7tmo

V1 complex lacking subunit C from Saccharomyces cerevisiae, State 1

Method: ELECTRON MICROSCOPY

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

H(+)-transporting two-sector ATPase

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	Vacuolar proton pump subunit B × 3 （A0A6A5Q585） V-type proton ATPase subunit E × 3 （A0A6A5Q7Y8） V-type proton ATPase subunit G × 3 （A0A6L0ZI53） V-type proton ATPase subunit D × 1 （A0A6A5Q1W2） V-type proton ATPase subunit F × 1 （A0A6A5PYF6） V-type proton ATPase subunit H × 1 （P41807） ADENOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 2 ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A6L0YX77_YEASX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–617； UniProt 1–617 Author chain C； PDBConstruct 1–617； UniProt 1–617 Author chain E； PDBConstruct 1–617； UniProt 1–617

Vacuolar proton pump subunit B

OrganismNot specified

UniProt A0A6A5Q585

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 15	H(+)-transporting two-sector ATPase × 3 （A0A6L0YX77） V-type proton ATPase subunit E × 3 （A0A6A5Q7Y8） V-type proton ATPase subunit G × 3 （A0A6L0ZI53） V-type proton ATPase subunit D × 1 （A0A6A5Q1W2） V-type proton ATPase subunit F × 1 （A0A6A5PYF6） V-type proton ATPase subunit H × 1 （P41807） ADENOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 2 ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A6A5Q585_YEASX
Isoform	—
PDB entities	2
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 E

OrganismNot specified

UniProt A0A6A5Q7Y8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 15	H(+)-transporting two-sector ATPase × 3 （A0A6L0YX77） Vacuolar proton pump subunit B × 3 （A0A6A5Q585） V-type proton ATPase subunit G × 3 （A0A6L0ZI53） V-type proton ATPase subunit D × 1 （A0A6A5Q1W2） V-type proton ATPase subunit F × 1 （A0A6A5PYF6） V-type proton ATPase subunit H × 1 （P41807） ADENOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 2 ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A6A5Q7Y8_YEASX
Isoform	—
PDB entities	3
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 G

OrganismNot specified

UniProt A0A6L0ZI53

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 15	H(+)-transporting two-sector ATPase × 3 （A0A6L0YX77） Vacuolar proton pump subunit B × 3 （A0A6A5Q585） V-type proton ATPase subunit E × 3 （A0A6A5Q7Y8） V-type proton ATPase subunit D × 1 （A0A6A5Q1W2） V-type proton ATPase subunit F × 1 （A0A6A5PYF6） V-type proton ATPase subunit H × 1 （P41807） ADENOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 2 ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A6L0ZI53_YEASX
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain H； PDBConstruct 1–114； UniProt 1–114 Author chain J； PDBConstruct 1–114； UniProt 1–114 Author chain L； PDBConstruct 1–114； UniProt 1–114

V-type proton ATPase subunit D

OrganismNot specified

UniProt A0A6A5Q1W2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 15	H(+)-transporting two-sector ATPase × 3 （A0A6L0YX77） Vacuolar proton pump subunit B × 3 （A0A6A5Q585） V-type proton ATPase subunit E × 3 （A0A6A5Q7Y8） V-type proton ATPase subunit G × 3 （A0A6L0ZI53） V-type proton ATPase subunit F × 1 （A0A6A5PYF6） V-type proton ATPase subunit H × 1 （P41807） ADENOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 2 ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A6A5Q1W2_YEASX
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain M； PDBConstruct 1–256； UniProt 1–256

V-type proton ATPase subunit F

OrganismNot specified

UniProt A0A6A5PYF6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 15	H(+)-transporting two-sector ATPase × 3 （A0A6L0YX77） Vacuolar proton pump subunit B × 3 （A0A6A5Q585） V-type proton ATPase subunit E × 3 （A0A6A5Q7Y8） V-type proton ATPase subunit G × 3 （A0A6L0ZI53） V-type proton ATPase subunit D × 1 （A0A6A5Q1W2） V-type proton ATPase subunit H × 1 （P41807） ADENOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 2 ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A6A5PYF6_YEASX
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain N； PDBConstruct 1–118； UniProt 1–118

V-type proton ATPase subunit H

OrganismNot specified

UniProt P41807

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 15	H(+)-transporting two-sector ATPase × 3 （A0A6L0YX77） Vacuolar proton pump subunit B × 3 （A0A6A5Q585） V-type proton ATPase subunit E × 3 （A0A6A5Q7Y8） V-type proton ATPase subunit G × 3 （A0A6L0ZI53） V-type proton ATPase subunit D × 1 （A0A6A5Q1W2） V-type proton ATPase subunit F × 1 （A0A6A5PYF6） ADENOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 2 ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VATH_YEAST
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain P； PDBConstruct 1–478； UniProt 1–478

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	7tmo
Deposition date deposition_date	2022-01-19
Structure title title	V1 complex lacking subunit C from Saccharomyces cerevisiae, State 1
Keywords keywords	V-ATPase, HYDROLASE; 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.

7tmo__assembly_1__model_1

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

Download this curve (.dat)

7tmo__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7tmo__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	53.76 Å
Rg (electron density)	52.42 Å
Total Rg	52.13 Å
Atom count	31559
Residues	4816
Excluded volume	555620 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7tmo__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 (10)

Entity 1 Entity 1 polymer

Description description	H(+)-transporting two-sector ATPase
Molecular weight formula_weight	70515.2 kDa
EC 编号 ec_number	7.1.2.2
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E
Atom count atom_count	31559

MAGAIENARKEIKRISLEDHAESEYGAIYSVSGPVVIAENMIGCAMYELVKVGHDNLVGEVIRIDGDKATIQVYEETAGLTVGDPVLRTGKPLSVELGPGLMETIYDGIQRPLKAIKEESQSIYIPRGIDTPALDRTIKWQFTPGKFQVGDHISGGDIYGSVFENSLISSHKILLPPRSRGTITWIAPAGEYTLDEKILEVEFDGKKSDFTLYHTWPVRVPRPVTEKLSADYPLLTGQRVLDALFPCVQGGTTCIPGAFGCGKTVISQSLSKYSNSDAIIYVGCGERGNEMAEVLMEFPELYTEMSGTKEPIMKRTTLVANTSNMPVAAREASIYTGITLAEYFRDQGKNVSMIADSSSRWAEALREISGRLGEMPADQGFPAYLGAKLASFYERAGKAVALGSPDRTGSVSIVAAVSPAGGDFSDPVTTATLGITQVFWGLDKKLAQRKHFPSINTSVSYSKYTNVLNKFYDSNYPEFPVLRDRMKEILSNAEELEQVVQLVGKSALSDSDKITLDVATLIKEDFLQQNGYSTYDAFCPIWKTFDMMRAFISYHDEAQKAVANGANWSKLADSTGDVKHAVSSSKFFEPSRGEKEVHGEFEKLLSTMQERFAESTDDYKDHDGDYKDHDIDYKDDDDK

Entity 2 Entity 2 polymer

Description description	Vacuolar proton pump 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 3 Entity 3 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,I,K

MSSAITALTPNQVNDELNKMQAFIRKEAEEKAKEIQLKADQEYEIEKTNIVRNETNNIDGNFKSKLKKAMLSQQITKSTIANKMRLKVLSAREQSLDGIFEETKEKLSGIANNRDEYKPILQSLIVEALLKLLEPKAIVKALERDVDLIESMKDDIMREYGEKAQRAPLEEIVISNDYLNKDLVSGGVVVSNASDKIEINNTLEERLKLLSEEALPAIRLELYGPSKTRKFFD

Entity 4 Entity 4 polymer

Description description	V-type proton ATPase subunit G
Molecular weight formula_weight	12738.7 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

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

MSQKNGIATLLQAEKEAHEIVSKARKYRQDKLKQAKTDAAKEIDSYKIQKDKELKEFEQKNAGGVGELEKKAEAGVQGELAEIKKIAEKKKDDVVKILIETVIKPSAEVHINAL

Entity 5 Entity 5 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 6 Entity 6 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 7 Entity 7 polymer

Description description	V-type proton ATPase subunit H
Molecular weight formula_weight	54482.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

MGATKILMDSTHFNEIRSIIRSRSVAWDALARSEELSEIDASTAKALESILVKKNIGDGLSSSNNAHSGFKVNGKTLIPLIHLLSTSDNEDCKKSVQNLIAELLSSDKYGDDTVKFFQEDPKQLEQLFDVSLKGDFQTVLISGFNVVSLLVQNGLHNVKLVEKLLKNNNLINILQNIEQMDTCYVCIRLLQELAVIPEYRDVIWLHEKKFMPTLFKILQRATDSQLATRIVATNSNHLGIQLQYHSLLLIWLLTFNPVFANELVQKYLSDFLDLLKLVKITIKEKVSRLCISIILQCCSTRVKQHKKVIKQLLLLGNALPTVQSLSERKYSDEELRQDISNLKEILENEYQELTSFDEYVAELDSKLLCWSPPHVDNGFWSDNIDEFKKDNYKIFRQLIELLQAKVRNGDVNAKQEKIIIQVALNDITHVVELLPESIDVLDKTGGKADIMELLNHSDSRVKYEALKATQAIIGYTFK

Entity 8 Entity 8 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 10 Entity 10 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	7tmoI01
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	7tmoM01
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	3.30 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	64329

V1 complex lacking subunit C from Saccharomyces cerevisiae, State 1

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

H(+)-transporting two-sector ATPase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Vacuolar proton pump 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 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 G

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

V-type proton ATPase subunit H

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

7tmo__assembly_1__model_1

7tmo__assembly_1__model_1 | I(q)

7tmo__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 (10)

Entity 1 Entity 1 polymer

Polymer Polymer

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