2019-11-06RELPDBePDBePDBe2019-03-312019-05-082019-05-082019-11-06Max Planck SocietyGermanyJapan Society for the Promotion of Science26291008;24000011;15KK0248;16H00748;17K07942JapanGerman Research FoundationFOR1905GermanyCryoEM structure and molecular model of squid hemocyanin (Todarodes pacificus , TpH)Tanaka YKato SStabrin MRaunser SMatsui TGatsogiannis CTanaka YKato SStabrin MRaunser SMatsui TGatsogiannis CCryo-EM reveals the asymmetric assembly of squid hemocyanin.IucrjUK6426437201931098023doi:10.1107/S205225251900321X2052-2525EMD-4750associated EM volumeCryoEM structure and molecular model of squid hemocyanin (Todarodes pacificus , TpH)6r83FULLOVERLAPSquid HemocyaninSquid Hemocyanin01TpH is a decamer of a 400 kDa subunit. Each subunit is composed by 8 paralogous O2 binding functional units (A,B,C,D,D*,E,F,G). The ten subunits of TpH acquire 4 different overall conformations.Todarodes pacificus3.8Hemocyanin subunit 1Japanese flying squid0.37974118810LEVONLLRKNVDTLTPDEILNLQVSLRAMQDDEGASGYQAISAYHGEPADCKAADGSTIVCCLHGMPTFPMWHRLYLVQFEQAL
VAHGSTLGIPYWDWTKPMTQLPELVQHPLFIDPTGKKAKKNVFYSGEIKFENKVTARAVDARLYQASQEGQKNFLLEGVL
NALEQEDFCHFEVQLEVAHNPIHYLVGGRFTHSMSSLEYTSYDPLFFLHHSNVERHFALWQALQKHRGLPTRPNCGLNLF
HSPMEPFGRDTNPFAITKDNSKASSLFDYEHLGYAFDDLSLNGMTIEELEALLKQRRSGARAFANFRLGGIKTSANVRIK
LCIPTEDKRQSDNCDNDAGQFFILGGTNEMPWNFAFPYLHEITDTVLSLGLALDSNYYVTAEVTAINGTLMPTQTIPRPI
VTYIPPQGFKDVNMVNMDTSSLRFRKDISSLTTEEEYELRVAMERFMSDKSINGYQALAEFHGLPAKCPRPDALNRVACC
IHGMATFPHWHRLVVMQFENALFTRGSPIGVPYWDWTKPFTALPSLLADETYVDPYTKETKPNPFFKAPIEFLKAGVHTS
RQIDERLFKQPSKGDHGFLYDGLSLAFEQDDFCDFEVQFEVTHNSIHAWTGGSEPYSMSSLHYTSFDPMFWLHHSQVDRL
WAIWQALQIQRGKPYKTYCANSEVYRPMKPFAFKSPLNNDEKTREHSVPTDVYDYQAELAYTYDTLFFGGLSIRELQRYV
EEAKSKDRVFAGFLLMGIQTSANVDLFVVAGGNEFFVGSIAVLGGSKEMTWRFDRVYKHEITDALGALGVDMFAEYTLRV
DIKDVNGTALPPTAIPPPIVIFVPGIADANVKFDEQHRSRKNVDSMTVSEMNALRTAMAAFAADKEVTGYQQVAAFHGST
QWCPSPDAAQKYACCHHGMATFPHWHRLIALNFENGLRRNGWSGGLPYWDWTRPIDALPALVLEAEYTDANGEAKPNPFF
SGAIDSIGASTSRAPTEALYEKPDFGKYTHLANEIISALEQEDFCDFEVQYEIAHNHIHALVGGTEAVSMASLEYSAFDP
IFMLHHSNVDRIWATWQALQKFRGKAYNSANCAIEILRKPMSPFSLASDINPDAMTREYSVPFDVFNYKKNFHYEYDTLE
LNGLSI(UNK)QLSREINRRKAKNRV(UNK)VTFMLEGLKKSLLVEYFIAADGTDQKMKAGEFYVLGSENEMPWKFDRPY
KSDITYVMDAMKLHYTDKYHVELRITDMTGAEVTDLKLVTSVIYEPGIGNFGEGRRWISPITSASRIRKNLLDFEDGEME
SLRNAFKQMADEGRYEEIASFHGVPAQCPSEDGTMVHTCCLHGMPVFPHWHRLYVSLVEDELLARGSGVAVPYWDWVEPF
DELPRLINEATFYNSRTLQIEPNPFFKGKISFENAETDRDTQPELFGNRYLYDHTLFVFEQTDFCEFEVHYEVLHNTIHS
WLGGRDVHSMSSLDYAAYDPVFFLHHSNVDRLWAIWQELQRYRKLSYNEANCALPLMNQPMRPFSNSTANNDRLTFTNSR
PNDVFDYQNVLHYKYDTLNFAGLSIPQLERILQKNQGRDRIFAGFLLHGIKASADVRIYICVPTGIGEENCGNYAGIFSV
LGGETEMPWQFDRLFRYEITDELKKLGLNQNSHFRVEMELTAVNGSKITQKIFPNPTIIFVPSDVEFEEDTWRDVVTSAN
RIRRNLKDLSKEDMFSLRAAFKRMTDDGRYEEIAAFHGLPAQCPNADGSNIHTCCLHGMPTFPHWHRLYLSLVENELLAR
GSDVAVPYWDWIEPFDSLPGLISDETYKHPKTNEDIENPFHHGKISFADAVTVRKPRDQLFNNRYLYEHALFAFEHTDFC
DFEVHFEVLHNSIHSWIGGPNPHSMSSLDFAAYDPIFFLHHSTVDRLWAIWQDLQRYRKLDYNVANCALNLLNDPMRPFN
NKTANQDHLTFTNSRPNDVFDYQNSLNYKFDSLSFSGLSIPRLDDLLESRQSHDRVFAGFWLSGIKASADVNIHICVPIG
VEHEDCDNYAGTFAVLGGETEMPWAFDRLFRYEISDEMKKLQLTEDSKFRLTTNIIASNGSKVSNDIFPTPTVIFVPKKE
RTEQVSTTKSVRGNLVRKNVDRLSLQEINSLIHALKRMQKDRSSDGFETIASFHALPPLCPNPTAKHRHACCLHGMATFP
QWHRLYVVQFEHSLNRHGAIVGVPYWDWTYPMTEVPGLLTSEKYTDPFTGIETFNPFNHGHISFISPETMTTREVSEHLF
EQPALGKQTWLFNNIILALEQTDYCDFEVQFEIVHNSIHSWLGGKELYSLNHLHYAAYDPAFFLHHSNVDRLWVVWQELQ
KFRGLPAYESNCAIELMSQPLKPFSFGAPYNLNPVTTKYSKPSDVFNYKQNFHYEYDMLEMNGMSIAQLESYIRQERQKD
RVFAGFLLEGFGSSAYATFQVCPDVGDCYEGSHFSVLGGSTEMPWAFDRLYKMEITDILQAMDLKFDSHFTIKTKIVAHN
GTELPESLLPEATIVRIPPSAQNLEVAIPLNRIRRNINSLESRDVQNLMSALKRLKEDESDFGFQTIAGYHGSLMCPTPE
APEYACCLHGMPTFMHWHRVYLLHFEESMRRHGASVAVPYWDWTMPSDNLPSLLGDADYYDAWTDSVIENPFLRGHIKYE
DTYTVREIQPELFALAEGQKESTLFKDVMLMFEQEDYCDFEVQAEVIHNSIHYLIGGHQKYAMSSLMFSSFDPIFYVHHS
MVDRLWAIWQELQKHRKLPHDKAYCALDQMAFPMKPFIWESNPNPTTRAVSTPSKLFDYKSLGYDYDHLNFHGMSIGQLE
ALIQKQKKADRVFAGFLLHGIKISADVHLKICIEADCQEAGVIFVLGGETEMPWHFDRNYKMDITDVLKKRNIPPEALFE
HDSKIRLEVEIKSVDGAVLDPNSLPKPSLIYAPAKGLIIQQVGEYDAGSMVRKNVNSLTPSEIENLRNALAAVQADKTDA
GYQKIASFHGMPLSCQYPDGTAFACCQHGMVTFPHWHRLYMKQMEDALKAKGAKIGIPYWDWTTAFHSLPILVTEPKNNP
FHHGYIDVADTKTTRDPRPQLFDDPEQGDQSFFYRQIAFALEQRDFCDFEIQFEMGHNAIHSWVGGPSPYGMSTLHYTSY
DPLFYVHHSNTDRIWAIWQALQKYRGLPYNSANCEINKLKKPMMPFSSEDNPNEVTKAHSTGYKSFDYQQLNYEYDNLNF
HGMTIPQLEVHLKKIQEKDRVFAGFLLRAIGQSADVNFDVCRKDGECTFGGTFCVLGGDYEMPWAFDRLFLYDISKSLVH
LRLDAHDDFDIKVTIMGIDGKSLPPNLLPSPTILFKPGTGKIsingleParticleparticle2.97.5100.0HEPES200.0CaCl2calcium chlorideQuantifoil R2/1COPPERGLOW DISCHARGEETHANEGATAN CRYOPLUNGE 3FEI TITAN KRIOSOTHERBRIGHT FIELDFIELD EMISSION GUN3000.0FEI TITAN KRIOS AUTOGRID HOLDERNITROGENMicroscope equipped with Cs correctorFEI FALCON II (4k x 4k)1-24150921.056.01359250SPHIRE1.0Initial model was computed from 2D class averages using VIPERC15.1FSC 0.143 CUT-OFFSPHIRE196315MAXIMUM LIKELIHOODSPHIRE1.0MAXIMUM LIKELIHOODSPHIRE1.0SPHIRE1.0RIGID BODY FITCross-correlation coefficient