Structure analysis

Human V-ATPase in state 2 with SidK and mEAK-7

Electron Microscopy
3.6Å resolution
Assembly composition:
hetero 36-mer (preferred)
Entry contents: 18 distinct polypeptide molecules

Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero 36-mer
Accessible surface area: 356325.1 Å2
Buried surface area: 136159.26 Å2
Dissociation area: 1,177.95 Å2
Dissociation energy (ΔGdiss): -3.77 kcal/mol
Dissociation entropy (TΔSdiss): 14.78 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-127432

Macromolecules

Chain: R
Length: 837 amino acids
Theoretical weight: 96.51 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q93050 (Residues: 1-837; Coverage: 100%)
Gene names: ATP6N1, ATP6N1A, ATP6V0A1, VPP1
Pfam: V-type ATPase 116kDa subunit family
InterPro:
PDBe-KB: UniProt Coverage View: Q93050  
1837100200300400500600700800
 
200400600800MGELFRSEEMTLAQLFLQSEAAYCCVSELGELGKVQFRDLNPDVNVFQRKFVNEVRRCEEMDRKLRFVEKEIRKANIPIMDTGENPEVPFPRDMIDLEANFEKIENELKEINTNQEALKRNFLELTELKFILRKTQQFFDEMADPDLLEESSSLLEPSEMGRGTPLRLGFVAGVINRERIPTFERMLWRVCRGNVFLRQAEIENPLEDPVTGDYVHKSVFIIFFQGDQLKNRVKKICEGFRASLYPCPETPQERKEMASGVNTRIDDLQMVLNQTEDHRQRVLQAAAKNIRVWFIKVRKMKAIYHTLNLCNIDVTQKCLIAEVWCPVTDLDSIQFALRRGTEHSGSTVPSILNRMQTNQTPPTYNKTNKFTYGFQNIVDAYGIGTYREINPAPYTIITFPFLFAVMFGDFGHGILMTLFAVWMVLRESRILSQKNENEMFSTVFSGRYIILLMGVFSMYTGLIYNDCFSKSLNIFGSSWSVRPMFTYNWTEETLRGNPVLQLNPALPGVFGGPYPFGIDPIWNIATNKLTFLNSFKMKMSVILGIIHMLFGVSLSLFNHIYFKKPLNIYFGFIPEIIFMTSLFGYLVILIFYKWTAYDAHTSENAPSLLIHFINMFLFSYPESGYSMLYSGQKGIQCFLVVVALLCVPWMLLFKPLVLRRQYLRRKHLGTLNFGGIRVGNGPTEEDAEIIQHDQLSTHSEDADEPSEDEVFDFGDTMVHQAIHTIEYCLGCISNTASYLRLWALSLAHAQLSEVLWTMVIHIGLSVKSLAGGLVLFFFFTAFATLTVAILLIMEGLSAFLHALRLHWVEFQNKFYSGTGFKFLPFSFEHIREGKFEE
UniProt
Q93050
Chains
Domains
Ligand binding sites
Interaction interfaces
Sequence conservation

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Chain: O
Length: 382 amino acids
Theoretical weight: 44 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P21283 (Residues: 1-382; Coverage: 100%)
Gene names: ATP6C, ATP6D, ATP6V1C1, VATC
Pfam: V-ATPase subunit C
InterPro:
PDBe-KB: UniProt Coverage View: P21283  
138250100150200250300350
 
100200300MTEFWLISAPGEKTCQQTWEKLHAATSKNNNLAVTSKFNIPDLKVGTLDVLVGLSDELAKLDAFVEGVVKKVAQYMADVLEDSKDKVQENLLANGVDLVTYITRFQWDMAKYPIKQSLKNISEIIAKGVTQIDNDLKSRASAYNNLKGNLQNLERKNAGSLLTRSLAEIVKKDDFVLDSEYLVTLLVVVPKLNHNDWIKQYETLAEMVVPRSSNVLSEDQDSYLCNVTLFRKAVDDFRHKARENKFIVRDFQYNEEEMKADKEEMNRLSTDKKKQFGPLVRWLKVNFSEAFIAWIHVKALRVFVESVLRYGLPVNFQAMLLQPNKKTLKKLREVLHELYKHLDSSAAAIIDAPMDIPGLNLSQQEYYPYVYYKIDCNLLEFK
UniProt
P21283
Chains
Domains
Sequence conservation

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Chains: H, I, J
Length: 226 amino acids
Theoretical weight: 26.18 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P36543 (Residues: 1-226; Coverage: 100%)
Gene names: ATP6E, ATP6E2, ATP6V1E1
Pfam: ATP synthase (E/31 kDa) subunit
InterPro:
PDBe-KB: UniProt Coverage View: P36543  
122620406080100120140160180200220
 
100200MALSDADVQKQIKHMMAFIEQEANEKAEEIDAKAEEEFNIEKGRLVQTQRLKIMEYYEKKEKQIEQQKKIQMSNLMNQARLKVLRARDDLITDLLNEAKQRLSKVVKDTTRYQVLLDGLVLQGLYQLLEPRMIVRCRKQDFPLVKAAVQKAIPMYKIATKNDVDVQIDQESYLPEDIAGGVEIYNGDRKIKVSNTLESRLDLIAQQMMPEVRGALFGANANRKFLD
UniProt
P36543
Chains
Domains
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Chains: K, L, M
Length: 118 amino acids
Theoretical weight: 13.78 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O75348 (Residues: 1-118; Coverage: 100%)
Gene names: ATP6G, ATP6G1, ATP6J, ATP6V1G1
Pfam: Vacuolar (H+)-ATPase G subunit
InterPro: Vacuolar (H+)-ATPase G subunit
PDBe-KB: UniProt Coverage View: O75348  
1118102030405060708090100110
 
50100MASQSQGIQQLLQAEKRAAEKVSEARKRKNRRLKQAKEEAQAEIEQYRLQREKEFKAKEAAALGSRGSCSTEVEKETQEKMTILQTYFRQNRDEVLDNLLAFVCDIRPEIHENYRING
UniProt
O75348
Chains
Domains
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Chain: S
Length: 81 amino acids
Theoretical weight: 9.38 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O15342 (Residues: 1-81; Coverage: 100%)
Gene names: ATP6H, ATP6V0E, ATP6V0E1
Pfam: ATP synthase subunit H
InterPro:
PDBe-KB: UniProt Coverage View: O15342  
1811020304050607080
 
20406080MAYHGLTVPLIVMSVFWGFVGFLVPWFIPKGPNRGVIITMLVTCSVCCYLFWLIAILAQLNPLFGPQLKNETIWYLKYHWP
UniProt
O15342
Chains
Domains
Ligand binding sites
Interaction interfaces
Sequence conservation

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Chain: T
Length: 137 amino acids
Theoretical weight: 15.44 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q6P5S7 (Residues: 1-137; Coverage: 100%)
Gene name: RNASEK
InterPro: Ribonuclease kappa
PDBe-KB: UniProt Coverage View: Q6P5S7  
1137102030405060708090100110120130
 
50100MGWLRPGPRPLCPPARASWAFSHRFPSPLAPRRSPTPFFMASLLCCGPKLAACGIVLSAWGVIMLIMLGIFFNVHSAVLIEDVPFTEKDFENGPQNIYNLYEQVSYNCFIAAGLYLLLGGFSFCQVRLNKRKEYMVR
UniProt
Q6P5S7
Chains
Domains
Interaction interfaces
Sequence conservation

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PDBe-KB: UniProt Coverage View: Q15904  
147050100150200250300350400450
 
200400MMAAMATARVRMGPRCAQALWRMPWLPVFLSLAAAAAAAAAEQQVPLVLWSSDRDLWAPAADTHEGHITSDLQLSTYLDPALELGPRNVLLFLQDKLSIEDFTAYGGVFGNKQDSAFSNLENALDLAPSSLVLPAVDWYAVSTLTTYLQEKLGASPLHVDLATLRELKLNASLPALLLIRLPYTASSGLMAPREVLTGNDEVIGQVLSTLKSEDVPYTAALTAVRPSRVARDVAVVAGGLGRQLLQKQPVSPVIHPPVSYNDTAPRILFWAQNFSVAYKDQWEDLTPLTFGVQELNLTGSFWNDSFARLSLTYERLFGTTVTFKFILANRLYPVSARHWFTMERLEVHSNGSVAYFNASQVTGPSIYSFHCEYVSSLSKKGSLLVARTQPSPWQMMLQDFQIQAFNVMGEQFSYASDCASFFSPGIWMGLLTSLFMLFIFTYGLHMILSLKTMDRFDDHKGPTISLTQIV
UniProt
Q15904
Chains
Domains
Ligand binding sites
Interaction interfaces
Sequence conservation

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Chain: V
Length: 350 amino acids
Theoretical weight: 39.05 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O75787 (Residues: 1-350; Coverage: 100%)
Gene names: ATP6AP2, ATP6IP2, CAPER, ELDF10, HT028, MSTP009, PSEC0072
Pfam: Renin receptor-like protein
InterPro: Renin receptor-like
PDBe-KB: UniProt Coverage View: O75787  
135050100150200250300350
 
100200300MAVFVVLLALVAGVLGNEFSILKSPGSVVFRNGNWPIPGERIPDVAALSMGFSVKEDLSWPGLAVGNLFHRPRATVMVMVKGVNKLALPPGSVISYPLENAVPFSLDSVANSIHSLFSEETPVVLQLAPSEERVYMVGKANSVFEDLSVTLRQLRNRLFQENSVLSSLPLNSLSRNNEVDLLFLSELQVLHDISSLLSRHKHLAKDHSPDLYSLELAGLDEIGKRYGEDSEQFRDASKILVDALQKFADDMYSLYGGNAVVELVTVKSFDTSLIRKTRTILEAKQAKNPASPYNLAYKYNFEYSVVFNMVLWIMIALALAVIITSYNIWNMDPGYDSIIYRMTNQKIRMD
UniProt
O75787
PRO_0000447864
PRO_0000447865
Chains
Domains
Interaction interfaces
Sequence conservation

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Chain: 0
Length: 205 amino acids
Theoretical weight: 21.42 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q99437 (Residues: 1-205; Coverage: 100%)
Gene names: ATP6F, ATP6V0B
Pfam: ATP synthase subunit C
InterPro:
PDBe-KB: UniProt Coverage View: Q99437  
120520406080100120140160180200
 
50100150200MTGLALLYSGVFVAFWACALAVGVCYTIFDLGFRFDVAWFLTETSPFMWSNLGIGLAISLSVVGAAWGIYITGSSIIGGGVKAPRIKTKNLVSIIFCEAVAIYGIIMAIVISNMAEPFSATDPKAIGHRNYHAGYSMFGAGLTVGLSNLFCGVCVGIVGSGAALADAQNPSLFVKILIVEIFGSAIGLFGVIVAILQTSRVKMGD
UniProt
Q99437
Chains
Domains
Interaction interfaces
Sequence conservation

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Chains: 1, 2, 3, 4, 5, 6, 7, 8, 9
Length: 155 amino acids
Theoretical weight: 15.74 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P27449 (Residues: 1-155; Coverage: 100%)
Gene names: ATP6C, ATP6L, ATP6V0C, ATPL
Pfam: ATP synthase subunit C
InterPro:
PDBe-KB: UniProt Coverage View: P27449  
115520406080100120140
 
50100150MSESKSGPEYASFFAVMGASAAMVFSALGAAYGTAKSGTGIAAMSVMRPEQIMKSIIPVVMAGIIAIYGLVVAVLIANSLNDDISLYKSFLQLGAGLSVGLSGLAAGFAIGIVGDAGVRGTAQQPRLFVGMILILIFAEVLGLYGLIVALILSTK
UniProt
P27449
Chains
Domains
Interaction interfaces
Sequence conservation

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PDBe-KB: UniProt Coverage View: P61421  
135150100150200250300350
 
100200300MSFFPELYFNVDNGYLEGLVRGLKAGVLSQADYLNLVQCETLEDLKLHLQSTDYGNFLANEASPLTVSVIDDRLKEKMVVEFRHMRNHAYEPLASFLDFITYSYMIDNVILLITGTLHQRSIAELVPKCHPLGSFEQMEAVNIAQTPAELYNAILVDTPLAAFFQDCISEQDLDEMNIEIIRNTLYKAYLESFYKFCTLLGGTTADAMCPILEFEADRRAFIITINSFGTELSKEDRAKLFPHCGRLYPEGLAQLARADDYEQVKNVADYYPEYKLLFEGAGSNPGDKTLEDRFFEHEVKLNKLAFLNQFHFGVFYAFVKLKEQECRNIVWIAECIAQRHRAKIDNYIPIF
UniProt
P61421
Chains
Domains
Interaction interfaces
Sequence conservation

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PDBe-KB: UniProt Coverage View: P38606  
161750100150200250300350400450500550600
 
200400600MDFSKLPKILDEDKESTFGYVHGVSGPVVTACDMAGAAMYELVRVGHSELVGEIIRLEGDMATIQVYEETSGVSVGDPVLRTGKPLSVELGPGIMGAIFDGIQRPLSDISSQTQSIYIPRGVNVSALSRDIKWDFTPCKNLRVGSHITGGDIYGIVSENSLIKHKIMLPPRNRGTVTYIAPPGNYDTSDVVLELEFEGVKEKFTMVQVWPVRQVRPVTEKLPANHPLLTGQRVLDALFPCVQGGTTAIPGAFGCGKTVISQSLSKYSNSDVIIYVGCGERGNEMSEVLRDFPELTMEVDGKVESIMKRTALVANTSNMPVAAREASIYTGITLSEYFRDMGYHVSMMADSTSRWAEALREISGRLAEMPADSGYPAYLGARLASFYERAGRVKCLGNPEREGSVSIVGAVSPPGGDFSDPVTSATLGIVQVFWGLDKKLAQRKHFPSVNWLISYSKYMRALDEYYDKHFTEFVPLRTKAKEILQEEEDLAEIVQLVGKASLAETDKITLEVAKLIKDDFLQQNGYTPYDRFCPFYKTVGMLSNMIAFYDMARRAVETTAQSDNKITWSIIREHMGDILYKLSSMKFKDPLKDGEAKIKSDYAQLLEDMQNAFRSLED
UniProt
P38606
Chains
Domains
Ligand binding sites
Interaction interfaces
Sequence conservation

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PDBe-KB: UniProt Coverage View: P21281  
151150100150200250300350400450500
 
200400MALRAMRGIVNGAAPELPVPTGGPAVGAREQALAVSRNYLSQPRLTYKTVSGVNGPLVILDHVKFPRYAEIVHLTLPDGTKRSGQVLEVSGSKAVVQVFEGTSGIDAKKTSCEFTGDILRTPVSEDMLGRVFNGSGKPIDRGPVVLAEDFLDIMGQPINPQCRIYPEEMIQTGISAIDGMNSIARGQKIPIFSAAGLPHNEIAAQICRQAGLVKKSKDVVDYSEENFAIVFAAMGVNMETARFFKSDFEENGSMDNVCLFLNLANDPTIERIITPRLALTTAEFLAYQCEKHVLVILTDMSSYAEALREVSAAREEVPGRRGFPGYMYTDLATIYERAGRVEGRNGSITQIPILTMPNDDITHPIPDLTGYITEGQIYVDRQLHNRQIYPPINVLPSLSRLMKSAIGEGMTRKDHADVSNQLYACYAIGKDVQAMKAVVGEEALTSDDLLYLEFLQKFERNFIAQGPYENRTVFETLDIGWQLLRIFPKEMLKRIPQSTLSEFYPRDSAKH
UniProt
P21281
Chains
Domains
Ligand binding sites
Interaction interfaces
Sequence conservation

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Chains: X, Y, Z
Length: 573 amino acids
Theoretical weight: 65.51 KDa
Source organism: Legionella pneumophila
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5ZWW6 (Residues: 1-573; Coverage: 100%)
Gene name: lpg0968
PDBe-KB: UniProt Coverage View: Q5ZWW6  
157350100150200250300350400450500550
 
200400MSFIKVGIKMGGLTSEQYHSQVVGKIGYIARCMQTIDPENNLKKIREDYQDVLIWAEKNYRFEEILEASKSGKCPNDLDALSRRSLILQELLRLVSSISPFKMKLDLIESQYEKMKQHVNLWKSDYHVKLNQLNQLTDYLKNAAPTPKNNFLRAMTSVLQMQIAQYGITEDNEGINQLFKLGLHLLAMANEKIDEQYHLFKGYVKDQPEESPFEGILPAEDQKILVKTMIDYAMPKLSSKVLQDKLSALSSSDVLTKTLLDSIDRIVKENEKLNALSKVKLGKFGLDIREIEVIYSQALKISPQDALQYTAQQCDAQLLSMAFPDSQNYIIESISNKKVKTIAELIHSKEFIYQIIKTEVFKQVDPNEKIRLQAATELYQLLGRIMDKQINLFTKMNLEQINEYIQTKTKAILDKIPERVELLTFMGFEIPTFKGIETLMTDISHSQDNETLAIAQEFYTNIKNAKNQLLGDKLIEDITPQDVEKFFNQCSQYGSEAAEKLADNRPVLTKIADILTAIARWAISLIGFNTPPQFLAPTRTCVDQVSDEITKIKLKLEDTLGSLQKVQEESLSL
UniProt
Q5ZWW6
Chains
Interaction interfaces
Sequence conservation

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Chain: G
Length: 247 amino acids
Theoretical weight: 28.31 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y5K8 (Residues: 1-247; Coverage: 100%)
Gene names: ATP6M, ATP6V1D, VATD
Pfam: ATP synthase subunit D
InterPro: ATPase, V1 complex, subunit D
PDBe-KB: UniProt Coverage View: Q9Y5K8  
124720406080100120140160180200220240
 
100200MSGKDRIEIFPSRMAQTIMKARLKGAQTGRNLLKKKSDALTLRFRQILKKIIETKMLMGEVMREAAFSLAEAKFTAGDFSTTVIQNVNKAQVKIRAKKDNVAGVTLPVFEHYHEGTDSYELTGLARGGEQLAKLKRNYAKAVELLVELASLQTSFVTLDEAIKITNRRVNAIEHVIIPRIERTLAYIITELDEREREEFYRLKKIQEKKKILKEKSEKDLEQRRAAGEVLEPANLLAEEKDEDLLFE
UniProt
Q9Y5K8
Chains
Domains
Interaction interfaces
Sequence conservation

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Chain: N
Length: 119 amino acids
Theoretical weight: 13.39 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q16864 (Residues: 1-119; Coverage: 100%)
Gene names: ATP6S14, ATP6V1F, VATF
Pfam: ATP synthase (F/14-kDa) subunit
InterPro:
PDBe-KB: UniProt Coverage View: Q16864  
1119102030405060708090100110
 
50100MAGRGKLIAVIGDEDTVTGFLLGGIGELNKNRHPNFLVVEKDTTINEIEDTFRQFLNRDDIGIILINQYIAEMVRHALDAHQQSIPAVLEIPSKEHPYDAAKDSILRRARGMFTAEDLR
UniProt
Q16864
Chains
Domains
Interaction interfaces
Sequence conservation

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Chain: P
Length: 483 amino acids
Theoretical weight: 55.95 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9UI12 (Residues: 1-483; Coverage: 100%)
Gene names: ATP6V1H, CGI-11
Pfam:
InterPro:
PDBe-KB: UniProt Coverage View: Q9UI12  
148350100150200250300350400450
 
200400MTKMDIRGAVDAAVPTNIIAAKAAEVRANKVNWQSYLQGQMISAEDCEFIQRFEMKRSPEEKQEMLQTEGSQCAKTFINLMTHICKEQTVQYILTMVDDMLQENHQRVSIFFDYARCSKNTAWPYFLPMLNRQDPFTVHMAARIIAKLAAWGKELMEGSDLNYYFNWIKTQLSSQKLRGSGVAVETGTVSSSDSSQYVQCVAGCLQLMLRVNEYRFAWVEADGVNCIMGVLSNKCGFQLQYQMIFSIWLLAFSPQMCEHLRRYNIIPVLSDILQESVKEKVTRIILAAFRNFLEKSTERETRQEYALAMIQCKVLKQLENLEQQKYDDEDISEDIKFLLEKLGESVQDLSSFDEYSSELKSGRLEWSPVHKSEKFWRENAVRLNEKNYELLKILTKLLEVSDDPQVLAVAAHDVGEYVRHYPRGKRVIEQLGGKQLVMNHMHHEDQQVRYNALLAVQKLMVHNWEYLGKQLQSEQPQTAAARS
UniProt
Q9UI12
Chains
Domains
Sequence conservation

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Chain: W
Length: 456 amino acids
Theoretical weight: 51.06 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q6P9B6 (Residues: 1-456; Coverage: 100%)
Gene names: KIAA1609, MEAK7, TLDC1
Pfam: TLD
InterPro: TLDc domain
PDBe-KB: UniProt Coverage View: Q6P9B6  
145650100150200250300350400450
 
200400MGNSRSRVGRSFCSQFLPEEQAEIDQLFDALSSDKNSPNVSSKSFSLKALQNHVGEALPPEMVTRLYDGMRRVDLTGKAKGPSENVSQEQFTASMSHLLKGNSEEKSLMIMKMISATEGPVKAREVQKFTEDLVGSVVHVLSHRQELRGWTGKEAPGPNPRVQVLAAQLLSDMKLQDGKRLLGPQWLDYDCDRAVIEDWVFRVPHVAIFLSVVICKGFLILCSSLDLTTLVPERQVDQGRGFESILDVLSVMYINAQLPREQRHRWCLLFSSELHGHSFSQLCGHITHRGPCVAVLEDHDKHVFGGFASCSWEVKPQFQGDNRCFLFSICPSMAVYTHTGYNDHYMYLNHGQQTIPNGLGMGGQHNYFGLWVDVDFGKGHSRAKPTCTTYNSPQLSAQENFQFDKMEVWAVGDPSEEQLAKGNKSILDADPEAQALLEISGHSRHSEGLREVPDDE
UniProt
Q6P9B6
Chains
Domains
Interaction interfaces
Sequence conservation

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