7tao

Cryo-EM structure of bafilomycin A1 bound to yeast VO V-ATPase

Method: ELECTRON MICROSCOPY

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

;V-type proton ATPase subunit c' ;

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 15	;V-type proton ATPase subunit c'' ; × 1 （P23968） V0 assembly protein 1 × 1 （P53262） V-type proton ATPase subunit e × 1 （Q3E7B6） V-type proton ATPase subunit c × 8 （P25515） Yeast V-ATPase subunit f × 1 （P0C5R9） V-type proton ATPase subunit d × 1 （P32366） V-type proton ATPase subunit a, vacuolar isoform × 1 （P32563） ;(5R)-2,4-dideoxy-1-C-{(2S,3R,4S)-3-hydroxy-4-[(2R,3S,4E,6E,9R,10S,11R,12E,14Z)-10-hydroxy-3,15-dimethoxy-7,9,11,13-tetramethyl-16-oxo-1-oxacyclohexadeca-4,6,12,14-tetraen-2-yl]pentan-2-yl}-4-methyl-5-propan-2-yl-alpha-D-threo-pentopyranose ; × 9	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VATL2_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain D； PDBConstruct 1–164； UniProt 1–164

;V-type proton ATPase subunit c'' ;

OrganismNot specified

UniProt P23968

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 15	;V-type proton ATPase subunit c' ; × 1 （P32842） V0 assembly protein 1 × 1 （P53262） V-type proton ATPase subunit e × 1 （Q3E7B6） V-type proton ATPase subunit c × 8 （P25515） Yeast V-ATPase subunit f × 1 （P0C5R9） V-type proton ATPase subunit d × 1 （P32366） V-type proton ATPase subunit a, vacuolar isoform × 1 （P32563） ;(5R)-2,4-dideoxy-1-C-{(2S,3R,4S)-3-hydroxy-4-[(2R,3S,4E,6E,9R,10S,11R,12E,14Z)-10-hydroxy-3,15-dimethoxy-7,9,11,13-tetramethyl-16-oxo-1-oxacyclohexadeca-4,6,12,14-tetraen-2-yl]pentan-2-yl}-4-methyl-5-propan-2-yl-alpha-D-threo-pentopyranose ; × 9	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VATO_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–213； UniProt 1–213

V0 assembly protein 1

OrganismNot specified

UniProt P53262

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 15	;V-type proton ATPase subunit c' ; × 1 （P32842） ;V-type proton ATPase subunit c'' ; × 1 （P23968） V-type proton ATPase subunit e × 1 （Q3E7B6） V-type proton ATPase subunit c × 8 （P25515） Yeast V-ATPase subunit f × 1 （P0C5R9） V-type proton ATPase subunit d × 1 （P32366） V-type proton ATPase subunit a, vacuolar isoform × 1 （P32563） ;(5R)-2,4-dideoxy-1-C-{(2S,3R,4S)-3-hydroxy-4-[(2R,3S,4E,6E,9R,10S,11R,12E,14Z)-10-hydroxy-3,15-dimethoxy-7,9,11,13-tetramethyl-16-oxo-1-oxacyclohexadeca-4,6,12,14-tetraen-2-yl]pentan-2-yl}-4-methyl-5-propan-2-yl-alpha-D-threo-pentopyranose ; × 9	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VOA1_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain N； PDBConstruct 1–265； UniProt 1–265

V-type proton ATPase subunit e

OrganismNot specified

UniProt Q3E7B6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 15	;V-type proton ATPase subunit c' ; × 1 （P32842） ;V-type proton ATPase subunit c'' ; × 1 （P23968） V0 assembly protein 1 × 1 （P53262） V-type proton ATPase subunit c × 8 （P25515） Yeast V-ATPase subunit f × 1 （P0C5R9） V-type proton ATPase subunit d × 1 （P32366） V-type proton ATPase subunit a, vacuolar isoform × 1 （P32563） ;(5R)-2,4-dideoxy-1-C-{(2S,3R,4S)-3-hydroxy-4-[(2R,3S,4E,6E,9R,10S,11R,12E,14Z)-10-hydroxy-3,15-dimethoxy-7,9,11,13-tetramethyl-16-oxo-1-oxacyclohexadeca-4,6,12,14-tetraen-2-yl]pentan-2-yl}-4-methyl-5-propan-2-yl-alpha-D-threo-pentopyranose ; × 9	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VA0E_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain M； PDBConstruct 1–73； UniProt 1–73

V-type proton ATPase subunit c

OrganismNot specified

UniProt P25515

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 15	;V-type proton ATPase subunit c' ; × 1 （P32842） ;V-type proton ATPase subunit c'' ; × 1 （P23968） V0 assembly protein 1 × 1 （P53262） V-type proton ATPase subunit e × 1 （Q3E7B6） Yeast V-ATPase subunit f × 1 （P0C5R9） V-type proton ATPase subunit d × 1 （P32366） V-type proton ATPase subunit a, vacuolar isoform × 1 （P32563） ;(5R)-2,4-dideoxy-1-C-{(2S,3R,4S)-3-hydroxy-4-[(2R,3S,4E,6E,9R,10S,11R,12E,14Z)-10-hydroxy-3,15-dimethoxy-7,9,11,13-tetramethyl-16-oxo-1-oxacyclohexadeca-4,6,12,14-tetraen-2-yl]pentan-2-yl}-4-methyl-5-propan-2-yl-alpha-D-threo-pentopyranose ; × 9	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VATL1_YEAST
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–160； UniProt 1–160 Author chain F； PDBConstruct 1–160； UniProt 1–160 Author chain G； PDBConstruct 1–160； UniProt 1–160 Author chain H； PDBConstruct 1–160； UniProt 1–160 Author chain I； PDBConstruct 1–160； UniProt 1–160 Author chain J； PDBConstruct 1–160； UniProt 1–160 Author chain K； PDBConstruct 1–160； UniProt 1–160 Author chain L； PDBConstruct 1–160； UniProt 1–160

Yeast V-ATPase subunit f

OrganismNot specified

UniProt P0C5R9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 15	;V-type proton ATPase subunit c' ; × 1 （P32842） ;V-type proton ATPase subunit c'' ; × 1 （P23968） V0 assembly protein 1 × 1 （P53262） V-type proton ATPase subunit e × 1 （Q3E7B6） V-type proton ATPase subunit c × 8 （P25515） V-type proton ATPase subunit d × 1 （P32366） V-type proton ATPase subunit a, vacuolar isoform × 1 （P32563） ;(5R)-2,4-dideoxy-1-C-{(2S,3R,4S)-3-hydroxy-4-[(2R,3S,4E,6E,9R,10S,11R,12E,14Z)-10-hydroxy-3,15-dimethoxy-7,9,11,13-tetramethyl-16-oxo-1-oxacyclohexadeca-4,6,12,14-tetraen-2-yl]pentan-2-yl}-4-methyl-5-propan-2-yl-alpha-D-threo-pentopyranose ; × 9	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YP17B_YEAST
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain O； PDBConstruct 1–85； UniProt 1–85

V-type proton ATPase subunit d

OrganismNot specified

UniProt P32366

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 15	;V-type proton ATPase subunit c' ; × 1 （P32842） ;V-type proton ATPase subunit c'' ; × 1 （P23968） V0 assembly protein 1 × 1 （P53262） V-type proton ATPase subunit e × 1 （Q3E7B6） V-type proton ATPase subunit c × 8 （P25515） Yeast V-ATPase subunit f × 1 （P0C5R9） V-type proton ATPase subunit a, vacuolar isoform × 1 （P32563） ;(5R)-2,4-dideoxy-1-C-{(2S,3R,4S)-3-hydroxy-4-[(2R,3S,4E,6E,9R,10S,11R,12E,14Z)-10-hydroxy-3,15-dimethoxy-7,9,11,13-tetramethyl-16-oxo-1-oxacyclohexadeca-4,6,12,14-tetraen-2-yl]pentan-2-yl}-4-methyl-5-propan-2-yl-alpha-D-threo-pentopyranose ; × 9	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VA0D_YEAST
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain B； PDBConstruct 1–345； UniProt 1–345

V-type proton ATPase subunit a, vacuolar isoform

OrganismNot specified

UniProt P32563

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 15	;V-type proton ATPase subunit c' ; × 1 （P32842） ;V-type proton ATPase subunit c'' ; × 1 （P23968） V0 assembly protein 1 × 1 （P53262） V-type proton ATPase subunit e × 1 （Q3E7B6） V-type proton ATPase subunit c × 8 （P25515） Yeast V-ATPase subunit f × 1 （P0C5R9） V-type proton ATPase subunit d × 1 （P32366） ;(5R)-2,4-dideoxy-1-C-{(2S,3R,4S)-3-hydroxy-4-[(2R,3S,4E,6E,9R,10S,11R,12E,14Z)-10-hydroxy-3,15-dimethoxy-7,9,11,13-tetramethyl-16-oxo-1-oxacyclohexadeca-4,6,12,14-tetraen-2-yl]pentan-2-yl}-4-methyl-5-propan-2-yl-alpha-D-threo-pentopyranose ; × 9	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VPH1_YEAST
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain A； PDBConstruct 1–840； UniProt 1–840

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	7tao
Deposition date deposition_date	2021-12-21
Structure title title	Cryo-EM structure of bafilomycin A1 bound to yeast VO V-ATPase
Keywords keywords	inhibitor, complex, proton pump, ATPase, MEMBRANE PROTEIN; MEMBRANE PROTEIN
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.

7tao__assembly_1__model_1

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

Download this curve (.dat)

7tao__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7tao__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	43.59 Å
Rg (electron density)	42.79 Å
Total Rg	43.20 Å
Atom count	22497
Residues	2915
Excluded volume	411710 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7tao__assembly_1__model_1`	pentadecameric （15）	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	;V-type proton ATPase subunit c' ;
Molecular weight formula_weight	17046.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D
Atom count atom_count	22497

MSTQLASNIYAPLYAPFFGFAGCAAAMVLSCLGAAIGTAKSGIGIAGIGTFKPELIMKSLIPVVMSGILAIYGLVVAVLIAGNLSPTEDYTLFNGFMHLSCGLCVGFACLSSGYAIGMVGDVGVRKYMHQPRLFVGIVLILIFSEVLGLYGMIVALILNTRGSE

Entity 2 Entity 2 polymer

Description description	;V-type proton ATPase subunit c'' ;
Molecular weight formula_weight	22610.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MNKESKDDDMSLGKFSFSHFLYYLVLIVVIVYGLYKLFTGHGSDINFGKFLLRTSPYMWANLGIALCVGLSVVGAAWGIFITGSSMIGAGVRAPRITTKNLISIIFCEVVAIYGLIIAIVFSSKLTVATAENMYSKSNLYTGYSLFWAGITVGASNLICGIAVGITGATAAISDAADSALFVKILVIEIFGSILGLLGLIVGLLMAGKASEFQ

Entity 3 Entity 3 polymer

Description description	V0 assembly protein 1
Molecular weight formula_weight	29694.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N

MVFGQLYALFIFTLSCCISKTVQADSSKESSSFISFDKESNWDTISTISSTADVISSVDSAIAVFEFDNFSLLDNLMIDEEYPFFNRFFANDVSLTVHDDSPLNISQSLSPIMEQFTVDELPESASDLLYEYSLDDKSIVLFKFTSDAYDLKKLDEFIDSCLSFLEDKSGDNLTVVINSLGWAFEDEDGDDEYATEETLSHHDNNKGKEGDDDILSSIWTEGLLMCLIVSALLLFILIVALSWISNLDITYGALEKSTNPIKKNN

Entity 4 Entity 4 polymer

Description description	V-type proton ATPase subunit e
Molecular weight formula_weight	8387.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

MSSFYTVVGVFIVVSAMSVLFWIMAPKNNQAVWRSTVILTLAMMFLMWAITFLCQLHPLVAPRRSDLRPEFAE

Entity 5 Entity 5 polymer

Description description	V-type proton ATPase subunit c
Molecular weight formula_weight	16357.5 kDa
Source method src_method	nat
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,G,H,I,J,K,L

MTELCPVYAPFFGAIGCASAIIFTSLGAAYGTAKSGVGICATCVLRPDLLFKNIVPVIMAGIIAIYGLVVSVLVCYSLGQKQALYTGFIQLGAGLSVGLSGLAAGFAIGIVGDAGVRGSSQQPRLFVGMILILIFAEVLGLYGLIVALLLNSRATQDVVC

Entity 6 Entity 6 polymer

Description description	Yeast V-ATPase subunit f
Molecular weight formula_weight	9369.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	O

MRPVVSTGKAWCCTVLSAFGVVILSVIAHLFNTNHESFVGSINDPEDGPAVAHTVYLAALVYLVFFVFCGFQVYLARRKPSIELR

Entity 7 Entity 7 polymer

Description description	V-type proton ATPase subunit d
Molecular weight formula_weight	39822.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MEGVYFNIDNGFIEGVVRGYRNGLLSNNQYINLTQCDTLEDLKLQLSSTDYGNFLSSVSSESLTTSLIQEYASSKLYHEFNYIRDQSSGSTRKFMDYITYGYMIDNVALMITGTIHDRDKGEILQRCHPLGWFDTLPTLSVATDLESLYETVLVDTPLAPYFKNCFDTAEELDDMNIEIIRNKLYKAYLEDFYNFVTEEIPEPAKECMQTLLGFEADRRSINIALNSLQSSDIDPDLKSDLLPNIGKLYPLATFHLAQAQDFEGVRAALANVYEYRGFLETGNLEDHFYQLEMELCRDAFTQQFAISTVWAWMKSKEQEVRNITWIAECIAQNQRERINNYISVY

Entity 8 Entity 8 polymer

Description description	V-type proton ATPase subunit a, vacuolar isoform
Molecular weight formula_weight	95625.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MAEKEEAIFRSAEMALVQFYIPQEISRDSAYTLGQLGLVQFRDLNSKVRAFQRTFVNEIRRLDNVERQYRYFYSLLKKHDIKLYEGDTDKYLDGSGELYVPPSGSVIDDYVRNASYLEERLIQMEDATDQIEVQKNDLEQYRFILQSGDEFFLKGDNTDSTSYMDEDMIDANGENIAAAIGASVNYVTGVIARDKVATLEQILWRVLRGNLFFKTVEIEQPVYDVKTREYKHKNAFIVFSHGDLIIKRIRKIAESLDANLYDVDSSNEGRSQQLAKVNKNLSDLYTVLKTTSTTLESELYAIAKELDSWFQDVTREKAIFEILNKSNYDTNRKILIAEGWIPRDELATLQARLGEMIARLGIDVPSIIQVLDTNHTPPTFHRTNKFTAGFQSICDCYGIAQYREINAGLPTIVTFPFMFAIMFGDMGHGFLMTLAALSLVLNEKKINKMKRGEIFDMAFTGRYIILLMGVFSMYTGFLYNDIFSKTMTIFKSGWKWPDHWKKGESITATSVGTYPIGLDWAWHGTENALLFSNSYKMKLSILMGFIHMTYSYFFSLANHLYFNSMIDIIGNFIPGLLFMQGIFGYLSVCIVYKWAVDWVKDGKPAPGLLNMLINMFLSPGTIDDELYPHQAKVQVFLLLMALVCIPWLLLVKPLHFKFTHKKKSHEPLPSTEADASSEDLEAQQLISAMDADDAEEEEVGSGSHGEDFGDIMIHQVIHTIEFCLNCVSHTASYLRLWALSLAHAQLSSVLWTMTIQIAFGFRGFVGVFMTVALFAMWFALTCAVLVLMEGTSAMLHSLRLHWVESMSKFFVGEGLPYEPFAFEYKDMEVAVASASSSASS

Entity 9 Entity 9 non-polymer

Description description	;(5R)-2,4-dideoxy-1-C-{(2S,3R,4S)-3-hydroxy-4-[(2R,3S,4E,6E,9R,10S,11R,12E,14Z)-10-hydroxy-3,15-dimethoxy-7,9,11,13-tetramethyl-16-oxo-1-oxacyclohexadeca-4,6,12,14-tetraen-2-yl]pentan-2-yl}-4-methyl-5-propan-2-yl-alpha-D-threo-pentopyranose ;
Molecular weight formula_weight	622.8 kDa
Source method src_method	syn
Copy count entity_count	9

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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	3.20 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	447983

Cryo-EM structure of bafilomycin A1 bound to yeast VO V-ATPase

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

;V-type proton ATPase subunit c' ;

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

;V-type proton ATPase subunit c'' ;

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

V0 assembly protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

V-type proton ATPase subunit e

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

V-type proton ATPase subunit c

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Yeast V-ATPase subunit f

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

V-type proton ATPase subunit d

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

V-type proton ATPase subunit a, vacuolar isoform

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

7tao__assembly_1__model_1

7tao__assembly_1__model_1 | I(q)

7tao__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer