+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12649 | ||||||||||||
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Title | cryoEM reconstruction of 1C9-sMAC | ||||||||||||
Map data | Locally sharpened 1C9-sMAC map | ||||||||||||
Sample |
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Function / homology | Function and homology information cell killing / Terminal pathway of complement / membrane attack complex / complement binding / other organism cell membrane / Activation of C3 and C5 / negative regulation of macrophage chemotaxis / complement activation, alternative pathway / complement activation / chemokine activity ...cell killing / Terminal pathway of complement / membrane attack complex / complement binding / other organism cell membrane / Activation of C3 and C5 / negative regulation of macrophage chemotaxis / complement activation, alternative pathway / complement activation / chemokine activity / retinol binding / endopeptidase inhibitor activity / positive regulation of vascular endothelial growth factor production / positive regulation of chemokine production / complement activation, classical pathway / Peptide ligand-binding receptors / Regulation of Complement cascade / protein homooligomerization / chemotaxis / positive regulation of immune response / extracellular vesicle / G alpha (i) signalling events / in utero embryonic development / killing of cells of another organism / blood microparticle / cell surface receptor signaling pathway / inflammatory response / immune response / G protein-coupled receptor signaling pathway / innate immune response / signaling receptor binding / protein-containing complex binding / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||||||||
Authors | Menny A / Couves EC / Bubeck D | ||||||||||||
Funding support | European Union, United Kingdom, 3 items
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Citation | Journal: Nat Commun / Year: 2021 Title: Structural basis of soluble membrane attack complex packaging for clearance. Authors: Anaïs Menny / Marie V Lukassen / Emma C Couves / Vojtech Franc / Albert J R Heck / Doryen Bubeck / Abstract: Unregulated complement activation causes inflammatory and immunological pathologies with consequences for human disease. To prevent bystander damage during an immune response, extracellular ...Unregulated complement activation causes inflammatory and immunological pathologies with consequences for human disease. To prevent bystander damage during an immune response, extracellular chaperones (clusterin and vitronectin) capture and clear soluble precursors to the membrane attack complex (sMAC). However, how these chaperones block further polymerization of MAC and prevent the complex from binding target membranes remains unclear. Here, we address that question by combining cryo electron microscopy (cryoEM) and cross-linking mass spectrometry (XL-MS) to solve the structure of sMAC. Together our data reveal how clusterin recognizes and inhibits polymerizing complement proteins by binding a negatively charged surface of sMAC. Furthermore, we show that the pore-forming C9 protein is trapped in an intermediate conformation whereby only one of its two transmembrane β-hairpins has unfurled. This structure provides molecular details for immune pore formation and helps explain a complement control mechanism that has potential implications for how cell clearance pathways mediate immune homeostasis. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12649.map.gz | 217.6 MB | EMDB map data format | |
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Header (meta data) | emd-12649-v30.xml emd-12649.xml | 23 KB 23 KB | Display Display | EMDB header |
Images | emd_12649.png | 51.4 KB | ||
Others | emd_12649_half_map_1.map.gz emd_12649_half_map_2.map.gz | 194.6 MB 194.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12649 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12649 | HTTPS FTP |
-Validation report
Summary document | emd_12649_validation.pdf.gz | 428.1 KB | Display | EMDB validaton report |
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Full document | emd_12649_full_validation.pdf.gz | 427.6 KB | Display | |
Data in XML | emd_12649_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | emd_12649_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12649 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12649 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12649.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Locally sharpened 1C9-sMAC map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.047 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: Half map 2 of 1C9-sMAC reconstruction
File | emd_12649_half_map_1.map | ||||||||||||
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Annotation | Half map 2 of 1C9-sMAC reconstruction | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1 of 1C9-sMAC reconstruction
File | emd_12649_half_map_2.map | ||||||||||||
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Annotation | Half map 1 of 1C9-sMAC reconstruction | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : 1C9-sMAC
Entire | Name: 1C9-sMAC |
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Components |
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-Supramolecule #1: 1C9-sMAC
Supramolecule | Name: 1C9-sMAC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: This sMAC oligomer contains one copy of C5b8 and 1 copy of C9, as well as multiple copies of the chaperones vitronectin and clusterin |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Experimental: 1 MDa |
-Macromolecule #1: Complement protein C5b
Macromolecule | Name: Complement protein C5b / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Sequence | String: QEQTYVISAP KIFRVGASEN IVIQVYGYTE AFDATISIKS YPDKKFSYSS GHVHLSSENK FQNSAILTI QPKQLPGGQN PVSYVYLEVV SKHFSKSKRM PITYDNGFLF IHTDKPVYTP D QSVKVRVY SLNDDLKPAK RETVLTFIDP EGSEVDMVEE IDHIGIISFP ...String: QEQTYVISAP KIFRVGASEN IVIQVYGYTE AFDATISIKS YPDKKFSYSS GHVHLSSENK FQNSAILTI QPKQLPGGQN PVSYVYLEVV SKHFSKSKRM PITYDNGFLF IHTDKPVYTP D QSVKVRVY SLNDDLKPAK RETVLTFIDP EGSEVDMVEE IDHIGIISFP DFKIPSNPRY GM WTIKAKY KEDFSTTGTA YFEVKEYVLP HFSVSIEPEY NFIGYKNFKN FEITIKARYF YNK VVTEAD VYITFGIRED LKDDQKEMMQ TAMQNTMLIN GIAQVTFDSE TAVKELSYYS LEDL NNKYL YIAVTVIEST GGFSEEAEIP GIKYVLSPYK LNLVATPLFL KPGIPYPIKV QVKDS LDQL VGGVPVTLNA QTIDVNQETS DLDPSKSVTR VDDGVASFVL NLPSGVTVLE FNVKTD APD LPEENQAREG YRAIAYSSLS QSYLYIDWTD NHKALLVGEH LNIIVTPKSP YIDKITH YN YLILSKGKII HFGTREKFSD ASYQSINIPV TQNMVPSSRL LVYYIVTGEQ TAELVSDS V WLNIEEKCGN QLQVHLSPDA DAYSPGQTVS LNMATGMDSW VALAAVDSAV YGVQRGAKK PLERVFQFLE KSDLGCGAGG GLNNANVFHL AGLTFLTNAN ADDSQENDEP CKEILRPRRT LQKKIEEIAA KYKHSVVKKC CYDGACVNND ETCEQRAARI SLGPRCIKAF TECCVVASQ LRANISHKDM QLGRLHMKTL LPVSKPEIRS YFPESWLWEV HLVPRRKQLQ FALPDSLTTW EIQGVGISN TGICVADTVK AKVFKDVFLE MNIPYSVVRG EQIQLKGTVY NYRTSGMQFC V KMSAVEGI CTSESPVIDH QGTKSSKCVR QKVEGSSSHL VTFTVLPLEI GLHNINFSLE TW FGKEILV KTLRVVPEGV KRESYSGVTL DPRGIYGTIS RRKEFPYRIP LDLVPKTEIK RIL SVKGLL VGEILSAVLS QEGINILTHL PKGSAEAELM SVVPVFYVFH YLETGNHWNI FHSD PLIEK QKLKKKLKEG MLSIMSYRNA DYSYSVWKGG SASTWLTAFA LRVLGQVNKY VEQNQ NSIC NSLLWLVENY QLDNGSFKEN SQYQPIKLQG TLPVEARENS LYLTAFTVIG IRKAFD ICP LVKIDTALIK ADNFLLENTL PAQSTFTLAI SAYALSLGDK THPQFRSIVS ALKREAL VK GNPPIYRFWK DNLQHKDSSV PNTGTARMVE TTAYALLTSL NLKDINYVNP VIKWLSEE Q RYGGGFYSTQ DTINAIEGLT EYSLLVKQLR LSMDIDVSYK HKGALHNYKM TDKNFLGRP VEVLLNDDLI VSTGFGSGLA TVHVTTVVHK TSTSEEVCSF YLKIDTQDIE ASHYRGYGNS DYKRIVACA SYKPSREESS SGSSHAVMDI SLPTGISANE EDLKALVEGV DQLFTDYQIK D GHVILQLN SIPSSDFLCV RFRIFELFEV GFLSPATFTV YEYHRPDKQC TMFYSTSNIK IQ KVCEGAA CKCVEADCGQ MQEELDLTIS AETRKQTACK PEIAYAYKVS ITSITVENVF VKY KATLLD IYKTGEAVAE KDSEITFIKK VTCTNAELVK GRQYLIMGKE ALQIKYNFSF RYIY PLDSL TWIEYWPRDT TCSSCQAFLA NLDEFAEDIF LNGC |
-Macromolecule #2: Complement protein C6
Macromolecule | Name: Complement protein C6 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Sequence | String: CFCDHYAWTQ WTSCSKTCNS GTQSRHRQIV VDKYYQENFC EQICSKQETR ECNWQRCPIN CLLGDFGPW SDCDPCIEKQ SKVRSVLRPS QFGGQPCTAP LVAFQPCIPS KLCKIEEADC K NKFRCDSG RCIARKLECN GENDCGDNSD ERDCGRTKAV CTRKYNPIPS ...String: CFCDHYAWTQ WTSCSKTCNS GTQSRHRQIV VDKYYQENFC EQICSKQETR ECNWQRCPIN CLLGDFGPW SDCDPCIEKQ SKVRSVLRPS QFGGQPCTAP LVAFQPCIPS KLCKIEEADC K NKFRCDSG RCIARKLECN GENDCGDNSD ERDCGRTKAV CTRKYNPIPS VQLMGNGFHF LA GEPRGEV LDNSFTGGIC KTVKSSRTSN PYRVPANLEN VGFEVQTAED DLKTDFYKDL TSL GHNENQ QGSFSSQGGS SFSVPIFYSS KRSENINHNS AFKQAIQASH KKDSSFIRIH KVMK VLNFT TKAKDLHLSD VFLKALNHLP LEYNSALYSR IFDDFGTHYF TSGSLGGVYD LLYQF SSEE LKNSGLTEEE AKHCVRIETK KRVLFAKKTK VEHRCTTNKL SEKHEGSFIQ GAEKSI SLI RGGRSEYGAA LAWEKGSSGL EEKTFSEWLE SVKENPAVID FELAPIVDLV RNIPCAV TK RNNLRKALQE YAAKFDPCQC APCPNNGRPT LSGTECLCVC QSGTYGENCE KQSPDYKS N AVDGQWGCWS SWSTCDATYK RSRTRECNNP APQRGGKRCE GEKRQEEDCT FSIMENNGQ PCINDDEEMK EVDLPEIEAD SGCPQPVPPE NGFIRNEKQL YLVGEDVEIS CLTGFETVGY QYFRCLPDG TWRQGDVECQ RTECIKPVVQ EVLTITPFQR LYRIGESIEL TCPKGFVVAG P SRYTCQGN SWTPPISNSL TCEKDTLTKL KGHCQLGQKQ SGSECICMSP EEDCSHHSED LC VFDTDSN DYFTSPACKF LAEKCLNNQQ LHFLHIGSCQ DGRQLEWGLE RTRLSSNSTK KES CGYDTC YDWEKCSAST SKCVCLLPPQ CFKGGNQLYC VKMGSSTSEK TLNICEVGTI RCAN RKMEI LHPGKCLA |
-Macromolecule #3: Complement protein C7
Macromolecule | Name: Complement protein C7 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Sequence | String: SSPVNCQWDF YAPWSECNGC TKTQTRRRSV AVYGQYGGQP CVGNAFETQS CEPTRGCPTE EGCGERFRC FSGQCISKSL VCNGDSDCDE DSADEDRCED SERRPSCDID KPPPNIELTG N GYNELTGQ FRNRVINTKS FGGQCRKVFS GDGKDFYRLS GNVLSYTFQV ...String: SSPVNCQWDF YAPWSECNGC TKTQTRRRSV AVYGQYGGQP CVGNAFETQS CEPTRGCPTE EGCGERFRC FSGQCISKSL VCNGDSDCDE DSADEDRCED SERRPSCDID KPPPNIELTG N GYNELTGQ FRNRVINTKS FGGQCRKVFS GDGKDFYRLS GNVLSYTFQV KINNDFNYEF YN STWSYVK HTSTEHTSSS RKRSFFRSSS SSSRSYTSHT NEIHKGKSYQ LLVVENTVEV AQF INNNPE FLQLAEPFWK ELSHLPSLYD YSAYRRLIDQ YGTHYLQSGS LGGEYRVLFY VDSE KLKQN DFNSVEEKKC KSSGWHFVVK FSSHGCKELE NALKAASGTQ NNVLRGEPFI RGGGA GFIS GLSYLELDNP AGNKRRYSAW AESVTNLPQV IKQKLTPLYE LVKEVPCASV KKLYLK WAL EEYLDEFDPC HCRPCQNGGL ATVEGTHCLC HCKPYTFGAA CEQGVLVGNQ AGGVDGG WS CWSSWSPCVQ GKKTRSRECN NPPPSGGGRS CVGETTESTQ CEDEELEHLR LLEPHCFP L SLVPTEFCPS PPALKDGFVQ DEGTMFPVGK NVVYTCNEGY SLIGNPVARC GEDLRWLVG EMHCQKIACV LPVLMDGIQS HPQKPFYTVG EKVTVSCSGG MSLEGPSAFL CGSSLKWSPE MKNARCVQK ENPLTQAVPK CQRWEKLQNS RCVCKMPYEC GPSLDVCAQD ERSKRILPLT V CKMHVLHC QGRNYTLTGR DSCTLPASAE KACGACPLWG KCDAESSKCV CREASECEEE GF SICVEVN GKEQTMSECE AGALRCRGQS ISVTSIRPCA AETQ |
-Macromolecule #4: Complement protein C8 beta
Macromolecule | Name: Complement protein C8 beta / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Sequence | String: SVDVTLMPID CELSSWSSWT TCDPCQKKRY RYAYLLQPSQ FHGEPCNFSD KEVEDCVTNR PCRSQVRCE GFVCAQTGRC VNRRLLCNGD NDCGDQSDEA NCRRIYKKCQ HEMDQYWGIG S LASGINLF TNSFEGPVLD HRYYAGGCSP HYILNTRFRK PYNVESYTPQ ...String: SVDVTLMPID CELSSWSSWT TCDPCQKKRY RYAYLLQPSQ FHGEPCNFSD KEVEDCVTNR PCRSQVRCE GFVCAQTGRC VNRRLLCNGD NDCGDQSDEA NCRRIYKKCQ HEMDQYWGIG S LASGINLF TNSFEGPVLD HRYYAGGCSP HYILNTRFRK PYNVESYTPQ TQGKYEFILK EY ESYSDFE RNVTEKMASK SGFSFGFKIP GIFELGISSQ SDRGKHYIRR TKRFSHTKSV FLH ARSDLE VAHYKLKPRS LMLHYEFLQR VKRLPLEYSY GEYRDLFRDF GTHYITEAVL GGIY EYTLV MNKEAMERGD YTLNNVHACA KNDFKIGGAI EEVYVSLGVS VGKCRGILNE IKDRN KRDT MVEDLVVLVR GGASEHITTL AYQELPTADL MQEWGDAVQY NPAIIKVKVE PLYELV TAT DFAYSSTVRQ NMKQALEEFQ KEVSSCHCAP CQGNGVPVLK GSRCDCICPV GSQGLAC EV SYRKNTPIDG KWNCWSNWSS CSGRRKTRQR QCNNPPPQNG GSPCSGPASE TLDCS |
-Macromolecule #5: Complement protein C8 alpha
Macromolecule | Name: Complement protein C8 alpha / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Sequence | String: AATPAAVTCQ LSNWSEWTDC FPCQDKKYRH RSLLQPNKFG GTICSGDIWD QASCSSSTTC VRQAQCGQD FQCKETGRCL KRHLVCNGDQ DCLDGSDEDD CEDVRAIDED CSQYEPIPGS Q KAALGYNI LTQEDAQSVY DASYYGGQCE TVYNGEWREL RYDSTCERLY ...String: AATPAAVTCQ LSNWSEWTDC FPCQDKKYRH RSLLQPNKFG GTICSGDIWD QASCSSSTTC VRQAQCGQD FQCKETGRCL KRHLVCNGDQ DCLDGSDEDD CEDVRAIDED CSQYEPIPGS Q KAALGYNI LTQEDAQSVY DASYYGGQCE TVYNGEWREL RYDSTCERLY YGDDEKYFRK PY NFLKYHF EALADTGISS EFYDNANDLL SKVKKDKSDS FGVTIGIGPA GSPLLVGVGV SHS QDTSFL NELNKYNEKK FIFTRIFTKV QTAHFKMRKD DIMLDEGMLQ SLMELPDQYN YGMY AKFIN DYGTHYITSG SMGGIYEYIL VIDKAKMESL GITSRDITTC FGGSLGIQYE DKINV GGGL SGDHCKKFGG GKTERARKAM AVEDIISRVR GGSSGWSGGL AQNRSTITYR SWGRSL KYN PVVIDFEMQP IHEVLRHTSL GPLEAKRQNL RRALDQYLME FNACRCGPCF NNGVPIL EG TSCRCQCRLG SLGAACEQTQ TEGAKADGSW SCWSSWSVCR AGIQERRREC DNPAPQNG G ASCPGRKVQT QAC |
-Macromolecule #6: Complement protein C8 gamma
Macromolecule | Name: Complement protein C8 gamma / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Sequence | String: QKPQRPRRPA SPISTIQPKA NFDAQQFAGT WLLVAVGSAC RFLQEQGHRA EATTLHVAPQ GTAMAVSTF RKLDGICWQV RQLYGDTGVL GRFLLQARDA RGAVHVVVAE TDYQSFAVLY L ERAGQLSV KLYARSLPVS DSVLSGFEQR VQEAHLTEDQ IFYFPKYGFC EAADQFHVLD EV RR |
-Macromolecule #7: Complement protein C9
Macromolecule | Name: Complement protein C9 / type: protein_or_peptide / ID: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Sequence | String: QYTTSYDPEL TESSGSASHI DCRMSPWSEW SQCDPCLRQM FRSRSIEVFG QFNGKRCTDA VGDRRQCVP TEPCEDAEDD CGNDFQCSTG RCIKMRLRCN GDNDCGDFSD EDDCESEPRP P CRDRVVEE SELARTAGYG INILGMDPLS TPFDNEFYNG LCNRDRDGNT ...String: QYTTSYDPEL TESSGSASHI DCRMSPWSEW SQCDPCLRQM FRSRSIEVFG QFNGKRCTDA VGDRRQCVP TEPCEDAEDD CGNDFQCSTG RCIKMRLRCN GDNDCGDFSD EDDCESEPRP P CRDRVVEE SELARTAGYG INILGMDPLS TPFDNEFYNG LCNRDRDGNT LTYYRRPWNV AS LIYETKG EKNFRTEHYE EQIEAFKSII QEKTSNFNAA ISLKFTPTET NKAEQCCEET ASS ISLHGK GSFRFSYSKN ETYQLFLSYS SKKEKMFLHV KGEIHLGRFV MRNRDVVLTT TFVD DIKAL PTTYEKGEYF AFLETYGTHY SSSGSLGGLY ELIYVLDKAS MKRKGVELKD IKRCL GYHL DVSLAFSEIS VGAEFNKDDC VKRGEGRAVN ITSENLIDDV VSLIRGGTRK YAFELK EKL LRGTVIDVTD FVNWASSIND APVLISQKLS PIYNLVPVKM KNAHLKKQNL ERAIEDY IN EFSVRKCHTC QNGGTVILMD GKCLCACPFK FEGIACEISK QKISEGLPAL EFPNEK |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.065 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |