9e76

Yeast V-ATPase Vo proton channel bound to nanobody 1WVA25

Method: ELECTRON MICROSCOPY

▼

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

V-type proton ATPase subunit d

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 19	;V-type proton ATPase subunit c'' ; × 1 （P23968） ;V-type proton ATPase subunit c' ; × 1 （P32842） V-type proton ATPase subunit c × 8 （P25515） V-type proton ATPase subunit e × 1 （Q3E7B6） V0 assembly protein 1 × 1 （P53262） Yeast V-ATPase subunit f × 1 （P0C5R9） Nanobody 1WVA25 × 4 V-type proton ATPase subunit a, vacuolar isoform × 1 （P32563）	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	1
Chains and sequence ranges	Author chain B； PDBConstruct 1–345； UniProt 1–345

;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 19	V-type proton ATPase subunit d × 1 （P32366） ;V-type proton ATPase subunit c' ; × 1 （P32842） V-type proton ATPase subunit c × 8 （P25515） V-type proton ATPase subunit e × 1 （Q3E7B6） V0 assembly protein 1 × 1 （P53262） Yeast V-ATPase subunit f × 1 （P0C5R9） Nanobody 1WVA25 × 4 V-type proton ATPase subunit a, vacuolar isoform × 1 （P32563）	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

;V-type proton ATPase subunit c' ;

OrganismNot specified

UniProt P32842

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 19	V-type proton ATPase subunit d × 1 （P32366） ;V-type proton ATPase subunit c'' ; × 1 （P23968） V-type proton ATPase subunit c × 8 （P25515） V-type proton ATPase subunit e × 1 （Q3E7B6） V0 assembly protein 1 × 1 （P53262） Yeast V-ATPase subunit f × 1 （P0C5R9） Nanobody 1WVA25 × 4 V-type proton ATPase subunit a, vacuolar isoform × 1 （P32563）	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	3
Chains and sequence ranges	Author chain D； PDBConstruct 1–164； UniProt 1–164

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 19	V-type proton ATPase subunit d × 1 （P32366） ;V-type proton ATPase subunit c'' ; × 1 （P23968） ;V-type proton ATPase subunit c' ; × 1 （P32842） V-type proton ATPase subunit e × 1 （Q3E7B6） V0 assembly protein 1 × 1 （P53262） Yeast V-ATPase subunit f × 1 （P0C5R9） Nanobody 1WVA25 × 4 V-type proton ATPase subunit a, vacuolar isoform × 1 （P32563）	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	4
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

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 19	V-type proton ATPase subunit d × 1 （P32366） ;V-type proton ATPase subunit c'' ; × 1 （P23968） ;V-type proton ATPase subunit c' ; × 1 （P32842） V-type proton ATPase subunit c × 8 （P25515） V0 assembly protein 1 × 1 （P53262） Yeast V-ATPase subunit f × 1 （P0C5R9） Nanobody 1WVA25 × 4 V-type proton ATPase subunit a, vacuolar isoform × 1 （P32563）	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	5
Chains and sequence ranges	Author chain M； PDBConstruct 1–73； UniProt 1–73

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 19	V-type proton ATPase subunit d × 1 （P32366） ;V-type proton ATPase subunit c'' ; × 1 （P23968） ;V-type proton ATPase subunit c' ; × 1 （P32842） V-type proton ATPase subunit c × 8 （P25515） V-type proton ATPase subunit e × 1 （Q3E7B6） Yeast V-ATPase subunit f × 1 （P0C5R9） Nanobody 1WVA25 × 4 V-type proton ATPase subunit a, vacuolar isoform × 1 （P32563）	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	6
Chains and sequence ranges	Author chain N； PDBConstruct 1–265； UniProt 1–265

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 19	V-type proton ATPase subunit d × 1 （P32366） ;V-type proton ATPase subunit c'' ; × 1 （P23968） ;V-type proton ATPase subunit c' ; × 1 （P32842） V-type proton ATPase subunit c × 8 （P25515） V-type proton ATPase subunit e × 1 （Q3E7B6） V0 assembly protein 1 × 1 （P53262） Nanobody 1WVA25 × 4 V-type proton ATPase subunit a, vacuolar isoform × 1 （P32563）	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	7
Chains and sequence ranges	Author chain O； PDBConstruct 1–85； UniProt 1–85

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 19	V-type proton ATPase subunit d × 1 （P32366） ;V-type proton ATPase subunit c'' ; × 1 （P23968） ;V-type proton ATPase subunit c' ; × 1 （P32842） V-type proton ATPase subunit c × 8 （P25515） V-type proton ATPase subunit e × 1 （Q3E7B6） V0 assembly protein 1 × 1 （P53262） Yeast V-ATPase subunit f × 1 （P0C5R9） Nanobody 1WVA25 × 4	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	9
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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9e76
Deposition date deposition_date	2024-10-31
Structure title title	Yeast V-ATPase Vo proton channel bound to nanobody 1WVA25
Keywords keywords	Vacuolar ATPase, Vo proton channel, lipid nanodisc, nanobody, PROTON TRANSPORT; PROTON TRANSPORT
Experimental Method method	ELECTRON MICROSCOPY

▼

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.

9e76__assembly_1__model_1

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

Download this curve (.dat)

9e76__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9e76__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	49.65 Å
Rg (electron density)	48.57 Å
Total Rg	48.77 Å
Atom count	52512
Residues	3423
Excluded volume	471990 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9e76__assembly_1__model_1`	19-meric （19）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 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
Atom count atom_count	52512

MEGVYFNIDNGFIEGVVRGYRNGLLSNNQYINLTQCDTLEDLKLQLSSTDYGNFLSSVSSESLTTSLIQEYASSKLYHEFNYIRDQSSGSTRKFMDYITYGYMIDNVALMITGTIHDRDKGEILQRCHPLGWFDTLPTLSVATDLESLYETVLVDTPLAPYFKNCFDTAEELDDMNIEIIRNKLYKAYLEDFYNFVTEEIPEPAKECMQTLLGFEADRRSINIALNSLQSSDIDPDLKSDLLPNIGKLYPLATFHLAQAQDFEGVRAALANVYEYRGFLETGNLEDHFYQLEMELCRDAFTQQFAISTVWAWMKSKEQEVRNITWIAECIAQNQRERINNYISVY

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	;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

MSTQLASNIYAPLYAPFFGFAGCAAAMVLSCLGAAIGTAKSGIGIAGIGTFKPELIMKSLIPVVMSGILAIYGLVVAVLIAGNLSPTEDYTLFNGFMHLSCGLCVGFACLSSGYAIGMVGDVGVRKYMHQPRLFVGIVLILIFSEVLGLYGMIVALILNTRGSE

Entity 4 Entity 4 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 5 Entity 5 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 6 Entity 6 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 7 Entity 7 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 8 Entity 8 polymer

Description description	Nanobody 1WVA25
Molecular weight formula_weight	16164.8 kDa
Mutation mutation	N-terminal pelB sequence
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Q,R,S,T

QVQLQESGGGLVQPGGSLRLSCVASGFTFSRYAMTWVRQAPGKGLEWVSDISSGGSSTFYTDSVKGRFTISRDNAKNTLYLQMNSLKPDDTAIYFCAKGVPSYYSDYERRSKRYDSRGQGTQVTVSSAAAYPYDVPDYGSHHHHHH

Source Source

Source organism organism	Lama glama
NCBI taxonomy ID ncbi_taxonomy_id	9844
Host organism host_organism	Escherichia coli

Entity 9 Entity 9 polymer

Description description	V-type proton ATPase subunit a, vacuolar isoform
Molecular weight formula_weight	95625.5 kDa
Mutation mutation	C-terminal calmodulin binding peptide
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MAEKEEAIFRSAEMALVQFYIPQEISRDSAYTLGQLGLVQFRDLNSKVRAFQRTFVNEIRRLDNVERQYRYFYSLLKKHDIKLYEGDTDKYLDGSGELYVPPSGSVIDDYVRNASYLEERLIQMEDATDQIEVQKNDLEQYRFILQSGDEFFLKGDNTDSTSYMDEDMIDANGENIAAAIGASVNYVTGVIARDKVATLEQILWRVLRGNLFFKTVEIEQPVYDVKTREYKHKNAFIVFSHGDLIIKRIRKIAESLDANLYDVDSSNEGRSQQLAKVNKNLSDLYTVLKTTSTTLESELYAIAKELDSWFQDVTREKAIFEILNKSNYDTNRKILIAEGWIPRDELATLQARLGEMIARLGIDVPSIIQVLDTNHTPPTFHRTNKFTAGFQSICDCYGIAQYREINAGLPTIVTFPFMFAIMFGDMGHGFLMTLAALSLVLNEKKINKMKRGEIFDMAFTGRYIILLMGVFSMYTGFLYNDIFSKTMTIFKSGWKWPDHWKKGESITATSVGTYPIGLDWAWHGTENALLFSNSYKMKLSILMGFIHMTYSYFFSLANHLYFNSMIDIIGNFIPGLLFMQGIFGYLSVCIVYKWAVDWVKDGKPAPGLLNMLINMFLSPGTIDDELYPHQAKVQVFLLLMALVCIPWLLLVKPLHFKFTHKKKSHEPLPSTEADASSEDLEAQQLISAMDADDAEEEEVGSGSHGEDFGDIMIHQVIHTIEFCLNCVSHTASYLRLWALSLAHAQLSSVLWTMTIQIAFGFRGFVGVFMTVALFAMWFALTCAVLVLMEGTSAMLHSLRLHWVESMSKFFVGEGLPYEPFAFEYKDMEVAVASASSSASS

▶

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	3.40 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	103691

Yeast V-ATPase Vo proton channel bound to nanobody 1WVA25

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

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 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

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 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

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

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 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

9e76__assembly_1__model_1

9e76__assembly_1__model_1 | I(q)

9e76__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