9vkp

Cryo-EM structure of F-ATP synthase from Mycobacteroides abscessus (Rotational State 1)

Method: ELECTRON MICROSCOPY

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1. Protein Identity and Related Structures Protein Identity & Related Structures

ATP synthase subunit alpha

Mycobacteroides abscessus subsp. abscessus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 10	ATP synthase subunit beta × 3 （B1MLW2） ATP synthase gamma chain × 1 （B1MLW1） ATP synthase epsilon chain × 1 （B1MLW3） ATP synthase subunit b × 1 （B1MLV8） ATP synthase subunit b-delta × 1 （B1MLV9） ADENOSINE-5'-TRIPHOSPHATE × 4 MAGNESIUM ION × 5 ADENOSINE-5'-DIPHOSPHATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ATPA_MYCA9
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–548； UniProt 1–548 Author chain B； PDBConstruct 1–548； UniProt 1–548 Author chain C； PDBConstruct 1–548； UniProt 1–548

ATP synthase subunit beta

Mycobacteroides abscessus subsp. abscessus

UniProt B1MLW2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 10	ATP synthase subunit alpha × 3 （B1MLW0） ATP synthase gamma chain × 1 （B1MLW1） ATP synthase epsilon chain × 1 （B1MLW3） ATP synthase subunit b × 1 （B1MLV8） ATP synthase subunit b-delta × 1 （B1MLV9） ADENOSINE-5'-TRIPHOSPHATE × 4 MAGNESIUM ION × 5 ADENOSINE-5'-DIPHOSPHATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B1MLW2_MYCA9
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–476； UniProt 1–476 Author chain E； PDBConstruct 1–476； UniProt 1–476 Author chain F； PDBConstruct 1–476； UniProt 1–476

ATP synthase gamma chain

Mycobacteroides abscessus subsp. abscessus

UniProt B1MLW1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 10	ATP synthase subunit alpha × 3 （B1MLW0） ATP synthase subunit beta × 3 （B1MLW2） ATP synthase epsilon chain × 1 （B1MLW3） ATP synthase subunit b × 1 （B1MLV8） ATP synthase subunit b-delta × 1 （B1MLV9） ADENOSINE-5'-TRIPHOSPHATE × 4 MAGNESIUM ION × 5 ADENOSINE-5'-DIPHOSPHATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ATPG_MYCA9
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain G； PDBConstruct 1–308； UniProt 1–308

ATP synthase epsilon chain

Mycobacteroides abscessus subsp. abscessus

UniProt B1MLW3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 10	ATP synthase subunit alpha × 3 （B1MLW0） ATP synthase subunit beta × 3 （B1MLW2） ATP synthase gamma chain × 1 （B1MLW1） ATP synthase subunit b × 1 （B1MLV8） ATP synthase subunit b-delta × 1 （B1MLV9） ADENOSINE-5'-TRIPHOSPHATE × 4 MAGNESIUM ION × 5 ADENOSINE-5'-DIPHOSPHATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ATPE_MYCA9
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain H； PDBConstruct 1–121； UniProt 1–121

ATP synthase subunit b

Mycobacteroides abscessus subsp. abscessus

UniProt B1MLV8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 10	ATP synthase subunit alpha × 3 （B1MLW0） ATP synthase subunit beta × 3 （B1MLW2） ATP synthase gamma chain × 1 （B1MLW1） ATP synthase epsilon chain × 1 （B1MLW3） ATP synthase subunit b-delta × 1 （B1MLV9） ADENOSINE-5'-TRIPHOSPHATE × 4 MAGNESIUM ION × 5 ADENOSINE-5'-DIPHOSPHATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ATPF_MYCA9
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain b； PDBConstruct 1–177； UniProt 1–177

ATP synthase subunit b-delta

Mycobacteroides abscessus subsp. abscessus

UniProt B1MLV9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 10	ATP synthase subunit alpha × 3 （B1MLW0） ATP synthase subunit beta × 3 （B1MLW2） ATP synthase gamma chain × 1 （B1MLW1） ATP synthase epsilon chain × 1 （B1MLW3） ATP synthase subunit b × 1 （B1MLV8） ADENOSINE-5'-TRIPHOSPHATE × 4 MAGNESIUM ION × 5 ADENOSINE-5'-DIPHOSPHATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ATPFD_MYCA9
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain d； PDBConstruct 1–448； UniProt 1–448

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9vkp
Deposition date deposition_date	2025-06-23
Structure title title	Cryo-EM structure of F-ATP synthase from Mycobacteroides abscessus (Rotational State 1)
Keywords keywords	Hydrolase, ATP synthase, membrane protein, mycobacterium abscessus, mycobacterial, nontuberculous mycobacteria; HYDROLASE
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9vkp__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9vkp__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9vkp__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	49.97 Å
Rg (electron density)	49.43 Å
Total Rg	49.61 Å
Atom count	29467
Residues	3859
Excluded volume	522250 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9vkp__assembly_1__model_1`	decameric （10）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	ATP synthase subunit alpha
Molecular weight formula_weight	58915.2 kDa
EC 编号 ec_number	7.1.2.2
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,C,A
Atom count atom_count	29467

MTELTISSADISGAIEQYVATFSADPTREEIGIVSDAGDGIAHVEGLPSVMTQELLEFPGGVLGVALNLDERSVGTVVLGDFQDIEEGQQVKRTGEVLSVPVGDAFLGRVINPLGQPIDGRGDIEAETRRALELQAPSVVQRQSVSEPLQTGIKAIDSQTPIGRGQRQLIIGDRKTGKTAVCIDTILNQKQAWETGDPAQQVRCIYVAVGQKGSTVAAVRRTLDEAGALEYTTIVAAPASDAAGFKWLAPYTGSALGQHWMYQGKHVLIVFDDLTKQAEAYRAISLLLRRPPGREAYPGDVFYLHSRLLERCAKLSDELGAGSLTGLPIIETKANDISAYIPTNVISITDGQCFLQTDLFNQGVRPAVNVGVSVSRVGGAAQIKAMKEVAGSLRLELSQYRELEAFAAFASDLDATSKAQLERGARLVELLKQPQNSPYPVEEQVVAIYLGTGGHLDSVPVEDVMRFEQEFLDHVRGSHADILADIRETKKFSEDTETKLTNAVNAFKKSFAATDGSSVEVKGVAAEALDESAVGQETVQVRKPAPKK

Source Source

Source organism organism	Mycobacteroides abscessus subsp. abscessus
NCBI taxonomy ID ncbi_taxonomy_id	1185650
Host organism host_organism	Mycobacteroides abscessus subsp. abscessus

Entity 2 Entity 2 polymer

Description description	ATP synthase subunit beta
Molecular weight formula_weight	56032.9 kDa
EC 编号 ec_number	7.1.2.2
Mutation mutation	FLAG-6xHis tag
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F

MTAPTANKTAGRVVRVTGPVVDVEFPRDAVPPLFSALNAEITYEAMAKTLTLEVAQHLGDNLVRTISMQPTDGLVRGVDVVSTGNTIAVPVGDGVKGHVFNALGNCLDEPGYGSDFEKWSIHRKPPAFDQLEPRTEMLETGLKVVDLLTPYVRGGKIALFGGAGVGKTVLIQEMINRIARNFGGTSVFAGVGERTREGNDLWVELADANVLKDTALVFGQMDEPPGTRMRVALSALTMAEYFRDEQGQDVLLFIDNIFRFTQAGSEVSTLLGRMPSAVGYQPTLADEMGELQERITSTRGRSITSMQAVYVPADDYTDPAPATTFAHLDATTELSRAVFSKGIFPAVDPLASSSTILLPSVVGEEHYRVAQEVIRILQRYQDLQDIIAILGIDELSEEDKQLVGRARRIERFLSQNMMAAEQFTGQPGSTVPLKETIEAFDKLTKGEFDHLPEQAFFLIGGLDDLAKKAESLGAKLGLSGQPPRSPSSGSSGGGGENLYFQDYKDDDDKHHHHHH

Source Source

Source organism organism	Mycobacteroides abscessus subsp. abscessus
NCBI taxonomy ID ncbi_taxonomy_id	1185650
Host organism host_organism	Mycobacteroides abscessus subsp. abscessus

Entity 3 Entity 3 polymer

Description description	ATP synthase gamma chain
Molecular weight formula_weight	33189.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

MGAQIRELRRRIKSAGAIKKITKAQELIATSRIAKAQARVVAARPYATEITNVLTALADDAALDHPLLVERPEPKRAGVLIVSSDRGLCGGYNANVLRVAEELYALLREQGKTPVVYVVGRKALNYYSFRNRKVTEAWTGFSERPEYASAQKIADTLVEAFLAGADDEGDDPGLDGILGVDELHIVYTEFKSMLTQAAVAKRIAPMEVEYVGEAAGPTTQYSFEPDATTLFGALLPRYLATRVYAALLEAAASESASRRRAMKAATDNADELIKGLTLEANGARQAQITQEISEIVGGVNALADAAGH

Source Source

Source organism organism	Mycobacteroides abscessus subsp. abscessus
NCBI taxonomy ID ncbi_taxonomy_id	1185650
Host organism host_organism	Mycobacteroides abscessus subsp. abscessus

Entity 4 Entity 4 polymer

Description description	ATP synthase epsilon chain
Molecular weight formula_weight	13074.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MSEIDVEIVAVEREIWSGKATFVFTRTTSGEIGILPHHIPLVAQLVDDAAVKIEREGSDDLWWAIDGGFLSITDTKVSILAESAQARADIDEAKAKTDSGSEDPRVAAQGRARLRALGQTV

Source Source

Source organism organism	Mycobacteroides abscessus subsp. abscessus
NCBI taxonomy ID ncbi_taxonomy_id	1185650
Host organism host_organism	Mycobacteroides abscessus subsp. abscessus

Entity 5 Entity 5 polymer

Description description	ATP synthase subunit b
Molecular weight formula_weight	18543.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	b

MGELHSVASAVTAVAAEAAEEGGKQNNFLIPNGTFFVVLAIFLIVLAVIGTFVVPPIQKVLKAREDMVTKTAEDNRNAAEQFTAAEADYKDELAKARGAATAVRDEARAEGRGILEDMRQRANAEATAVTETAAAELARQGEVTAGELATNVDSLSRTLAERVLGVSLSEPANAGRG

Source Source

Source organism organism	Mycobacteroides abscessus subsp. abscessus
NCBI taxonomy ID ncbi_taxonomy_id	1185650
Host organism host_organism	Mycobacteroides abscessus subsp. abscessus

Entity 6 Entity 6 polymer

Description description	ATP synthase subunit b-delta
Molecular weight formula_weight	47696.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	d

MSTFIGQLIGFAVIVFLVVKYVVPPVRTLMAKQQDAVRQQLADSKTAADKLVEAEGAHAKAIEDAKADAAQIAEEAKADAVQISKQLREQADAEVERIKVHGQEQIVLQRQQLIRQLRGDLGAESVRRAGDLVRSHVADPSAQSATVDRFLDELSQMAGSVGAAKRPVPGGYSGMHAASRESLAAQVSTFRETAASLDSSALSALAEDIAAVAELLISELVLRKHLSEPVDASENEAKLTLVNSLLGNKIGAPALAIVRSAVTARWSASSDLITSLEYIARLALLERAERDGQIEDVEDQLFRVSRVLDAEPQLATLLSDSTAPAQGRVALLTNVLGGRANEVTTALLAQTVRLLYSVRAEVAVLDVAELAVARRDESVAHVKAAAPITDAQRTRLAQVLGQIYGRTIAVQLDVDPELLGGLVVNIGDEEIDGSLSTRLSAAALHLPN

Source Source

Source organism organism	Mycobacteroides abscessus subsp. abscessus
NCBI taxonomy ID ncbi_taxonomy_id	1185650
Host organism host_organism	Mycobacteroides abscessus subsp. abscessus

Entity 7 Entity 7 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 8 Entity 8 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 9 Entity 9 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	2

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.940 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	2.94 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	45839

Cryo-EM structure of F-ATP synthase from Mycobacteroides abscessus (Rotational State 1)

1. Protein Identity and Related Structures Protein Identity & Related Structures

ATP synthase subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

ATP synthase subunit beta

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

ATP synthase gamma chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

ATP synthase epsilon chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

ATP synthase subunit b

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

ATP synthase subunit b-delta

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9vkp__assembly_1__model_1

9vkp__assembly_1__model_1 | I(q)

9vkp__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 non-polymer