CryoEM structure of C5b8-CD59

2024-11-06 REL PDBe PDBe PDBe 2022-09-07 2023-02-22 2023-02-22 2024-11-06 European Research Council (ERC) 864751 European Union Cancer Research UK C24523/A26234 United Kingdom CryoEM structure of C5b8-CD59 Bubeck D Couves EC Gardner S Complement, inhibitor, complex, pore-forming, IMMUNE SYSTEM Couves EC Gardner S Voisin TB Bickel JK Stansfeld PJ Tate EW Bubeck D Structural basis for membrane attack complex inhibition by CD59. Nat Commun UK 14 890 890 2023 36797260 doi:10.1038/s41467-023-36441-z 2041-1723 Afonine PV Poon BK Read RJ Sobolev OV Terwilliger TC Urzhumtsev A Adams PD Real-space refinement in PHENIX for cryo-EM and crystallography Acta Crystallogr., Sect. D: Biol. Crystallogr. DK 74 531 544 2018 0907-4449 0766 ABCRE6 8b0f FULLOVERLAP C5b8-CD59 C5b8-CD59 0 1 2 3 4 5 6 7

Inhibited complement membrane attack complex

Complement components C5, C6, C7 and C8 1 1 2 3 4 5 6 Homo sapiens CD59 glycoprotein 1 7 Escherichia coli Complement C5 Homo sapiens 0.188512094 1 LEVO MGLLGILCFLIFLGKTWGQEQTYVISAPKIFRVGASENIVIQVYGYTEAFDATISIKSYPDKKFSYSSGHVHLSSENKFQ NSAILTIQPKQLPGGQNPVSYVYLEVVSKHFSKSKRMPITYDNGFLFIHTDKPVYTPDQSVKVRVYSLNDDLKPAKRETV LTFIDPEGSEVDMVEEIDHIGIISFPDFKIPSNPRYGMWTIKAKYKEDFSTTGTAYFEVKEYVLPHFSVSIEPEYNFIGY KNFKNFEITIKARYFYNKVVTEADVYITFGIREDLKDDQKEMMQTAMQNTMLINGIAQVTFDSETAVKELSYYSLEDLNN KYLYIAVTVIESTGGFSEEAEIPGIKYVLSPYKLNLVATPLFLKPGIPYPIKVQVKDSLDQLVGGVPVTLNAQTIDVNQE TSDLDPSKSVTRVDDGVASFVLNLPSGVTVLEFNVKTDAPDLPEENQAREGYRAIAYSSLSQSYLYIDWTDNHKALLVGE HLNIIVTPKSPYIDKITHYNYLILSKGKIIHFGTREKFSDASYQSINIPVTQNMVPSSRLLVYYIVTGEQTAELVSDSVW LNIEEKCGNQLQVHLSPDADAYSPGQTVSLNMATGMDSWVALAAVDSAVYGVQRGAKKPLERVFQFLEKSDLGCGAGGGL NNANVFHLAGLTFLTNANADDSQENDEPCKEILRPRRTLQKKIEEIAAKYKHSVVKKCCYDGACVNNDETCEQRAARISL GPRCIKAFTECCVVASQLRANISHKDMQLGRLHMKTLLPVSKPEIRSYFPESWLWEVHLVPRRKQLQFALPDSLTTWEIQ GVGISNTGICVADTVKAKVFKDVFLEMNIPYSVVRGEQIQLKGTVYNYRTSGMQFCVKMSAVEGICTSESPVIDHQGTKS SKCVRQKVEGSSSHLVTFTVLPLEIGLHNINFSLETWFGKEILVKTLRVVPEGVKRESYSGVTLDPRGIYGTISRRKEFP YRIPLDLVPKTEIKRILSVKGLLVGEILSAVLSQEGINILTHLPKGSAEAELMSVVPVFYVFHYLETGNHWNIFHSDPLI EKQKLKKKLKEGMLSIMSYRNADYSYSVWKGGSASTWLTAFALRVLGQVNKYVEQNQNSICNSLLWLVENYQLDNGSFKE NSQYQPIKLQGTLPVEARENSLYLTAFTVIGIRKAFDICPLVKIDTALIKADNFLLENTLPAQSTFTLAISAYALSLGDK THPQFRSIVSALKREALVKGNPPIYRFWKDNLQHKDSSVPNTGTARMVETTAYALLTSLNLKDINYVNPVIKWLSEEQRY GGGFYSTQDTINAIEGLTEYSLLVKQLRLSMDIDVSYKHKGALHNYKMTDKNFLGRPVEVLLNDDLIVSTGFGSGLATVH VTTVVHKTSTSEEVCSFYLKIDTQDIEASHYRGYGNSDYKRIVACASYKPSREESSSGSSHAVMDISLPTGISANEEDLK ALVEGVDQLFTDYQIKDGHVILQLNSIPSSDFLCVRFRIFELFEVGFLSPATFTVYEYHRPDKQCTMFYSTSNIKIQKVC EGAACKCVEADCGQMQEELDLTISAETRKQTACKPEIAYAYKVSITSITVENVFVKYKATLLDIYKTGEAVAEKDSEITF IKKVTCTNAELVKGRQYLIMGKEALQIKYNFSFRYIYPLDSLTWIEYWPRDTTCSSCQAFLANLDEFAEDIFLNGC P01031 Complement component C6 Homo sapiens 0.10491817999999999 1 LEVO MARRSVLYFILLNALINKGQACFCDHYAWTQWTSCSKTCNSGTQSRHRQIVVDKYYQENFCEQICSKQETRECNWQRCPI NCLLGDFGPWSDCDPCIEKQSKVRSVLRPSQFGGQPCTAPLVAFQPCIPSKLCKIEEADCKNKFRCDSGRCIARKLECNG ENDCGDNSDERDCGRTKAVCTRKYNPIPSVQLMGNGFHFLAGEPRGEVLDNSFTGGICKTVKSSRTSNPYRVPANLENVG FEVQTAEDDLKTDFYKDLTSLGHNENQQGSFSSQGGSSFSVPIFYSSKRSENINHNSAFKQAIQASHKKDSSFIRIHKVM KVLNFTTKAKDLHLSDVFLKALNHLPLEYNSALYSRIFDDFGTHYFTSGSLGGVYDLLYQFSSEELKNSGLTEEEAKHCV RIETKKRVLFAKKTKVEHRCTTNKLSEKHEGSFIQGAEKSISLIRGGRSEYGAALAWEKGSSGLEEKTFSEWLESVKENP AVIDFELAPIVDLVRNIPCAVTKRNNLRKALQEYAAKFDPCQCAPCPNNGRPTLSGTECLCVCQSGTYGENCEKQSPDYK SNAVDGQWGCWSSWSTCDATYKRSRTRECNNPAPQRGGKRCEGEKRQEEDCTFSIMENNGQPCINDDEEMKEVDLPEIEA DSGCPQPVPPENGFIRNEKQLYLVGEDVEISCLTGFETVGYQYFRCLPDGTWRQGDVECQRTECIKPVVQEVLTITPFQR LYRIGESIELTCPKGFVVAGPSRYTCQGNSWTPPISNSLTCEKDTLTKLKGHCQLGQKQSGSECICMSPEEDCSHHSEDL CVFDTDSNDYFTSPACKFLAEKCLNNQQLHFLHIGSCQDGRQLEWGLERTRLSSNSTKKESCGYDTCYDWEKCSASTSKC VCLLPPQCFKGGNQLYCVKMGSSTSEKTLNICEVGTIRCANRKMEILHPGKCLA P13671 Complement component C7 Homo sapiens 0.093625328 1 LEVO MKVISLFILVGFIGEFQSFSSASSPVNCQWDFYAPWSECNGCTKTQTRRRSVAVYGQYGGQPCVGNAFETQSCEPTRGCP TEEGCGERFRCFSGQCISKSLVCNGDSDCDEDSADEDRCEDSERRPSCDIDKPPPNIELTGNGYNELTGQFRNRVINTKS FGGQCRKVFSGDGKDFYRLSGNVLSYTFQVKINNDFNYEFYNSTWSYVKHTSTEHTSSSRKRSFFRSSSSSSRSYTSHTN EIHKGKSYQLLVVENTVEVAQFINNNPEFLQLAEPFWKELSHLPSLYDYSAYRRLIDQYGTHYLQSGSLGGEYRVLFYVD SEKLKQNDFNSVEEKKCKSSGWHFVVKFSSHGCKELENALKAASGTQNNVLRGEPFIRGGGAGFISGLSYLELDNPAGNK RRYSAWAESVTNLPQVIKQKLTPLYELVKEVPCASVKKLYLKWALEEYLDEFDPCHCRPCQNGGLATVEGTHCLCHCKPY TFGAACEQGVLVGNQAGGVDGGWSCWSSWSPCVQGKKTRSRECNNPPPSGGGRSCVGETTESTQCEDEELEHLRLLEPHC FPLSLVPTEFCPSPPALKDGFVQDEGTMFPVGKNVVYTCNEGYSLIGNPVARCGEDLRWLVGEMHCQKIACVLPVLMDGI QSHPQKPFYTVGEKVTVSCSGGMSLEGPSAFLCGSSLKWSPEMKNARCVQKENPLTQAVPKCQRWEKLQNSRCVCKMPYE CGPSLDVCAQDERSKRILPLTVCKMHVLHCQGRNYTLTGRDSCTLPASAEKACGACPLWGKCDAESSKCVCREASECEEE GFSICVEVNGKEQTMSECEAGALRCRGQSISVTSIRPCAAETQ P10643 Complement component C8 beta chain Homo sapiens 0.067136891 1 LEVO MKNSRTWAWRAPVELFLLCAALGCLSLPGSRGERPHSFGSNAVNKSFAKSRQMRSVDVTLMPIDCELSSWSSWTTCDPCQ KKRYRYAYLLQPSQFHGEPCNFSDKEVEDCVTNRPCRSQVRCEGFVCAQTGRCVNRRLLCNGDNDCGDQSDEANCRRIYK KCQHEMDQYWGIGSLASGINLFTNSFEGPVLDHRYYAGGCSPHYILNTRFRKPYNVESYTPQTQGKYEFILKEYESYSDF ERNVTEKMASKSGFSFGFKIPGIFELGISSQSDRGKHYIRRTKRFSHTKSVFLHARSDLEVAHYKLKPRSLMLHYEFLQR VKRLPLEYSYGEYRDLFRDFGTHYITEAVLGGIYEYTLVMNKEAMERGDYTLNNVHACAKNDFKIGGAIEEVYVSLGVSV GKCRGILNEIKDRNKRDTMVEDLVVLVRGGASEHITTLAYQELPTADLMQEWGDAVQYNPAIIKVKVEPLYELVTATDFA YSSTVRQNMKQALEEFQKEVSSCHCAPCQGNGVPVLKGSRCDCICPVGSQGLACEVSYRKNTPIDGKWNCWSNWSSCSGR RKTRQRQCNNPPPQNGGSPCSGPASETLDCS P07358 Complement component C8 alpha chain Homo sapiens 0.065239152 1 LEVO MFAVVFFILSLMTCQPGVTAQEKVNQRVRRAATPAAVTCQLSNWSEWTDCFPCQDKKYRHRSLLQPNKFGGTICSGDIWD QASCSSSTTCVRQAQCGQDFQCKETGRCLKRHLVCNGDQDCLDGSDEDDCEDVRAIDEDCSQYEPIPGSQKAALGYNILT QEDAQSVYDASYYGGQCETVYNGEWRELRYDSTCERLYYGDDEKYFRKPYNFLKYHFEALADTGISSEFYDNANDLLSKV KKDKSDSFGVTIGIGPAGSPLLVGVGVSHSQDTSFLNELNKYNEKKFIFTRIFTKVQTAHFKMRKDDIMLDEGMLQSLME LPDQYNYGMYAKFINDYGTHYITSGSMGGIYEYILVIDKAKMESLGITSRDITTCFGGSLGIQYEDKINVGGGLSGDHCK KFGGGKTERARKAMAVEDIISRVRGGSSGWSGGLAQNRSTITYRSWGRSLKYNPVVIDFEMQPIHEVLRHTSLGPLEAKR QNLRRALDQYLMEFNACRCGPCFNNGVPILEGTSCRCQCRLGSLGAACEQTQTEGAKADGSWSCWSSWSVCRAGIQERRR ECDNPAPQNGGASCPGRKVQTQAC P07357 Complement component C8 gamma chain Homo sapiens 0.022302423999999998 1 LEVO MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQFAGTWLLVAVGSACRFLQEQGHRAEATTLHVAPQ GTAMAVSTFRKLDGICWQVRQLYGDTGVLGRFLLQARDARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDS VLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQFHVLDEVRR P07360 CD59 glycoprotein Escherichia coli 0.013355329999999999 1 Escherichia coli LEVO MGIQGGSVLFGLLLVLAVFCHSGHSLQCYNCPNPTADCKTAVNCSSDFDACLITKAGLQVYNKCWKFEHCNFNDVTTRLR ENELTYYCCKKDLCNFNEQLENGGTSLSEKTVLLLVTPFL P13987 CALCIUM ION 4.0078e-05 2 CA 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 1 NAG singleParticle particle 7.5 Quantifoil R1.2/1.3 COPPER 300 GRAPHENE OXIDE HOLEY GLOW DISCHARGE 60 NITROGEN ETHANE 95 294 FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 100.0 2.7 0.9 2.4 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN FEI FALCON IV (4k x 4k) 4096 4096 2 12805 9.8 50.0 1 1138825

CrYOLO neural network based particle picking, standard model, low threshold (0.01).

An initial model was generated using ab-inito reconstruction in cryoSPARC. 2 BACK PROJECTION 3.0 FSC 0.143 CUT-OFF RELION 3.1 206782 MAXIMUM LIKELIHOOD cryoSPARC 3.3.2 MAXIMUM LIKELIHOOD cryoSPARC 3.3.2 4 51965.0 RELION 3.1

3D Classification was used to remove junk particles and particles with graphene oxide edges.

emd_15779.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 448 448 448 0 0 0 448 448 448 524.60803 524.60803 524.60803 90.0 90.0 90.0 X Y Z -4.269096 9.492267999999999 0.00413231 0.12551086 1.1710001 1.1710001 1.1710001 0.75 AUTHOR ::::EMDATABANK.org::::EMD-15779:::: CryoEM reconstruction of C5b8-CD59. FLEXIBLE FIT

Initial rigid body fits were performed using UCSF Chimera and UCSF ChimeraX. Carbohydrates were added using Coot. Models were refined iteratively using Isolde and Phenix Real Space Refine.

REAL 87.0 emd_15779_msk_1.map emd_15779_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 448 448 448 0 0 0 448 448 448 524.60803 524.60803 524.60803 90.0 90.0 90.0 X Y Z -1.4060645 5.4077115 0.00435016 0.14204846 1.1710001 1.1710001 1.1710001 AUTHOR ::::EMDATABANK.org::::EMD-15779:::: CryoEM reconstruction of C5b8-CD59. emd_15779_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 448 448 448 0 0 0 448 448 448 524.60803 524.60803 524.60803 90.0 90.0 90.0 X Y Z -1.5115308 5.1129675 0.0044070715 0.14199418 1.1710001 1.1710001 1.1710001 AUTHOR ::::EMDATABANK.org::::EMD-15779:::: CryoEM reconstruction of C5b8-CD59.