobacteroides abscessus subsp. abscessus
ncbi_taxonomy_id	1185650
host_organism	Mycobacteroides abscessus subsp. abscessus

Entity 2 polymer

description	ATP synthase subunit beta
formula_weight	56032.9 kDa
ec_number	7.1.2.2
mutation	FLAG-6xHis tag
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	D,E,F

MTAPTANKTAGRVVRVTGPVVDVEFPRDAVPPLFSALNAEITYEAMAKTLTLEVAQHLGDNLVRTISMQPTDGLVRGVDVVSTGNTIAVPVGDGVKGHVFNALGNCLDEPGYGSDFEKWSIHRKPPAFDQLEPRTEMLETGLKVVDLLTPYVRGGKIALFGGAGVGKTVLIQEMINRIARNFGGTSVFAGVGERTREGNDLWVELADANVLKDTALVFGQMDEPPGTRMRVALSALTMAEYFRDEQGQDVLLFIDNIFRFTQAGSEVSTLLGRMPSAVGYQPTLADEMGELQERITSTRGRSITSMQAVYVPADDYTDPAPATTFAHLDATTELSRAVFSKGIFPAVDPLASSSTILLPSVVGEEHYRVAQEVIRILQRYQDLQDIIAILGIDELSEEDKQLVGRARRIERFLSQNMMAAEQFTGQPGSTVPLKETIEAFDKLTKGEFDHLPEQAFFLIGGLDDLAKKAESLGAKLGLSGQPPRSPSSGSSGGGGENLYFQDYKDDDDKHHHHHH

Source

organism	Mycobacteroides abscessus subsp. abscessus
ncbi_taxonomy_id	1185650
host_organism	Mycobacteroides abscessus subsp. abscessus

Entity 3 polymer

description	ATP synthase gamma chain
formula_weight	33189.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	G

MGAQIRELRRRIKSAGAIKKITKAQELIATSRIAKAQARVVAARPYATEITNVLTALADDAALDHPLLVERPEPKRAGVLIVSSDRGLCGGYNANVLRVAEELYALLREQGKTPVVYVVGRKALNYYSFRNRKVTEAWTGFSERPEYASAQKIADTLVEAFLAGADDEGDDPGLDGILGVDELHIVYTEFKSMLTQAAVAKRIAPMEVEYVGEAAGPTTQYSFEPDATTLFGALLPRYLATRVYAALLEAAASESASRRRAMKAATDNADELIKGLTLEANGARQAQITQEISEIVGGVNALADAAGH

Source

organism	Mycobacteroides abscessus subsp. abscessus
ncbi_taxonomy_id	1185650
host_organism	Mycobacteroides abscessus subsp. abscessus

Entity 4 polymer

description	ATP synthase epsilon chain
formula_weight	13074.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

MSEIDVEIVAVEREIWSGKATFVFTRTTSGEIGILPHHIPLVAQLVDDAAVKIEREGSDDLWWAIDGGFLSITDTKVSILAESAQARADIDEAKAKTDSGSEDPRVAAQGRARLRALGQTV

Source

organism	Mycobacteroides abscessus subsp. abscessus
ncbi_taxonomy_id	1185650
host_organism	Mycobacteroides abscessus subsp. abscessus

Entity 5 polymer

description	ATP synthase subunit b
formula_weight	18543.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	b

MGELHSVASAVTAVAAEAAEEGGKQNNFLIPNGTFFVVLAIFLIVLAVIGTFVVPPIQKVLKAREDMVTKTAEDNRNAAEQFTAAEADYKDELAKARGAATAVRDEARAEGRGILEDMRQRANAEATAVTETAAAELARQGEVTAGELATNVDSLSRTLAERVLGVSLSEPANAGRG

Source

organism	Mycobacteroides abscessus subsp. abscessus
ncbi_taxonomy_id	1185650
host_organism	Mycobacteroides abscessus subsp. abscessus

Entity 6 polymer

description	ATP synthase subunit b-delta
formula_weight	47696.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	d

MSTFIGQLIGFAVIVFLVVKYVVPPVRTLMAKQQDAVRQQLADSKTAADKLVEAEGAHAKAIEDAKADAAQIAEEAKADAVQISKQLREQADAEVERIKVHGQEQIVLQRQQLIRQLRGDLGAESVRRAGDLVRSHVADPSAQSATVDRFLDELSQMAGSVGAAKRPVPGGYSGMHAASRESLAAQVSTFRETAASLDSSALSALAEDIAAVAELLISELVLRKHLSEPVDASENEAKLTLVNSLLGNKIGAPALAIVRSAVTARWSASSDLITSLEYIARLALLERAERDGQIEDVEDQLFRVSRVLDAEPQLATLLSDSTAPAQGRVALLTNVLGGRANEVTTALLAQTVRLLYSVRAEVAVLDVAELAVARRDESVAHVKAAAPITDAQRTRLAQVLGQIYGRTIAVQLDVDPELLGGLVVNIGDEEIDGSLSTRLSAAALHLPN

Source

organism	Mycobacteroides abscessus subsp. abscessus
ncbi_taxonomy_id	1185650
host_organism	Mycobacteroides abscessus subsp. abscessus

Entity 7 non-polymer

description	ADENOSINE-5'-TRIPHOSPHATE
formula_weight	507.2 kDa
src_method	syn
entity_count	4

Entity 8 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	5

Entity 9 non-polymer

description	ADENOSINE-5'-DIPHOSPHATE
formula_weight	427.2 kDa
src_method	syn
entity_count	2

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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	2.790 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.79 Å
resolution_method	—
num_particles	54067

fit	/app/data/saxs_computation/vk/9vkr/9vkr.fit
pddf	/app/data/pr_computation/vk/9vkr/9vkr.pr.out
profile	/app/data/saxs_computation/vk/9vkr/9vkr.dat

Cryo-EM structure of F-ATP synthase from Mycobacteroides abscessus (Rotational State 3)

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 (9)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

Entity 6 polymer

Polymer

Source

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)