7fde

CryoEM Structures of Reconstituted V-ATPase, Oxr1 bound V1

Method: ELECTRON MICROSCOPY

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

V-type proton ATPase subunit C

Saccharomyces cerevisiae S288C

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 16	V-type proton ATPase subunit E × 3 （P22203） V-type proton ATPase subunit G × 3 Yeast Vacuolar ATPase A subunit × 3 V-type proton ATPase subunit B × 3 （P16140） V-type proton ATPase subunit D × 1 （P32610） V-type proton ATPase subunit F × 1 （P39111） Oxidation resistance protein 1 × 1 （Q08952）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VATC_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain O； PDBConstruct 1–392； UniProt 1–392

V-type proton ATPase subunit E

OrganismNot specified

UniProt P22203

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 16	V-type proton ATPase subunit C × 1 （P31412） V-type proton ATPase subunit G × 3 Yeast Vacuolar ATPase A subunit × 3 V-type proton ATPase subunit B × 3 （P16140） V-type proton ATPase subunit D × 1 （P32610） V-type proton ATPase subunit F × 1 （P39111） Oxidation resistance protein 1 × 1 （Q08952）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VATE_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain G； PDBConstruct 1–233； UniProt 1–233 Author chain I； PDBConstruct 1–233； UniProt 1–233 Author chain K； PDBConstruct 1–233； UniProt 1–233

V-type proton ATPase subunit B

OrganismNot specified

UniProt P16140

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 16	V-type proton ATPase subunit C × 1 （P31412） V-type proton ATPase subunit E × 3 （P22203） V-type proton ATPase subunit G × 3 Yeast Vacuolar ATPase A subunit × 3 V-type proton ATPase subunit D × 1 （P32610） V-type proton ATPase subunit F × 1 （P39111） Oxidation resistance protein 1 × 1 （Q08952）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VATB_YEAST
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain B； PDBConstruct 1–517； UniProt 1–517 Author chain D； PDBConstruct 1–517； UniProt 1–517 Author chain F； PDBConstruct 1–517； UniProt 1–517

V-type proton ATPase subunit D

OrganismNot specified

UniProt P32610

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 16	V-type proton ATPase subunit C × 1 （P31412） V-type proton ATPase subunit E × 3 （P22203） V-type proton ATPase subunit G × 3 Yeast Vacuolar ATPase A subunit × 3 V-type proton ATPase subunit B × 3 （P16140） V-type proton ATPase subunit F × 1 （P39111） Oxidation resistance protein 1 × 1 （Q08952）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VATD_YEAST
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain M； PDBConstruct 1–256； UniProt 1–256

V-type proton ATPase subunit F

OrganismNot specified

UniProt P39111

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 16	V-type proton ATPase subunit C × 1 （P31412） V-type proton ATPase subunit E × 3 （P22203） V-type proton ATPase subunit G × 3 Yeast Vacuolar ATPase A subunit × 3 V-type proton ATPase subunit B × 3 （P16140） V-type proton ATPase subunit D × 1 （P32610） Oxidation resistance protein 1 × 1 （Q08952）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VATF_YEAST
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain N； PDBConstruct 1–118； UniProt 1–118

Oxidation resistance protein 1

OrganismNot specified

UniProt Q08952

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 16	V-type proton ATPase subunit C × 1 （P31412） V-type proton ATPase subunit E × 3 （P22203） V-type proton ATPase subunit G × 3 Yeast Vacuolar ATPase A subunit × 3 V-type proton ATPase subunit B × 3 （P16140） V-type proton ATPase subunit D × 1 （P32610） V-type proton ATPase subunit F × 1 （P39111）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	OXR1_YEAST
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain P； PDBConstruct 1–273； UniProt 1–273

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	7fde
Deposition date deposition_date	2021-07-16
Structure title title	CryoEM Structures of Reconstituted V-ATPase, Oxr1 bound V1
Keywords keywords	ATPase, proton pump, rotary motor enzyme, membrane protein, MOTOR PROTEIN; MOTOR 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.

7fde__assembly_1__model_1

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

Download this curve (.dat)

7fde__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7fde__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	58.03 Å
Rg (electron density)	57.87 Å
Total Rg	58.00 Å
Atom count	39557
Residues	5045
Excluded volume	706380 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7fde__assembly_1__model_1`	hexadecameric （16）	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 (8)

Entity 1 Entity 1 polymer

Description description	V-type proton ATPase subunit C
Molecular weight formula_weight	44241.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	O
Atom count atom_count	39557

MATALYTANDFILISLPQNAQPVTAPGSKTDSWFNETLIGGRAFVSDFKIPEFKIGSLDTLIVESEELSKVDNQIGASIGKIIEILQGLNETSTNAYRTLPINNMPVPEYLENFQWQTRKFKLDKSIKDLITLISNESSQLDADVRATYANYNSAKTNLAAAERKKTGDLSVRSLHDIVKPEDFVLNSEHLTTVLVAVPKSLKSDFEKSYETLSKNVVPASASVIAEDAEYVLFNVHLFKKNVQEFTTAAREKKFIPREFNYSEELIDQLKKEHDSAASLEQSLRVQLVRLAKTAYVDVFINWFHIKALRVYVESVLRYGLPPHFNIKIIAVPPKNLSKCKSELIDAFGFLGGNAFMKDKKGKINKQDTSLHQYASLVDTEYEPFVMYIINL

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	V-type proton ATPase subunit E
Molecular weight formula_weight	26508.4 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,K,I

MSSAITALTPNQVNDELNKMQAFIRKEAEEKAKEIQLKADQEYEIEKTNIVRNETNNIDGNFKSKLKKAMLSQQITKSTIANKMRLKVLSAREQSLDGIFEETKEKLSGIANNRDEYKPILQSLIVEALLKLLEPKAIVKALERDVDLIESMKDDIMREYGEKAQRAPLEEIVISNDYLNKDLVSGGVVVSNASDKIEINNTLEERLKLLSEEALPAIRLELYGPSKTRKFFD

Entity 3 Entity 3 polymer

Description description	V-type proton ATPase subunit G
Molecular weight formula_weight	13735.7 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,L,J

MDYKDDDDKSQKNGIATLLQAEKEAHEIVSKARKYRQDKLKQAKTDAAKEIDSYKIQKDKELKEFEQKNAGGVGELEKKAEAGVQGELAEIKKIAEKKKDDVVKILIETVIKPSAEVHINAL

Entity 4 Entity 4 polymer

Description description	Yeast Vacuolar ATPase A subunit
Molecular weight formula_weight	67796.5 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E

MAGAIENARKEIKRISLEDHAESEYGAIYSVSGPVVIAENMIGCAMYELVKVGHDNLVGEVIRIDGDKATIQVYEETAGLTVGDPVLRTGKPLSVELGPGLMETIYDGIQRPLKAIKEESQSIYIPRGIDTPALDRTIKWQFTPGKFQVGDHISGGDIYGSVFENSLISSHKILLPPRSRGTITWIAPAGEYTLDEKILEVEFDGKKSDFTLYHTWPVRVPRPVTEKLSADYPLLTGQRVLDALFPCVQGGTTCIPGAFGCGKTVISQSLSKYSNSDAIIYVGCGERGNEMAEVLMEFPELYTEMSGTKEPIMKRTTLVANTSNMPVAAREASIYTGITLAEYFRDQGKNVSMIADSSSRWAEALREISGRLGEMPADQGFPAYLGAKLASFYERAGKAVALGSPDRTGSVSIVAAVSPAGGDFSDPVTTATLGITQVFWGLDKKLAQRKHFPSINTSVSYSKYTNVLNKFYDSNYPEFPVLRDRMKEILSNAEELEQVVQLVGKSALSDSDKITLDVATLIKEDFLQQNGYSTYDAFCPIWKTFDMMRAFISYHDEAQKAVANGANWSKLADSTGDVKHAVSSSKFFEPSRGEKEVHGEFEKLLSTMQERFAESTD

Entity 5 Entity 5 polymer

Description description	V-type proton ATPase subunit B
Molecular weight formula_weight	57815.0 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

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

MVLSDKELFAINKKAVEQGFNVKPRLNYNTVSGVNGPLVILEKVKFPRYNEIVNLTLPDGTVRQGQVLEIRGDRAIVQVFEGTSGIDVKKTTVEFTGESLRIPVSEDMLGRIFDGSGRPIDNGPKVFAEDYLDINGSPINPYARIYPEEMISTGVSAIDTMNSIARGQKIPIFSASGLPHNEIAAQICRQAGLVRPTKDVHDGHEENFSIVFAAMGVNLETARFFKQDFEENGSLERTSLFLNLANDPTIERIITPRLALTTAEYLAYQTERHVLTILTDMSSYADALREVSAAREEVPGRRGYPGYMYTDLSTIYERAGRVEGRNGSITQIPILTMPNDDITHPIPDLTGYITEGQIFVDRQLHNKGIYPPINVLPSLSRLMKSAIGEGMTRKDHGDVSNQLYAKYAIGKDAAAMKAVVGEEALSIEDKLSLEFLEKFEKTFITQGAYEDRTVFESLDQAWSLLRIYPKEMLNRISPKILDEFYDRARDDADEDEEDPDTRSSGKKKDASQEESLI

Entity 6 Entity 6 polymer

Description description	V-type proton ATPase subunit D
Molecular weight formula_weight	29235.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

MSGNREQVFPTRMTLGLMKTKLKGANQGYSLLKRKSEALTKRFRDITKRIDDAKQKMGRVMQTAAFSLAEVSYATGENIGYQVQESVSTARFKVRARQENVSGVYLSQFESYIDPEINDFRLTGLGRGGQQVQRAKEIYSRAVETLVELASLQTAFIILDEVIKVTNRRVNAIEHVIIPRTENTIAYINSELDELDREEFYRLKKVQEKKQNETAKLDAEMKLKRDRAEQDASEVAADEEPQGETLVADQEDDVIF

Entity 7 Entity 7 polymer

Description description	V-type proton ATPase subunit F
Molecular weight formula_weight	13479.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N

MAEKRTLIAVIADEDTTTGLLLAGIGQITPETQEKNFFVYQEGKTTKEEITDKFNHFTEERDDIAILLINQHIAENIRARVDSFTNAFPAILEIPSKDHPYDPEKDSVLKRVRKLFGE

Entity 8 Entity 8 polymer

Description description	Oxidation resistance protein 1
Molecular weight formula_weight	30818.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

MFGVKDAIFKIKRSIAGTDSSDSTAYTTASESSPQLKDSHNPFRNKTTSERTIVEEGSLPPVRLNGYLPSTKNKLLTPEMCDEIRTLMPTRIQLYTEWNLLYSLEQHGSSLHSLYSNVAPDSKEFRRVGYVLVIKDRKNGIFGAYSNEAFHPNEHRQYTGNGECFLWKLDKVPDVNISEKEESEQEGKEGKEEGDKEERWRFSGYPYTGVNEFAIYCTSEFLSMGAGDGHYGLLCDDGLLHGVSNPCQTYGNEVLSKEGKKFSIVALEVWRVG

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	7fdeG01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2320 — hypothetical protein PF0899 fold
Homologous superfamily homologous superfamily	30 — ATP synthase, E subunit, C-terminal

Domain ID domain_id	7fdeM01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	3240 —

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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	3.80 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	20447

CryoEM Structures of Reconstituted V-ATPase, Oxr1 bound V1

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 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 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

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 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

Oxidation resistance 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7fde__assembly_1__model_1

7fde__assembly_1__model_1 | I(q)

7fde__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 polymer

Polymer Polymer

Entity 8 Entity 8 polymer

Polymer Polymer

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)