9nn1

Yeast V1-ATPase bound to Rtc5p

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	V-type proton ATPase subunit E × 3 （P22203） Yeast V-ATPase subunit G × 3 V-type proton ATPase subunit D × 1 （P32610） V-type proton ATPase subunit F × 1 （P39111） Restriction of telomere capping protein 5 × 1 （B3LJG1） V-type proton ATPase subunit B × 3 （P16140） ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B3LH69_YEAS1
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

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	H(+)-transporting two-sector ATPase × 3 （B3LH69） Yeast V-ATPase subunit G × 3 V-type proton ATPase subunit D × 1 （P32610） V-type proton ATPase subunit F × 1 （P39111） Restriction of telomere capping protein 5 × 1 （B3LJG1） V-type proton ATPase subunit B × 3 （P16140） ADENOSINE-5'-DIPHOSPHATE × 1	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 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	H(+)-transporting two-sector ATPase × 3 （B3LH69） V-type proton ATPase subunit E × 3 （P22203） Yeast V-ATPase subunit G × 3 V-type proton ATPase subunit F × 1 （P39111） Restriction of telomere capping protein 5 × 1 （B3LJG1） V-type proton ATPase subunit B × 3 （P16140） ADENOSINE-5'-DIPHOSPHATE × 1	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	4
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 15	H(+)-transporting two-sector ATPase × 3 （B3LH69） V-type proton ATPase subunit E × 3 （P22203） Yeast V-ATPase subunit G × 3 V-type proton ATPase subunit D × 1 （P32610） Restriction of telomere capping protein 5 × 1 （B3LJG1） V-type proton ATPase subunit B × 3 （P16140） ADENOSINE-5'-DIPHOSPHATE × 1	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	5
Chains and sequence ranges	Author chain N； PDBConstruct 1–118； UniProt 1–118

Restriction of telomere capping protein 5

Saccharomyces cerevisiae

UniProt B3LJG1

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 （B3LH69） V-type proton ATPase subunit E × 3 （P22203） Yeast V-ATPase subunit G × 3 V-type proton ATPase subunit D × 1 （P32610） V-type proton ATPase subunit F × 1 （P39111） V-type proton ATPase subunit B × 3 （P16140） ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RTC5_YEAS1
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain R； PDBConstruct 1–567； UniProt 1–567

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	H(+)-transporting two-sector ATPase × 3 （B3LH69） V-type proton ATPase subunit E × 3 （P22203） Yeast V-ATPase subunit G × 3 V-type proton ATPase subunit D × 1 （P32610） V-type proton ATPase subunit F × 1 （P39111） Restriction of telomere capping protein 5 × 1 （B3LJG1） ADENOSINE-5'-DIPHOSPHATE × 1	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	7
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

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	9nn1
Deposition date deposition_date	2025-03-04
Structure title title	Yeast V1-ATPase bound to Rtc5p
Keywords keywords	Vacuolar ATPase, V1-ATPase, Rtc5p, protein structure, PROTON TRANSPORT; PROTON TRANSPORT
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.

9nn1__assembly_1__model_1

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

Download this curve (.dat)

9nn1__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9nn1__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	56.36 Å
Rg (electron density)	56.15 Å
Total Rg	56.34 Å
Atom count	77843
Residues	4941
Excluded volume	693230 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9nn1__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 (8)

Entity 1 Entity 1 polymer

Description description	H(+)-transporting two-sector ATPase
Molecular weight formula_weight	67796.5 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	77843

MAGAIENARKEIKRISLEDHAESEYGAIYSVSGPVVIAENMIGCAMYELVKVGHDNLVGEVIRIDGDKATIQVYEETAGLTVGDPVLRTGKPLSVELGPGLMETIYDGIQRPLKAIKEESQSIYIPRGIDTPALDRTIKWQFTPGKFQVGDHISGGDIYGSVFENSLISSHKILLPPRSRGTITWIAPAGEYTLDEKILEVEFDGKKSDFTLYHTWPVRVPRPVTEKLSADYPLLTGQRVLDALFPCVQGGTTCIPGAFGCGKTVISQSLSKYSNSDAIIYVGCGERGNEMAEVLMEFPELYTEMSGTKEPIMKRTTLVANTSNMPVAAREASIYTGITLAEYFRDQGKNVSMIADSSSRWAEALREISGRLGEMPADQGFPAYLGAKLASFYERAGKAVALGSPDRTGSVSIVAAVSPAGGDFSDPVTTATLGITQVFWGLDKKLAQRKHFPSINTSVSYSKYTNVLNKFYDSNYPEFPVLRDRMKEILSNAEELEQVVQLVGKSALSDSDKITLDVATLIKEDFLQQNGYSTYDAFCPIWKTFDMMRAFISYHDEAQKAVANGANWSKLADSTGDVKHAVSSSKFFEPSRGEKEVHGEFEKLLSTMQERFAESTD

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,I,K

MSSAITALTPNQVNDELNKMQAFIRKEAEEKAKEIQLKADQEYEIEKTNIVRNETNNIDGNFKSKLKKAMLSQQITKSTIANKMRLKVLSAREQSLDGIFEETKEKLSGIANNRDEYKPILQSLIVEALLKLLEPKAIVKALERDVDLIESMKDDIMREYGEKAQRAPLEEIVISNDYLNKDLVSGGVVVSNASDKIEINNTLEERLKLLSEEALPAIRLELYGPSKTRKFFD

Entity 3 Entity 3 polymer

Description description	Yeast V-ATPase subunit G
Molecular weight formula_weight	13735.7 kDa
Mutation mutation	N-terminal FLAG tag
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

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

MDYKDDDDKSQKNGIATLLQAEKEAHEIVSKARKYRQDKLKQAKTDAAKEIDSYKIQKDKELKEFEQKNAGGVGELEKKAEAGVQGELAEIKKIAEKKKDDVVKILIETVIKPSAEVHINAL

Entity 4 Entity 4 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 5 Entity 5 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 6 Entity 6 polymer

Description description	Restriction of telomere capping protein 5
Molecular weight formula_weight	64368.3 kDa
Mutation mutation	N-terminal His tag
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	R

MGQSSSISSSNEEGSSHSKKFTNSKDILAYFNNKAQQQVTIPELVSFKGNLQIEDLNTPISHKALCNSLYFPQNHAMIVGIVTNMLRVLSNFPLMKSSYEPITGYGLLKCILLLNRARCAKFLKTKSYDQLKLLFISLSLQKTDKEELSEESENDGNKELTIKQIITGFDDVDTEMLCIPADFMLQFLTWLLILTVDCPTTNSKLDNTETHDQWGNFKVSALNLLRTMNPDVVGDIESHSITFQQFSTAIRTVMPNLLKPLENLMEHFFYLQHDLVDHDTNLSSIQDSKVMTPALLAQLSTGLPKELFIHKLQSLYIGRKSGFSMRSLQAKVFKWMAPSILVVSGMRITNSEEYAAEKNPRYRHFLEEFPKLKESDQMMDASHLNKRKTTFAVYIDDPWKVTNKDYFGDLNTRIIEISPRQDIYKVNQKGTIYFNTIGGGIGIGDKQPLIKPASKRYIPGNVSLTFDSTLEFAVFRNTGYGGSLDPGLLSMERKEENSPYELHFLIQDVEVWGCGGEKELEEQIKQLEWEEAESKRRQQINLRSLGEDRALLEMAGLVGQHQGGGSM

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;brewer's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 7 Entity 7 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 8 Entity 8 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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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	triclinic

Resolution resolution	3.70 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	67351

Yeast V1-ATPase bound to Rtc5p

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

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

Restriction of telomere capping protein 5

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9nn1__assembly_1__model_1

9nn1__assembly_1__model_1 | I(q)

9nn1__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

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

Source Source

Entity 7 Entity 7 polymer

Polymer Polymer

Entity 8 Entity 8 non-polymer

7. Citations (1)