3J9U: Yeast V-ATPase state 2

Yeast V-ATPase state 2. Determined by electron microscopy at 7.6 Å resolution. Released 13 May 2015.

Method: Electron microscopy
Resolution: 7.6 Å
Organism: Saccharomyces cerevisiae
Chains: 28
Atoms: 57,659
Mol. weight: 934.64 kDa
Released: 13 May 2015

Explore 3J9U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3J9U contains 302 α-helices and 204 β-strands across 28 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chains a and U: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	13-45	33
α-helix	50-58	9
α-helix	63-76	14
α-helix	84-121	38
α-helix	126-154	29

Chain A: 24 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	25-31	7	4
β-strand	34-38	5	4
β-strand	47-51	5	4
β-strand	56-64	9	4
β-strand	67-72	6	4
β-strand	80	1	28
β-strand	84-91	8	4
β-strand	93-96	4	29
β-strand	104-105	2	30
β-strand	111	1	30
α-helix	112-119	8
β-strand	139-143	5	31
β-strand	151-153	3	32
β-strand	157-162	6	31
β-strand	168-173	6	31
α-helix	174-175	2
β-strand	179-185	7	32
β-strand	189-191	3	31
β-strand	196-201	6	32
β-strand	205-210	6	32
β-strand	213-216	4	29
α-helix	220-222	3
β-strand	225-227	3	30
β-strand	232	1	33
α-helix	238-243	6
β-strand	247	1	33
β-strand	251-254	4	30
α-helix	262-272	11
β-strand	277-282	6	30
β-strand	285	1	34
α-helix	288-299	12
α-helix	311-314	4
β-strand	315-318	4	30
β-strand	321	1	34
α-helix	326-346	21
β-strand	349-355	7	30
α-helix	357-371	15
α-helix	377-379	3
α-helix	384-393	10
β-strand	396-399	4	30
α-helix	400	1
β-strand	407-415	9	30
α-helix	426-434	9
β-strand	437-438	2	30
α-helix	443-447	5
β-strand	460-461	2	30
α-helix	464-474	11
α-helix	478-501	24
α-helix	509-521	13
α-helix	522-526	5
α-helix	534-536	3
α-helix	540-562	23
α-helix	567-574	8
α-helix	576-582	7
α-helix	588	1
α-helix	598-615	18

Chain b: 10 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	15-21	7	41
α-helix	26-37	12
β-strand	39-44	6	41
α-helix	50-52	3
α-helix	56-79	24
α-helix	94-98	5
α-helix	107-150	44
β-strand	185-191	7	42
α-helix	194-207	14
β-strand	215-218	4	42
β-strand	235-241	7	42
α-helix	246-255	10
β-strand	261	1	42
α-helix	273-323	51
α-helix	327-330	4
β-strand	335-341	7	41
α-helix	346-351	6

Chain B: 19 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	30-35	6	4
β-strand	38-42	5	4
β-strand	48	1	28
β-strand	51-56	6	4
β-strand	62-71	10	4
β-strand	74-79	6	4
β-strand	92-99	8	4
β-strand	102-104	3	35
β-strand	112-114	3	36
α-helix	123	1
α-helix	125	1
β-strand	130-132	3	35
β-strand	150	1	37
α-helix	156-159	4
β-strand	165	1	37
β-strand	169	1	36
α-helix	171	1
β-strand	172-174	3	38
α-helix	180-201	22
β-strand	208-217	10	36
α-helix	219-232	14
β-strand	238-244	7	36
α-helix	249-270	22
β-strand	273-279	7	36
α-helix	281-293	13
α-helix	297-298	2
β-strand	299	1	39
α-helix	301-303	3
β-strand	305	1	39
α-helix	308-317	10
β-strand	320-322	3	36
β-strand	327-333	7	36
β-strand	334-336	3	38
α-helix	345-353	9
β-strand	357-360	4	38
α-helix	362-367	6
β-strand	373-379	7	38
α-helix	383-386	4
α-helix	396-420	25
α-helix	427-438	12
α-helix	439-443	5
α-helix	454-466	13
α-helix	478-483	6

Chain C: 23 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	25-31	7	4
β-strand	34-38	5	4
β-strand	47-51	5	4
β-strand	56-64	9	4
β-strand	67-72	6	4
β-strand	84-91	8	4
β-strand	94-96	3	5
β-strand	104-105	2	6
β-strand	111	1	6
α-helix	112-119	8
α-helix	124-125	2
β-strand	138-143	6	7
β-strand	151-152	2	8
β-strand	157-161	5	7
β-strand	171-173	3	7
α-helix	174-175	2
β-strand	180-185	6	8
β-strand	189-192	4	7
β-strand	196-201	6	8
β-strand	205-210	6	8
β-strand	213-215	3	5
α-helix	220-222	3
β-strand	225-227	3	6
β-strand	231	1	9
α-helix	238-243	6
β-strand	248	1	9
β-strand	251-255	5	6
α-helix	262-272	11
β-strand	277-285	9	6
α-helix	288-299	12
α-helix	312-314	3
β-strand	315-321	7	6
α-helix	326-344	19
β-strand	349-355	7	6
α-helix	357-371	15
α-helix	377-379	3
α-helix	383-394	12
β-strand	396-400	5	6
β-strand	406-416	11	6
α-helix	426-434	9
β-strand	437-441	5	6
α-helix	443-447	5
β-strand	454-461	8	6
α-helix	464-474	11
α-helix	478-501	24
α-helix	509-521	13
α-helix	522-526	5
α-helix	540-562	23
α-helix	567-574	8
α-helix	576-582	7
α-helix	583-586	4
α-helix	598-615	18

Chain D: 17 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	31-35	5	4
β-strand	38-41	4	4
α-helix	48	1
β-strand	51-56	6	4
β-strand	62-71	10	4
β-strand	74-79	6	4
β-strand	92-99	8	4
β-strand	101-104	4	10
β-strand	112-114	3	11
β-strand	119	1	11
β-strand	130-133	4	10
β-strand	142	1	12
β-strand	150-151	2	13
α-helix	156-161	6
β-strand	164-165	2	13
β-strand	169	1	11
β-strand	172-175	4	14
α-helix	180-190	11
α-helix	194-201	8
β-strand	208-217	10	11
α-helix	219-232	14
β-strand	238-244	7	11
α-helix	249-269	21
β-strand	273-279	7	11
α-helix	281-292	12
α-helix	301-303	3
α-helix	308-317	10
β-strand	320-321	2	11
β-strand	322	1	12
β-strand	328-333	6	11
β-strand	334-337	4	14
α-helix	345-353	9
β-strand	356-360	5	14
α-helix	361	1
α-helix	362-367	6
β-strand	373-380	8	14
α-helix	396-420	25
α-helix	427-438	12
α-helix	439-444	6
α-helix	454-465	12
α-helix	478-483	6

Chain E: 23 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	25-31	7	4
β-strand	34-38	5	4
β-strand	47-51	5	4
β-strand	56-64	9	4
β-strand	67-72	6	4
α-helix	79	1
β-strand	80	1	15
β-strand	84-91	8	4
β-strand	93-96	4	16
β-strand	104-105	2	17
α-helix	112-118	7
α-helix	124-125	2
β-strand	139-141	3	18
β-strand	142-143	2	19
β-strand	151-153	3	20
β-strand	157-161	5	19
β-strand	170-173	4	19
α-helix	174-175	2
β-strand	179-185	7	20
β-strand	189-191	3	18
β-strand	198-201	4	20
β-strand	205-209	5	20
β-strand	213-216	4	16
α-helix	220-222	3
β-strand	225-226	2	17
α-helix	238-243	6
β-strand	251-254	4	17
α-helix	262-272	11
β-strand	277-285	9	17
α-helix	288-296	9
β-strand	315-321	7	17
α-helix	326-346	21
β-strand	349-355	7	17
α-helix	357-371	15
β-strand	377	1	21
β-strand	380	1	21
α-helix	384-392	9
β-strand	396-399	4	17
α-helix	400	1
β-strand	407-415	9	17
α-helix	426-434	9
β-strand	437-438	2	17
α-helix	443-446	4
β-strand	460-461	2	17
α-helix	464-474	11
α-helix	479-498	20
α-helix	499-503	5
α-helix	509-521	13
α-helix	522-526	5
α-helix	540-562	23
α-helix	567-582	16
α-helix	584-586	3
α-helix	598-615	18

Chain F: 18 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	31-35	5	4
β-strand	38-41	4	4
α-helix	47	1
β-strand	48	1	15
β-strand	51-56	6	4
β-strand	62-71	10	4
β-strand	74-79	6	4
β-strand	92-99	8	4
β-strand	101-104	4	22
β-strand	111-114	4	23
β-strand	118	1	24
β-strand	123	1	24
β-strand	130-133	4	22
β-strand	150	1	25
α-helix	156-159	4
β-strand	165	1	25
β-strand	169	1	23
α-helix	171	1
β-strand	172-175	4	23
α-helix	180-190	11
α-helix	194-201	8
β-strand	208-215	8	23
α-helix	219-232	14
β-strand	238-243	6	23
α-helix	249-269	21
β-strand	273-279	7	23
α-helix	281-290	10
α-helix	301-303	3
α-helix	308-316	9
β-strand	320-321	2	23
α-helix	323-325	3
β-strand	328-337	10	23
α-helix	345-353	9
β-strand	357	1	26
β-strand	358-359	2	23
β-strand	360	1	27
α-helix	362-367	6
β-strand	373	1	27
β-strand	379	1	26
α-helix	383-386	4
α-helix	396-419	24
α-helix	427-440	14
α-helix	454-464	11
α-helix	478-483	6

19 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
V-type proton ATPase subunit D	M	protein	256	Saccharomyces cerevisiae	P32610 (AlphaFold model)
V-type proton ATPase subunit F	N	protein	118	Saccharomyces cerevisiae	P39111 (AlphaFold model)
V-type proton ATPase catalytic subunit A	A, C, E	protein	616	Saccharomyces cerevisiae	P17255 (AlphaFold model)
V-type proton ATPase subunit B	B, D, F	protein	517	Saccharomyces cerevisiae	P16140 (AlphaFold model)
V-type proton ATPase subunit d	Q	protein	345	Saccharomyces cerevisiae	P32366
V-type proton ATPase subunit G	H, J, L	protein	114	Saccharomyces cerevisiae	P48836
V-type proton ATPase subunit E	G, I, K	protein	233	Saccharomyces cerevisiae	P22203
V-type proton ATPase subunit H	P	protein	478	Saccharomyces cerevisiae	P41807
V-type proton ATPase subunit a, vacuolar isoform	b	protein	840	Saccharomyces cerevisiae	P32563
V-type proton ATPase subunit C	O	protein	392	Saccharomyces cerevisiae	P31412
V-type proton ATPase subunit c	R, S, T, U, V, W, X, Y, Z, a	protein	160	Saccharomyces cerevisiae	P25515

Sequence of entity 1 (M), FASTA

>3J9U_1 V-type proton ATPase subunit D (chains M)
MSGNREQVFPTRMTLGLMKTKLKGANQGYSLLKRKSEALTKRFRDITKRIDDAKQKMGRV
MQTAAFSLAEVSYATGENIGYQVQESVSTARFKVRARQENVSGVYLSQFESYIDPEINDF
RLTGLGRGGQQVQRAKEIYSRAVETLVELASLQTAFIILDEVIKVTNRRVNAIEHVIIPR
TENTIAYINSELDELDREEFYRLKKVQEKKQNETAKLDAEMKLKRDRAEQDASEVAADEE
PQGETLVADQEDDVIF

Sequence of entity 2 (N), FASTA

>3J9U_2 V-type proton ATPase subunit F (chains N)
MAEKRTLIAVIADEDTTTGLLLAGIGQITPETQEKNFFVYQEGKTTKEEITDKFNHFTEE
RDDIAILLINQHIAENIRARVDSFTNAFPAILEIPSKDHPYDPEKDSVLKRVRKLFGE

Sequence of entity 3 (A, C, E), FASTA

>3J9U_3 V-type proton ATPase catalytic subunit A (chains A, C, E)
AGAIENARKEIKRISLEDHAESEYGAIYSVSGPVVIAENMIGCAMYELVKVGHDNLVGEV
IRIDGDKATIQVYEETAGLTVGDPVLRTGKPLSVELGPGLMETIYDGIQRPLKAIKEESQ
SIYIPRGIDTPALDRTIKWQFTPGKFQVGDHISGGDIYGSVFENSLISSHKILLPPRSRG
TITWIAPAGEYTLDEKILEVEFDGKKSDFTLYHTWPVRVPRPVTEKLSADYPLLTGQRVL
DALFPCVQGGTTCIPGAFGCGKTVISQSLSKYSNSDAIIYVGCGERGNEMAEVLMEFPEL
YTEMSGTKEPIMKRTTLVANTSNMPVAAREASIYTGITLAEYFRDQGKNVSMIADSSSRW
AEALREISGRLGEMPADQGFPAYLGAKLASFYERAGKAVALGSPDRTGSVSIVAAVSPAG
GDFSDPVTTATLGITQVFWGLDKKLAQRKHFPSINTSVSYSKYTNVLNKFYDSNYPEFPV
LRDRMKEILSNAEELEQVVQLVGKSALSDSDKITLDVATLIKEDFLQQNGYSTYDAFCPI
WKTFDMMRAFISYHDEAQKAVANGANWSKLADSTGDVKHAVSSSKFFEPSRGEKEVHGEF
EKLLSTMQERFAESTD

Sequence of entity 4 (B, D, F), FASTA

>3J9U_4 V-type proton ATPase subunit B (chains B, D, F)
MVLSDKELFAINKKAVEQGFNVKPRLNYNTVSGVNGPLVILEKVKFPRYNEIVNLTLPDG
TVRQGQVLEIRGDRAIVQVFEGTSGIDVKKTTVEFTGESLRIPVSEDMLGRIFDGSGRPI
DNGPKVFAEDYLDINGSPINPYARIYPEEMISTGVSAIDTMNSIARGQKIPIFSASGLPH
NEIAAQICRQAGLVRPTKDVHDGHEENFSIVFAAMGVNLETARFFKQDFEENGSLERTSL
FLNLANDPTIERIITPRLALTTAEYLAYQTERHVLTILTDMSSYADALREVSAAREEVPG
RRGYPGYMYTDLSTIYERAGRVEGRNGSITQIPILTMPNDDITHPIPDLTGYITEGQIFV
DRQLHNKGIYPPINVLPSLSRLMKSAIGEGMTRKDHGDVSNQLYAKYAIGKDAAAMKAVV
GEEALSIEDKLSLEFLEKFEKTFITQGAYEDRTVFESLDQAWSLLRIYPKEMLNRISPKI
LDEFYDRARDDADEDEEDPDTRSSGKKKDASQEESLI

Sequence of entity 5 (Q), FASTA

>3J9U_5 V-type proton ATPase subunit d (chains Q)
MEGVYFNIDNGFIEGVVRGYRNGLLSNNQYINLTQCDTLEDLKLQLSSTDYGNFLSSVSS
ESLTTSLIQEYASSKLYHEFNYIRDQSSGSTRKFMDYITYGYMIDNVALMITGTIHDRDK
GEILQRCHPLGWFDTLPTLSVATDLESLYETVLVDTPLAPYFKNCFDTAEELDDMNIEII
RNKLYKAYLEDFYNFVTEEIPEPAKECMQTLLGFEADRRSINIALNSLQSSDIDPDLKSD
LLPNIGKLYPLATFHLAQAQDFEGVRAALANVYEYRGFLETGNLEDHFYQLEMELCRDAF
TQQFAISTVWAWMKSKEQEVRNITWIAECIAQNQRERINNYISVY

Sequence of entity 6 (H, J, L), FASTA

>3J9U_6 V-type proton ATPase subunit G (chains H, J, L)
MSQKNGIATLLQAEKEAHEIVSKARKYRQDKLKQAKTDAAKEIDSYKIQKDKELKEFEQK
NAGGVGELEKKAEAGVQGELAEIKKIAEKKKDDVVKILIETVIKPSAEVHINAL

Sequence of entity 7 (G, I, K), FASTA

>3J9U_7 V-type proton ATPase subunit E (chains G, I, K)
MSSAITALTPNQVNDELNKMQAFIRKEAEEKAKEIQLKADQEYEIEKTNIVRNETNNIDG
NFKSKLKKAMLSQQITKSTIANKMRLKVLSAREQSLDGIFEETKEKLSGIANNRDEYKPI
LQSLIVEALLKLLEPKAIVKALERDVDLIESMKDDIMREYGEKAQRAPLEEIVISNDYLN
KDLVSGGVVVSNASDKIEINNTLEERLKLLSEEALPAIRLELYGPSKTRKFFD

Sequence of entity 8 (P), FASTA

>3J9U_8 V-type proton ATPase subunit H (chains P)
MGATKILMDSTHFNEIRSIIRSRSVAWDALARSEELSEIDASTAKALESILVKKNIGDGL
SSSNNAHSGFKVNGKTLIPLIHLLSTSDNEDCKKSVQNLIAELLSSDKYGDDTVKFFQED
PKQLEQLFDVSLKGDFQTVLISGFNVVSLLVQNGLHNVKLVEKLLKNNNLINILQNIEQM
DTCYVCIRLLQELAVIPEYRDVIWLHEKKFMPTLFKILQRATDSQLATRIVATNSNHLGI
QLQYHSLLLIWLLTFNPVFANELVQKYLSDFLDLLKLVKITIKEKVSRLCISIILQCCST
RVKQHKKVIKQLLLLGNALPTVQSLSERKYSDEELRQDISNLKEILENEYQELTSFDEYV
AELDSKLLCWSPPHVDNGFWSDNIDEFKKDNYKIFRQLIELLQAKVRNGDVNAKQEKIII
QVALNDITHVVELLPESIDVLDKTGGKADIMELLNHSDSRVKYEALKATQAIIGYTFK

Sequence of entity 9 (b), FASTA

>3J9U_9 V-type proton ATPase subunit a, vacuolar isoform (chains b)
MAEKEEAIFRSAEMALVQFYIPQEISRDSAYTLGQLGLVQFRDLNSKVRAFQRTFVNEIR
RLDNVERQYRYFYSLLKKHDIKLYEGDTDKYLDGSGELYVPPSGSVIDDYVRNASYLEER
LIQMEDATDQIEVQKNDLEQYRFILQSGDEFFLKGDNTDSTSYMDEDMIDANGENIAAAI
GASVNYVTGVIARDKVATLEQILWRVLRGNLFFKTVEIEQPVYDVKTREYKHKNAFIVFS
HGDLIIKRIRKIAESLDANLYDVDSSNEGRSQQLAKVNKNLSDLYTVLKTTSTTLESELY
AIAKELDSWFQDVTREKAIFEILNKSNYDTNRKILIAEGWIPRDELATLQARLGEMIARL
GIDVPSIIQVLDTNHTPPTFHRTNKFTAGFQSICDCYGIAQYREINAGLPTIVTFPFMFA
IMFGDMGHGFLMTLAALSLVLNEKKINKMKRGEIFDMAFTGRYIILLMGVFSMYTGFLYN
DIFSKTMTIFKSGWKWPDHWKKGESITATSVGTYPIGLDWAWHGTENALLFSNSYKMKLS
ILMGFIHMTYSYFFSLANHLYFNSMIDIIGNFIPGLLFMQGIFGYLSVCIVYKWAVDWVK
DGKPAPGLLNMLINMFLSPGTIDDELYPHQAKVQVFLLLMALVCIPWLLLVKPLHFKFTH
KKKSHEPLPSTEADASSEDLEAQQLISAMDADDAEEEEVGSGSHGEDFGDIMIHQVIHTI
EFCLNCVSHTASYLRLWALSLAHAQLSSVLWTMTIQIAFGFRGFVGVFMTVALFAMWFAL
TCAVLVLMEGTSAMLHSLRLHWVESMSKFFVGEGLPYEPFAFEYKDMEVAVASASSSASS

Sequence of entity 10 (O), FASTA

>3J9U_10 V-type proton ATPase subunit C (chains O)
MATALYTANDFILISLPQNAQPVTAPGSKTDSWFNETLIGGRAFVSDFKIPEFKIGSLDT
LIVESEELSKVDNQIGASIGKIIEILQGLNETSTNAYRTLPINNMPVPEYLENFQWQTRK
FKLDKSIKDLITLISNESSQLDADVRATYANYNSAKTNLAAAERKKTGDLSVRSLHDIVK
PEDFVLNSEHLTTVLVAVPKSLKSDFEKSYETLSKNVVPASASVIAEDAEYVLFNVHLFK
KNVQEFTTAAREKKFIPREFNYSEELIDQLKKEHDSAASLEQSLRVQLVRLAKTAYVDVF
INWFHIKALRVYVESVLRYGLPPHFNIKIIAVPPKNLSKCKSELIDAFGFLGGNAFMKDK
KGKINKQDTSLHQYASLVDTEYEPFVMYIINL

Sequence of entity 11 (R, S, T, U, V, W, X, Y, Z, a), FASTA

>3J9U_11 V-type proton ATPase subunit c (chains R, S, T, U, V, W, X, Y, Z, a)
MTELCPVYAPFFGAIGCASAIIFTSLGAAYGTAKSGVGICATCVLRPDLLFKNIVPVIMA
GIIAIYGLVVSVLVCYSLGQKQALYTGFIQLGAGLSVGLSGLAAGFAIGIVGDAGVRGSS
QQPRLFVGMILILIFAEVLGLYGLIVALLLNSRATQDVVC

Primary citation

Electron cryomicroscopy observation of rotational states in a eukaryotic V-ATPase. Zhao, J., Benlekbir, S., Rubinstein, J.L. Nature (2015) 521:241-245. DOI 10.1038/nature14365 · PubMed

Other PDB entries of the same protein (UniProt P32610 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9COP 2.7 Å, Yeast RAVE bound to V-ATPase V1 complex
4RND 3.18 Å, Crystal Structure of the subunit DF-assembly of the eukaryotic V-ATPase.
7TMO 3.3 Å, V1 complex lacking subunit C from Saccharomyces cerevisiae, State 1
7TMP 3.3 Å, V1 complex lacking subunit C from Saccharomyces cerevisiae, State 2
7TMQ 3.3 Å, V1 complex lacking subunit C from Saccharomyces cerevisiae, State 3
7TMM 3.5 Å, Complete V1 Complex from Saccharomyces cerevisiae
7TMR 3.5 Å, V-ATPase from Saccharomyces cerevisiae, State 1
9MOY 3.6 Å, Reconstituted yeast V-ATPase bound to Rtc5p
9NN1 3.7 Å, Yeast V1-ATPase bound to Rtc5p
7FDE 3.8 Å, CryoEM Structures of Reconstituted V-ATPase, Oxr1 bound V1
9ODU 3.9 Å, Yeast V-ATPase bound to Rtc5p, rotary state 2
7FDA 4.2 Å, CryoEM Structure of Reconstituted V-ATPase, state1

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