5d80

Crystal Structure of Yeast V1-ATPase in the Autoinhibited Form

Method: X-RAY DIFFRACTION

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

V-type proton ATPase catalytic subunit A

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 B × 3 （P16140） V-type proton ATPase subunit H × 1 （P41807） V-type proton ATPase subunit G × 3 （P48836） V-type proton ATPase subunit E × 3 （P22203） V-type proton ATPase subunit D × 1 （P32610） V-type proton ATPase subunit F × 1 （P39111）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 15	V-type proton ATPase subunit B × 3 （P16140） V-type proton ATPase subunit H × 1 （P41807） V-type proton ATPase subunit G × 3 （P48836） V-type proton ATPase subunit E × 3 （P22203） 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	VATA_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–283； UniProt 1–283 Author chain A； PDBConstruct 284–617； UniProt 738–1071 Author chain B； PDBConstruct 1–283； UniProt 1–283 Author chain B； PDBConstruct 284–617； UniProt 738–1071 Author chain C； PDBConstruct 1–283； UniProt 1–283 Author chain C； PDBConstruct 284–617； UniProt 738–1071 Author chain a； PDBConstruct 1–283； UniProt 1–283 Author chain a； PDBConstruct 284–617； UniProt 738–1071 Author chain b； PDBConstruct 1–283； UniProt 1–283 Author chain b； PDBConstruct 284–617； UniProt 738–1071 Author chain c； PDBConstruct 1–283； UniProt 1–283 Author chain c； PDBConstruct 284–617； UniProt 738–1071

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 15	V-type proton ATPase catalytic subunit A × 3 （P17255） V-type proton ATPase subunit H × 1 （P41807） V-type proton ATPase subunit G × 3 （P48836） V-type proton ATPase subunit E × 3 （P22203） V-type proton ATPase subunit D × 1 （P32610） V-type proton ATPase subunit F × 1 （P39111）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 15	V-type proton ATPase catalytic subunit A × 3 （P17255） V-type proton ATPase subunit H × 1 （P41807） V-type proton ATPase subunit G × 3 （P48836） V-type proton ATPase subunit E × 3 （P22203） 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	VATB_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–517； UniProt 1–517 Author chain E； PDBConstruct 1–517； UniProt 1–517 Author chain F； PDBConstruct 1–517； UniProt 1–517 Author chain d； PDBConstruct 1–517； UniProt 1–517 Author chain e； PDBConstruct 1–517； UniProt 1–517 Author chain f； PDBConstruct 1–517； UniProt 1–517

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	V-type proton ATPase catalytic subunit A × 3 （P17255） V-type proton ATPase subunit B × 3 （P16140） V-type proton ATPase subunit G × 3 （P48836） V-type proton ATPase subunit E × 3 （P22203） V-type proton ATPase subunit D × 1 （P32610） V-type proton ATPase subunit F × 1 （P39111）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 15	V-type proton ATPase catalytic subunit A × 3 （P17255） V-type proton ATPase subunit B × 3 （P16140） V-type proton ATPase subunit G × 3 （P48836） V-type proton ATPase subunit E × 3 （P22203） 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	VATH_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain H； PDBConstruct 1–478； UniProt 1–478 Author chain h； PDBConstruct 1–478； UniProt 1–478

V-type proton ATPase subunit G

OrganismNot specified

UniProt P48836

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 catalytic subunit A × 3 （P17255） V-type proton ATPase subunit B × 3 （P16140） V-type proton ATPase subunit H × 1 （P41807） V-type proton ATPase subunit E × 3 （P22203） V-type proton ATPase subunit D × 1 （P32610） V-type proton ATPase subunit F × 1 （P39111）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 15	V-type proton ATPase catalytic subunit A × 3 （P17255） V-type proton ATPase subunit B × 3 （P16140） V-type proton ATPase subunit H × 1 （P41807） V-type proton ATPase subunit E × 3 （P22203） 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	VATG_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain J； PDBConstruct 10–122； UniProt 2–114 Author chain L； PDBConstruct 10–122； UniProt 2–114 Author chain N； PDBConstruct 10–122； UniProt 2–114 Author chain j； PDBConstruct 10–122； UniProt 2–114 Author chain l； PDBConstruct 10–122； UniProt 2–114 Author chain n； PDBConstruct 10–122； UniProt 2–114

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 15	V-type proton ATPase catalytic subunit A × 3 （P17255） V-type proton ATPase subunit B × 3 （P16140） V-type proton ATPase subunit H × 1 （P41807） V-type proton ATPase subunit G × 3 （P48836） V-type proton ATPase subunit D × 1 （P32610） V-type proton ATPase subunit F × 1 （P39111）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 15	V-type proton ATPase catalytic subunit A × 3 （P17255） V-type proton ATPase subunit B × 3 （P16140） V-type proton ATPase subunit H × 1 （P41807） V-type proton ATPase subunit G × 3 （P48836） 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	VATE_YEAST
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain I； PDBConstruct 1–233； UniProt 1–233 Author chain K； PDBConstruct 1–233； UniProt 1–233 Author chain M； PDBConstruct 1–233； UniProt 1–233 Author chain i； PDBConstruct 1–233； UniProt 1–233 Author chain k； PDBConstruct 1–233； UniProt 1–233 Author chain m； PDBConstruct 1–233； UniProt 1–233

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 15	V-type proton ATPase catalytic subunit A × 3 （P17255） V-type proton ATPase subunit B × 3 （P16140） V-type proton ATPase subunit H × 1 （P41807） V-type proton ATPase subunit G × 3 （P48836） V-type proton ATPase subunit E × 3 （P22203） V-type proton ATPase subunit F × 1 （P39111）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 15	V-type proton ATPase catalytic subunit A × 3 （P17255） V-type proton ATPase subunit B × 3 （P16140） V-type proton ATPase subunit H × 1 （P41807） V-type proton ATPase subunit G × 3 （P48836） V-type proton ATPase subunit E × 3 （P22203） 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	VATD_YEAST
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain G； PDBConstruct 1–256； UniProt 1–256 Author chain g； 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 15	V-type proton ATPase catalytic subunit A × 3 （P17255） V-type proton ATPase subunit B × 3 （P16140） V-type proton ATPase subunit H × 1 （P41807） V-type proton ATPase subunit G × 3 （P48836） V-type proton ATPase subunit E × 3 （P22203） V-type proton ATPase subunit D × 1 （P32610）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 15	V-type proton ATPase catalytic subunit A × 3 （P17255） V-type proton ATPase subunit B × 3 （P16140） V-type proton ATPase subunit H × 1 （P41807） V-type proton ATPase subunit G × 3 （P48836） V-type proton ATPase subunit E × 3 （P22203） V-type proton ATPase subunit D × 1 （P32610）	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 O； PDBConstruct 1–118； UniProt 1–118 Author chain o； PDBConstruct 1–118； UniProt 1–118

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	5d80
Deposition date deposition_date	2015-08-14
Structure title title	Crystal Structure of Yeast V1-ATPase in the Autoinhibited Form
Keywords keywords	Hydrolase, Autoinhibition; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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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.

5d80__assembly_1__model_1

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

Download this curve (.dat)

5d80__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5d80__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	56.87 Å
Rg (electron density)	57.02 Å
Total Rg	57.13 Å
Atom count	23747
Residues	4813
Excluded volume	381960 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5d80__assembly_1__model_1`	pentadecameric （15）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5d80__assembly_2__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 (7)

Entity 1 Entity 1 polymer

Description description	V-type proton ATPase catalytic subunit A
Molecular weight formula_weight	67796.5 kDa
EC 编号 ec_number	3.6.3.14,3.1.-.-
Source method src_method	nat
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,a,b,c
Atom count atom_count	47363

MAGAIENARKEIKRISLEDHAESEYGAIYSVSGPVVIAENMIGCAMYELVKVGHDNLVGEVIRIDGDKATIQVYEETAGLTVGDPVLRTGKPLSVELGPGLMETIYDGIQRPLKAIKEESQSIYIPRGIDTPALDRTIKWQFTPGKFQVGDHISGGDIYGSVFENSLISSHKILLPPRSRGTITWIAPAGEYTLDEKILEVEFDGKKSDFTLYHTWPVRVPRPVTEKLSADYPLLTGQRVLDALFPCVQGGTTCIPGAFGCGKTVISQSLSKYSNSDAIIYVGCGERGNEMAEVLMEFPELYTEMSGTKEPIMKRTTLVANTSNMPVAAREASIYTGITLAEYFRDQGKNVSMIADSSSRWAEALREISGRLGEMPADQGFPAYLGAKLASFYERAGKAVALGSPDRTGSVSIVAAVSPAGGDFSDPVTTATLGITQVFWGLDKKLAQRKHFPSINTSVSYSKYTNVLNKFYDSNYPEFPVLRDRMKEILSNAEELEQVVQLVGKSALSDSDKITLDVATLIKEDFLQQNGYSTYDAFCPIWKTFDMMRAFISYHDEAQKAVANGANWSKLADSTGDVKHAVSSSKFFEPSRGEKEVHGEFEKLLSTMQERFAESTD

Entity 2 Entity 2 polymer

Description description	V-type proton ATPase subunit B
Molecular weight formula_weight	57815.0 kDa
EC 编号 ec_number	3.6.3.14
Source method src_method	nat
Copy count entity_count	6

Polymer Polymer

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

MVLSDKELFAINKKAVEQGFNVKPRLNYNTVSGVNGPLVILEKVKFPRYNEIVNLTLPDGTVRQGQVLEIRGDRAIVQVFEGTSGIDVKKTTVEFTGESLRIPVSEDMLGRIFDGSGRPIDNGPKVFAEDYLDINGSPINPYARIYPEEMISTGVSAIDTMNSIARGQKIPIFSASGLPHNEIAAQICRQAGLVRPTKDVHDGHEENFSIVFAAMGVNLETARFFKQDFEENGSLERTSLFLNLANDPTIERIITPRLALTTAEYLAYQTERHVLTILTDMSSYADALREVSAAREEVPGRRGYPGYMYTDLSTIYERAGRVEGRNGSITQIPILTMPNDDITHPIPDLTGYITEGQIFVDRQLHNKGIYPPINVLPSLSRLMKSAIGEGMTRKDHGDVSNQLYAKYAIGKDAAAMKAVVGEEALSIEDKLSLEFLEKFEKTFITQGAYEDRTVFESLDQAWSLLRIYPKEMLNRISPKILDEFYDRARDDADEDEEDPDTRSSGKKKDASQEESLI

Entity 3 Entity 3 polymer

Description description	V-type proton ATPase subunit H
Molecular weight formula_weight	54482.6 kDa
EC 编号 ec_number	3.6.3.14
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

MGATKILMDSTHFNEIRSIIRSRSVAWDALARSEELSEIDASTAKALESILVKKNIGDGLSSSNNAHSGFKVNGKTLIPLIHLLSTSDNEDCKKSVQNLIAELLSSDKYGDDTVKFFQEDPKQLEQLFDVSLKGDFQTVLISGFNVVSLLVQNGLHNVKLVEKLLKNNNLINILQNIEQMDTCYVCIRLLQELAVIPEYRDVIWLHEKKFMPTLFKILQRATDSQLATRIVATNSNHLGIQLQYHSLLLIWLLTFNPVFANELVQKYLSDFLDLLKLVKITIKEKVSRLCISIILQCCSTRVKQHKKVIKQLLLLGNALPTVQSLSERKYSDEELRQDISNLKEILENEYQELTSFDEYVAELDSKLLCWSPPHVDNGFWSDNIDEFKKDNYKIFRQLIELLQAKVRNGDVNAKQEKIIIQVALNDITHVVELLPESIDVLDKTGGKADIMELLNHSDSRVKYEALKATQAIIGYTFK

Entity 4 Entity 4 polymer

Description description	V-type proton ATPase subunit G
Molecular weight formula_weight	13735.7 kDa
EC 编号 ec_number	3.6.3.14
Source method src_method	nat
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J,L,N,j,l,n

MDYKDDDDKSQKNGIATLLQAEKEAHEIVSKARKYRQDKLKQAKTDAAKEIDSYKIQKDKELKEFEQKNAGGVGELEKKAEAGVQGELAEIKKIAEKKKDDVVKILIETVIKPSAEVHINAL

Entity 5 Entity 5 polymer

Description description	V-type proton ATPase subunit E
Molecular weight formula_weight	26508.4 kDa
EC 编号 ec_number	3.6.3.14
Source method src_method	nat
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,K,M,i,k,m

MSSAITALTPNQVNDELNKMQAFIRKEAEEKAKEIQLKADQEYEIEKTNIVRNETNNIDGNFKSKLKKAMLSQQITKSTIANKMRLKVLSAREQSLDGIFEETKEKLSGIANNRDEYKPILQSLIVEALLKLLEPKAIVKALERDVDLIESMKDDIMREYGEKAQRAPLEEIVISNDYLNKDLVSGGVVVSNASDKIEINNTLEERLKLLSEEALPAIRLELYGPSKTRKFFD

Entity 6 Entity 6 polymer

Description description	V-type proton ATPase subunit D
Molecular weight formula_weight	29235.0 kDa
EC 编号 ec_number	3.6.3.14
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,g

MSGNREQVFPTRMTLGLMKTKLKGANQGYSLLKRKSEALTKRFRDITKRIDDAKQKMGRVMQTAAFSLAEVSYATGENIGYQVQESVSTARFKVRARQENVSGVYLSQFESYIDPEINDFRLTGLGRGGQQVQRAKEIYSRAVETLVELASLQTAFIILDEVIKVTNRRVNAIEHVIIPRTENTIAYINSELDELDREEFYRLKKVQEKKQNETAKLDAEMKLKRDRAEQDASEVAADEEPQGETLVADQEDDVIF

Entity 7 Entity 7 polymer

Description description	V-type proton ATPase subunit F
Molecular weight formula_weight	13479.2 kDa
EC 编号 ec_number	3.6.3.14
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	o,O

MAEKRTLIAVIADEDTTTGLLLAGIGQITPETQEKNFFVYQEGKTTKEEITDKFNHFTEERDDIAILLINQHIAENIRARVDSFTNAFPAILEIPSKDHPYDPEKDSVLKRVRKLFGE

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Unit-cell length a length_a	468.020 Å
Unit-cell length b length_b	159.650 Å
Unit-cell length c length_c	248.270 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	113.75 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	6.202 Å
Low-resolution limit resolution_low	39.720 Å
R factor r_factor	0.2573
R_work r_work	0.2545
R_free r_free	0.3018

Crystal Structure of Yeast V1-ATPase in the Autoinhibited Form

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

V-type proton ATPase catalytic subunit A

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 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

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 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 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5d80__assembly_1__model_1

5d80__assembly_1__model_1 | I(q)

5d80__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

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