9COP: Yeast RAVE

Yeast RAVE bound to V-ATPase V1 complex. Determined by electron microscopy at 2.7 Å resolution. Released 20 Nov 2024.

Method: Electron microscopy
Resolution: 2.7 Å
Organism: Saccharomyces cerevisiae
Chains: 14
Atoms: 36,495
Mol. weight: 747.2 kDa
Ligands: ADP, MG
Released: 20 Nov 2024

Explore 9COP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9COP contains 255 α-helices and 241 β-strands across 14 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.

Chain A: 27 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	25-32	8	1
β-strand	35-39	5	1
α-helix	44	1
β-strand	45	1	2
β-strand	49-52	4	1
β-strand	57-65	9	1
β-strand	68-73	6	1
β-strand	81	1	3
β-strand	85-88	4	1
β-strand	94-97	4	4
β-strand	105-106	2	5
α-helix	113-120	8
β-strand	124	1	6
β-strand	140-144	5	7
β-strand	152	1	8
β-strand	158-162	5	7
β-strand	171-174	4	7
α-helix	175-176	2
β-strand	182-186	5	8
α-helix	187-188	2
β-strand	190-192	3	7
β-strand	197-202	6	8
β-strand	207-211	5	8
β-strand	214-217	4	4
α-helix	221-223	3
β-strand	226-228	3	5
β-strand	233-234	2	9
α-helix	239-243	5
β-strand	247-248	2	9
β-strand	252-256	5	5
α-helix	263-273	11
β-strand	278-740	463	5
α-helix	742-751	10
α-helix	752-754	3
β-strand	756-757	2	10
β-strand	764-765	2	10
α-helix	766-769	4
β-strand	770-776	7	5
α-helix	782-799	18
β-strand	804-810	7	5
α-helix	812-826	15
α-helix	828-830	3
α-helix	832-834	3
α-helix	839-847	9
β-strand	851-854	4	5
β-strand	862-871	10	5
α-helix	874-876	3
α-helix	881-889	9
β-strand	892-893	2	5
β-strand	896	1	11
α-helix	898-902	5
β-strand	909	1	11
β-strand	915-916	2	5
α-helix	923-929	7
α-helix	933-957	25
α-helix	964-979	16
α-helix	995-1017	23
α-helix	1022-1028	7
α-helix	1030-1038	9
α-helix	1039-1041	3
α-helix	1044-1046	3
α-helix	1048-1068	21

Chain B: 29 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	11-16	6
β-strand	26-28	3	1
β-strand	31-35	5	1
β-strand	38-41	4	1
β-strand	48	1	3
β-strand	52-56	5	1
β-strand	62-71	10	1
β-strand	74-79	6	1
β-strand	92-95	4	1
β-strand	101-104	4	12
α-helix	106-108	3
β-strand	111-114	4	13
β-strand	119	1	13
α-helix	124-126	3
β-strand	130-133	4	12
α-helix	138	1
β-strand	139	1	6
α-helix	140	1
α-helix	141-143	3
β-strand	144-145	2	14
β-strand	150	1	15
β-strand	151	1	16
α-helix	156-159	4
α-helix	164	1
β-strand	165	1	15
β-strand	169	1	13
β-strand	172-174	3	13
α-helix	180-190	11
β-strand	193	1	16
α-helix	207-208	2
β-strand	209-217	9	13
α-helix	219-232	14
α-helix	235-237	3
β-strand	238-244	7	13
α-helix	250-253	4
α-helix	255-270	16
β-strand	273-279	7	13
α-helix	281-294	14
β-strand	299	1	17
α-helix	301-303	3
β-strand	305	1	17
α-helix	308-316	9
β-strand	320	1	13
β-strand	321-322	2	14
β-strand	328-336	9	13
α-helix	337	1
α-helix	338-340	3
α-helix	345-353	9
β-strand	356-357	2	18
β-strand	358-359	2	13
β-strand	360	1	19
α-helix	362-366	5
β-strand	373	1	19
β-strand	379-380	2	18
α-helix	383-386	4
α-helix	396-420	25
α-helix	422-424	3
α-helix	427-438	12
α-helix	439-444	6
α-helix	454-465	12
α-helix	470-472	3
α-helix	478-485	8

Chain E: 28 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	25-32	8	1
β-strand	35-39	5	1
β-strand	48-52	5	1
β-strand	57-65	9	1
β-strand	68-73	6	1
β-strand	81	1	20
β-strand	85-92	8	1
β-strand	94-97	4	21
β-strand	105	1	22
β-strand	106	1	23
β-strand	112	1	23
α-helix	113-120	8
β-strand	124	1	24
α-helix	138-139	2
β-strand	140-144	5	25
β-strand	152-154	3	26
β-strand	158-162	5	25
β-strand	171-174	4	25
α-helix	175-176	2
β-strand	180-186	7	26
α-helix	187-188	2
β-strand	190-192	3	25
β-strand	199-203	5	26
β-strand	206-210	5	26
β-strand	214-217	4	21
α-helix	221-223	3
β-strand	224-227	4	22
β-strand	233	1	27
α-helix	239-243	5
β-strand	248	1	27
β-strand	252-254	3	22
α-helix	263-273	11
β-strand	278-738	461	22
α-helix	744-751	8
β-strand	756-757	2	28
β-strand	764-765	2	28
α-helix	766-768	3
β-strand	770-775	6	22
α-helix	781-783	3
α-helix	785-799	15
β-strand	804-810	7	22
α-helix	813-826	14
α-helix	829-830	2
α-helix	839-847	9
β-strand	851-855	5	22
β-strand	862-870	9	22
α-helix	874-876	3
α-helix	881-889	9
β-strand	892-893	2	22
β-strand	896	1	29
α-helix	898-902	5
β-strand	909	1	29
β-strand	915-916	2	22
α-helix	919-929	11
α-helix	933-957	25
α-helix	959-961	3
α-helix	964-975	12
α-helix	976-981	6
α-helix	995-1017	23
α-helix	1022-1028	7
α-helix	1030-1038	9
α-helix	1039-1041	3
α-helix	1051-1053	3
α-helix	1054-1057	4

Chain F: 29 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	16-19	4
β-strand	26-27	2	1
β-strand	31-35	5	1
β-strand	38-41	4	1
β-strand	48	1	20
β-strand	52-56	5	1
α-helix	57	1
β-strand	62-71	10	1
β-strand	74-79	6	1
β-strand	87	1	2
β-strand	92-95	4	1
β-strand	101-104	4	30
α-helix	106-108	3
β-strand	111-114	4	31
β-strand	119	1	31
α-helix	124-126	3
β-strand	130-133	4	30
α-helix	138	1
β-strand	139	1	24
α-helix	140	1
β-strand	144-145	2	31
α-helix	146-147	2
β-strand	150	1	32
β-strand	151-152	2	33
α-helix	156-159	4
α-helix	163-164	2
β-strand	165	1	32
β-strand	169	1	31
β-strand	172-174	3	34
α-helix	180-190	11
β-strand	192-193	2	33
α-helix	207-208	2
β-strand	209-217	9	31
α-helix	219-231	13
β-strand	238-244	7	31
α-helix	250-253	4
α-helix	255-264	10
α-helix	265-269	5
β-strand	273-279	7	31
α-helix	281-294	14
α-helix	297-298	2
β-strand	299	1	35
α-helix	301-303	3
β-strand	305	1	35
α-helix	308-316	9
β-strand	320-322	3	31
β-strand	328-331	4	31
β-strand	334-336	3	34
α-helix	338-340	3
α-helix	345-351	7
β-strand	356-357	2	36
β-strand	358-359	2	34
β-strand	360	1	37
α-helix	362-366	5
β-strand	373	1	37
β-strand	379-380	2	36
α-helix	383-386	4
α-helix	396-420	25
α-helix	422-424	3
α-helix	427-438	12
α-helix	439-444	6
α-helix	454-465	12
α-helix	478-484	7

Chain I: 7 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	28-112	85
α-helix	114-132	19
β-strand	136-141	6	1
α-helix	146-150	5
α-helix	153-163	11
α-helix	168-169	2
β-strand	171-174	4	1
β-strand	187-192	6	1
β-strand	198-202	5	1
α-helix	203-213	11
α-helix	215-223	9

Chain J: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	18-22	5
α-helix	25-58	34
α-helix	61-66	6
α-helix	72-103	32

Chain K: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	37-54	18
α-helix	56-59	4
α-helix	60-112	53
α-helix	114-132	19
β-strand	136-141	6	1
α-helix	146-163	18
α-helix	168-169	2
β-strand	171-174	4	1
α-helix	175	1
α-helix	178-180	3
β-strand	187	1	38
β-strand	188-192	5	1
β-strand	197-199	3	1
β-strand	202	1	38
α-helix	203-213	11
α-helix	215-223	9

Chain L: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	31-36	6
α-helix	42-51	10
α-helix	53-102	50

6 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 catalytic subunit A	A, E	protein	1071	Saccharomyces cerevisiae	P17255 (AlphaFold model)
V-type proton ATPase subunit B	B, F	protein	517	Saccharomyces cerevisiae	P16140 (AlphaFold model)
V-type proton ATPase subunit E	I, K	protein	233	Saccharomyces cerevisiae	P22203 (AlphaFold model)
V-type proton ATPase subunit G	J, L	protein	114	Saccharomyces cerevisiae	P48836 (AlphaFold model)
V-type proton ATPase subunit D	M	protein	256	Saccharomyces cerevisiae	P32610
V-type proton ATPase subunit F	N	protein	117	Saccharomyces cerevisiae	P39111
V-type proton ATPase subunit H	P	protein	478	Saccharomyces cerevisiae	P41807
Regulator of V-ATPase in vacuolar membrane protein 1	x	protein	1357	Saccharomyces cerevisiae	P47104
Regulator of V-ATPase in vacuolar membrane protein 2	y	protein	351	Saccharomyces cerevisiae	Q03956
Suppressor of kinetochore protein 1	z	protein	194	Saccharomyces cerevisiae	P52286

Sequence of entity 1 (A, E), FASTA

>9COP_1 V-type proton ATPase catalytic subunit A (chains A, E)
MAGAIENARKEIKRISLEDHAESEYGAIYSVSGPVVIAENMIGCAMYELVKVGHDNLVGE
VIRIDGDKATIQVYEETAGLTVGDPVLRTGKPLSVELGPGLMETIYDGIQRPLKAIKEES
QSIYIPRGIDTPALDRTIKWQFTPGKFQVGDHISGGDIYGSVFENSLISSHKILLPPRSR
GTITWIAPAGEYTLDEKILEVEFDGKKSDFTLYHTWPVRVPRPVTEKLSADYPLLTGQRV
LDALFPCVQGGTTCIPGAFGCGKTVISQSLSKYSNSDAIIYVGCFAKGTNVLMADGSIEC
IENIEVGNKVMGKDGRPREVIKLPRGRETMYSVVQKSQHRAHKSDSSREVPELLKFTCNA
THELVVRTPRSVRRLSRTIKGVEYFEVITFEMGQKKAPDGRIVELVKEVSKSYPISEGPE
RANELVESYRKASNKAYFEWTIEARDLSLLGSHVRKATYQTYAPILYENDHFFDYMQKSK
FHLTIEGPKVLAYLLGLWIGDGLSDRATFSVDSRDTSLMERVTEYAEKLNLCAEYKDRKE
PQVAKTVNLYSKVVRGNGIRNNLNTENPLWDAIVGLGFLKDGVKNIPSFLSTDNIGTRET
FLAGLIDSDGYVTDEHGIKATIKTIHTSVRDGLVSLARSLGLVVSVNAEPAKVDMNGTKH
KISYAIYMSGGDVLLNVLSKCAGSKKFRPAPAAAFARECRGFYFELQELKEDDYYGITLS
DDSDHQFLLANQVVVHNCGERGNEMAEVLMEFPELYTEMSGTKEPIMKRTTLVANTSNMP
VAAREASIYTGITLAEYFRDQGKNVSMIADSSSRWAEALREISGRLGEMPADQGFPAYLG
AKLASFYERAGKAVALGSPDRTGSVSIVAAVSPAGGDFSDPVTTATLGITQVFWGLDKKL
AQRKHFPSINTSVSYSKYTNVLNKFYDSNYPEFPVLRDRMKEILSNAEELEQVVQLVGKS
ALSDSDKITLDVATLIKEDFLQQNGYSTYDAFCPIWKTFDMMRAFISYHDEAQKAVANGA
NWSKLADSTGDVKHAVSSSKFFEPSRGEKEVHGEFEKLLSTMQERFAESTD

Sequence of entity 2 (B, F), FASTA

>9COP_2 V-type proton ATPase subunit B (chains B, F)
MVLSDKELFAINKKAVEQGFNVKPRLNYNTVSGVNGPLVILEKVKFPRYNEIVNLTLPDG
TVRQGQVLEIRGDRAIVQVFEGTSGIDVKKTTVEFTGESLRIPVSEDMLGRIFDGSGRPI
DNGPKVFAEDYLDINGSPINPYARIYPEEMISTGVSAIDTMNSIARGQKIPIFSASGLPH
NEIAAQICRQAGLVRPTKDVHDGHEENFSIVFAAMGVNLETARFFKQDFEENGSLERTSL
FLNLANDPTIERIITPRLALTTAEYLAYQTERHVLTILTDMSSYADALREVSAAREEVPG
RRGYPGYMYTDLSTIYERAGRVEGRNGSITQIPILTMPNDDITHPIPDLTGYITEGQIFV
DRQLHNKGIYPPINVLPSLSRLMKSAIGEGMTRKDHGDVSNQLYAKYAIGKDAAAMKAVV
GEEALSIEDKLSLEFLEKFEKTFITQGAYEDRTVFESLDQAWSLLRIYPKEMLNRISPKI
LDEFYDRARDDADEDEEDPDTRSSGKKKDASQEESLI

Sequence of entity 3 (I, K), FASTA

>9COP_3 V-type proton ATPase subunit E (chains I, K)
MSSAITALTPNQVNDELNKMQAFIRKEAEEKAKEIQLKADQEYEIEKTNIVRNETNNIDG
NFKSKLKKAMLSQQITKSTIANKMRLKVLSAREQSLDGIFEETKEKLSGIANNRDEYKPI
LQSLIVEALLKLLEPKAIVKALERDVDLIESMKDDIMREYGEKAQRAPLEEIVISNDYLN
KDLVSGGVVVSNASDKIEINNTLEERLKLLSEEALPAIRLELYGPSKTRKFFD

Sequence of entity 4 (J, L), FASTA

>9COP_4 V-type proton ATPase subunit G (chains J, L)
MSQKNGIATLLQAEKEAHEIVSKARKYRQDKLKQAKTDAAKEIDSYKIQKDKELKEFEQK
NAGGVGELEKKAEAGVQGELAEIKKIAEKKKDDVVKILIETVIKPSAEVHINAL

Sequence of entity 5 (M), FASTA

>9COP_5 V-type proton ATPase subunit D (chains M)
MSGNREQVFPTRMTLGLMKTKLKGANQGYSLLKRKSEALTKRFRDITKRIDDAKQKMGRV
MQTAAFSLAEVSYATGENIGYQVQESVSTARFKVRARQENVSGVYLSQFESYIDPEINDF
RLTGLGRGGQQVQRAKEIYSRAVETLVELASLQTAFIILDEVIKVTNRRVNAIEHVIIPR
TENTIAYINSELDELDREEFYRLKKVQEKKQNETAKLDAEMKLKRDRAEQDASEVAADEE
PQGETLVADQEDDVIF

Sequence of entity 6 (N), FASTA

>9COP_6 V-type proton ATPase subunit F (chains N)
AEKRTLIAVIADEDTTTGLLLAGIGQITPETQEKNFFVYQEGKTTKEEITDKFNHFTEER
DDIAILLINQHIAENIRARVDSFTNAFPAILEIPSKDHPYDPEKDSVLKRVRKLFGE

Sequence of entity 7 (P), FASTA

>9COP_7 V-type proton ATPase subunit H (chains P)
MGATKILMDSTHFNEIRSIIRSRSVAWDALARSEELSEIDASTAKALESILVKKNIGDGL
SSSNNAHSGFKVNGKTLIPLIHLLSTSDNEDCKKSVQNLIAELLSSDKYGDDTVKFFQED
PKQLEQLFDVSLKGDFQTVLISGFNVVSLLVQNGLHNVKLVEKLLKNNNLINILQNIEQM
DTCYVCIRLLQELAVIPEYRDVIWLHEKKFMPTLFKILQRATDSQLATRIVATNSNHLGI
QLQYHSLLLIWLLTFNPVFANELVQKYLSDFLDLLKLVKITIKEKVSRLCISIILQCCST
RVKQHKKVIKQLLLLGNALPTVQSLSERKYSDEELRQDISNLKEILENEYQELTSFDEYV
AELDSKLLCWSPPHVDNGFWSDNIDEFKKDNYKIFRQLIELLQAKVRNGDVNAKQEKIII
QVALNDITHVVELLPESIDVLDKTGGKADIMELLNHSDSRVKYEALKATQAIIGYTFK

Sequence of entity 8 (x), FASTA

>9COP_8 Regulator of V-ATPase in vacuolar membrane protein 1 (chains x)
MSLNFLPGRPNATPQTACQATWQNHTIFAYCSGNNLIILTNKFTRLQTIYTQSDCTAVDI
NSQNGFIALSFHNRVLIYKPIHQIMQNPKWTQCCQLFHDDTPVNCLRWSSDNELAIGSDF
LSFWKIKDNFGVYQPILQWNQKQPKPVYNVIISQDSQLIVSIGKYDCNAKLWKRVSIVGE
QAIFNLTMLPHPKPITAMRWKKEPDQVSKNNTASHALYTLCEDKVLRIWSCFEMEKNHTV
QIWGEVPLSPTQKFCVIIDNWIIRQTLSVKDSEIFDISDSDIVILGSMTGEMEVLALNNL
SQDPPKPMTKKTISHKKVKKATMLNDTRYLYLPEIQPYDNVKGKLSFLVHDLQGVIRHLL
IDILQLINNKTEDLSAALEHKFTGHNKSVQKLVRSSDGEALLTTSRFSENGVWYPQKLNH
GVSLRLQNTIQTESPIKFAVVHELGKQVICLLENGALQAWECPTNRKEDSEQKQSYLRVE
TRLKEEKKIHPIVMLNTPEPKHSHERHFTALIFSDGSIKAFEVSLTRGIFEVKSDSLDID
GDDIYKISIIDPVHQTFVSNRPLISLITKKGLTRTYKAIVNYNDRHVQWIKACEINTGIM
NCTCIRGSSTGKLCIVNSTGKVMSLWDLNRGVLEYEETFHNPIEDIDWTSTEYGQSIVSI
GFTGYALLYTQLRYDYTNNTPSYLPIEKIDITAHTAHNIGDSVWMKNGTFVVASGNQFYI
KDKSLDLTDPFTYQSIGSRKILSNDILHLSSVLNGPLPVYHPQFLIQAIYANKLQLVKEL
LLRLFLALRKLDFESQDVSNLDSNLGMDPLKYFIAKDRDYPVESFPDPYPCFNKTVSLAL
TEQLTKTTLPYLTRHQQITLITVIEAVDEVTKNENIVDYNGVRFLLGVKLFLSHKNIQKS
ILMRDVSWALHSDNKEILLSSIDRHITSWNRAREYRIAYWIKEQDLVKKFEDIAKYEFSK
DDKRDPSRCAIFYLALKKKQILLSLWKMAIGHPEQQKMVRFISNDFTVPRWRTAALKNAF
VLLSKHRYMDAAVFFLLTDSLKDCVNVLCKQVHDMDLAIGVCRVYEGDNGPVLGELLTAQ
MLPETIKENDRWKASFIYWKLRKQEVAIKALLTAPIDLENNSSIVDKEVCVNRSFLVEDP
ALLYLYNHLRNRNLKYFIGSLNVEAKIECTLILRVTDILCRMGCNYLAVSLVKNWKFIER
NSIPVQKLLKSPTKDRAYSAIGAMASEPISTARMRPSLFDKFGSPSASDIESPNPKLPNS
LLDDFLQPPPNSTSSNSLAQSSSSAPRSILDEFVSPSYSQHKENLTPKAPNDSVGETDNS
ENRKDKLSKDILDDLSSQKPQKPKKSAITKNLLDDFV

Sequence of entity 9 (y), FASTA

>9COP_9 Regulator of V-ATPase in vacuolar membrane protein 2 (chains y)
MSVDLFPNDRFGAEDKYDNFKDAVKECSWLIEEIVKPQLPNIIDNFSKCLEMLESDQIFK
MPVSNGIPNESNKQNDSPTVKGVITRQGQYIVDFHIVVRFPQFQRGKQVMFRMNTGLNFL
LIQFSKIMTHLKNILEILNQLQVATDVSEFVSKFGVAMELLNHSLILLQNPPRDLVFPED
NNFAMKEMFQDCYSVCESTAHILGLELTLCRNELCIELRNLIKVTKKPWCEIDSKTGRSF
CDQIRNQVTNERNKTLSKILSENGVQVQDSTLLNHIISSFQSEAITLPEAQELLRRGVTF
DNRVVMECEKLIVSTSDPTLISISAKLNSLKASMANHQANLVASKQLSTYK

Sequence of entity 10 (z), FASTA

>9COP_10 Suppressor of kinetochore protein 1 (chains z)
MVTSNVVLVSGEGERFTVDKKIAERSLLLKNYLNDMHDSNLQNNSDSESDSDSETNHKSK
DNNNGDDDDEDDDEIVMPVPNVRSSVLQKVIEWAEHHRDSNFPDEDDDDSRKSAPVDSWD
REFLKVDQEMLYEIILAANYLNIKPLLDAGCKVVAEMIRGRSPEEIRRTFNIVNDFTPEE
EAAIRRENEWAEDR

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	2
MG	Magnesium ion	Mg	2

Primary citation

Structure of yeast RAVE bound to a partial V 1 complex. Wang, H., Tarsio, M., Kane, P.M. et al. Proc Natl Acad Sci U S A (2024) 121:e2414511121-e2414511121. DOI 10.1073/pnas.2414511121 · PubMed

Other PDB entries of the same protein (UniProt P17255 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1GPP 1.35 Å, Crystal structure of the S.cerevisiae Homing Endonuclease PI-SceI Domain I
1DFA 2.0 Å, Crystal structure of pi-scei in C2 space group
1EF0 2.1 Å, Crystal structure of pi-scei miniprecursor
1JVA 2.1 Å, Crystal structure of the VMA1-derived endonuclease bearing the N and C extein propeptides
1VDE 2.4 Å, Pi-scei, a homing endonuclease with protein splicing activity
1UM2 2.9 Å, Crystal Structure of the Vma1-Derived Endonuclease with the Ligated Extein Segment
1LWT 3.2 Å, Crystal structure of the intein homing endonuclease PI-SceI bound to its substrate DNA…
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
1LWS 3.5 Å, Crystal structure of the intein homing endonuclease PI-SceI bound to its recognition…
7TMM 3.5 Å, Complete V1 Complex from Saccharomyces cerevisiae

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