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- EMDB-15781: 2C9, C5b9-CD59 cryoEM structure -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-15781
Title2C9, C5b9-CD59 cryoEM structure
Map dataLocally filtered 2C9-CD59 map
Sample
  • Complex: 2C9, CD59 inhibited MAC Complex
    • Complex: CD59 glycoprotein
      • Protein or peptide: CD59 glycoprotein
    • Complex: Complement components C5, C6, C7, C8 and C9
      • Protein or peptide: Complement component C8 beta chain
      • Protein or peptide: Complement component C8 gamma chain
      • Protein or peptide: Complement component C8 alpha chain
      • Protein or peptide: Complement C5Complement component 5
      • Protein or peptide: Complement component C7
      • Protein or peptide: Complement component C6
      • Protein or peptide: Complement component C9
Function / homology
Function and homology information


negative regulation of activation of membrane attack complex / cell killing / Terminal pathway of complement / membrane attack complex / complement binding / regulation of complement-dependent cytotoxicity / other organism cell membrane / regulation of complement activation / Activation of C3 and C5 / negative regulation of macrophage chemotaxis ...negative regulation of activation of membrane attack complex / cell killing / Terminal pathway of complement / membrane attack complex / complement binding / regulation of complement-dependent cytotoxicity / other organism cell membrane / regulation of complement activation / Activation of C3 and C5 / negative regulation of macrophage chemotaxis / Cargo concentration in the ER / complement activation, alternative pathway / complement activation / chemokine activity / COPII-mediated vesicle transport / retinol binding / endopeptidase inhibitor activity / tertiary granule membrane / positive regulation of vascular endothelial growth factor production / specific granule membrane / COPI-mediated anterograde transport / complement activation, classical pathway / positive regulation of chemokine production / transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / Peptide ligand-binding receptors / Regulation of Complement cascade / ER to Golgi transport vesicle membrane / protein homooligomerization / chemotaxis / positive regulation of immune response / extracellular vesicle / blood coagulation / G alpha (i) signalling events / blood microparticle / killing of cells of another organism / in utero embryonic development / vesicle / cell surface receptor signaling pathway / immune response / inflammatory response / G protein-coupled receptor signaling pathway / external side of plasma membrane / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response / Neutrophil degranulation / protein-containing complex binding / endoplasmic reticulum membrane / cell surface / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane
Similarity search - Function
Kazal-type serine protease inhibitor domain / : / : / Kazal-type serine protease inhibitor domain / Complement component C7, FIM2 N-terminal / Complement component C7, Kazal domain / : / Complement component C6, KAZAL domain / Complement component C8 gamma chain / : ...Kazal-type serine protease inhibitor domain / : / : / Kazal-type serine protease inhibitor domain / Complement component C7, FIM2 N-terminal / Complement component C7, Kazal domain / : / Complement component C6, KAZAL domain / Complement component C8 gamma chain / : / Complement components C8A/B/C6, EGF-like domain / Membrane attack complex component/perforin/complement C9 / Alpha-1-microglobulin / Factor I / membrane attack complex / factor I membrane attack complex / CD59 antigen, conserved site / Membrane attack complex component/perforin domain, conserved site / Membrane attack complex/perforin (MACPF) domain signature. / Ly-6 / u-PAR domain signature. / Ly-6 antigen / uPA receptor -like domain / u-PAR/Ly-6 domain / Ly-6 antigen/uPA receptor-like / : / Complement component 5, CUB domain / membrane-attack complex / perforin / Membrane attack complex/perforin (MACPF) domain profile. / MAC/Perforin domain / Membrane attack complex component/perforin (MACPF) domain / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Anaphylatoxin, complement system domain / Anaphylatoxin domain signature. / Anaphylatoxin/fibulin / Anaphylatoxin, complement system / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Kazal domain / Kazal domain profile. / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor binding domain / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor / Netrin domain / NTR domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / Alpha-2-macroglobulin / Macroglobulin domain / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / Thrombospondin type 1 domain / LDL-receptor class A (LDLRA) domain profile. / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Lipocalin family conserved site / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/SCR/CCP superfamily / Sushi/CCP/SCR domain profile. / Snake toxin-like superfamily / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / Calycin / Lipocalin signature. / Immunoglobulin-like fold
Similarity search - Domain/homology
Complement C5 / Complement component C9 / Complement component C8 alpha chain / Complement component C8 beta chain / Complement component C8 gamma chain / Complement component C7 / Complement component C6 / CD59 glycoprotein
Similarity search - Component
Biological speciesHomo sapiens (human) / human (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsCouves EC / Gardner S / Bubeck D
Funding supportEuropean Union, United Kingdom, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)No. 864751European Union
Cancer Research UKC24523/A26234 United Kingdom
CitationJournal: Nat Commun / Year: 2023
Title: Structural basis for membrane attack complex inhibition by CD59.
Authors: Emma C Couves / Scott Gardner / Tomas B Voisin / Jasmine K Bickel / Phillip J Stansfeld / Edward W Tate / Doryen Bubeck /
Abstract: CD59 is an abundant immuno-regulatory receptor that protects human cells from damage during complement activation. Here we show how the receptor binds complement proteins C8 and C9 at the membrane to ...CD59 is an abundant immuno-regulatory receptor that protects human cells from damage during complement activation. Here we show how the receptor binds complement proteins C8 and C9 at the membrane to prevent insertion and polymerization of membrane attack complex (MAC) pores. We present cryo-electron microscopy structures of two inhibited MAC precursors known as C5b8 and C5b9. We discover that in both complexes, CD59 binds the pore-forming β-hairpins of C8 to form an intermolecular β-sheet that prevents membrane perforation. While bound to C8, CD59 deflects the cascading C9 β-hairpins, rerouting their trajectory into the membrane. Preventing insertion of C9 restricts structural transitions of subsequent monomers and indirectly halts MAC polymerization. We combine our structural data with cellular assays and molecular dynamics simulations to explain how the membrane environment impacts the dual roles of CD59 in controlling pore formation of MAC, and as a target of bacterial virulence factors which hijack CD59 to lyse human cells.
History
DepositionSep 7, 2022-
Header (metadata) releaseFeb 22, 2023-
Map releaseFeb 22, 2023-
UpdateMar 1, 2023-
Current statusMar 1, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15781.png

Downloads & links

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Map

FileDownload / File: emd_15781.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocally filtered 2C9-CD59 map
Voxel sizeX=Y=Z: 0.831 Å
Density
Contour LevelBy AUTHOR: 0.00481
Minimum - Maximum-0.084219486 - 0.13041718
Average (Standard dev.)5.668714e-05 (±0.0017382303)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions540540540
Spacing540540540
CellA=B=C: 448.74 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15781_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Relion refinement map of 2C9-CD59 (full structure)

Fileemd_15781_additional_1.map
AnnotationRelion refinement map of 2C9-CD59 (full structure)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Relion refinement map of 2C9-CD59 (full structure) unfiltered...

Fileemd_15781_half_map_1.map
AnnotationRelion refinement map of 2C9-CD59 (full structure) unfiltered half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Relion refinement map of 2C9-CD59 (full structure) unfiltered...

Fileemd_15781_half_map_2.map
AnnotationRelion refinement map of 2C9-CD59 (full structure) unfiltered half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 2C9, CD59 inhibited MAC Complex

EntireName: 2C9, CD59 inhibited MAC Complex
Components
  • Complex: 2C9, CD59 inhibited MAC Complex
    • Complex: CD59 glycoprotein
      • Protein or peptide: CD59 glycoprotein
    • Complex: Complement components C5, C6, C7, C8 and C9
      • Protein or peptide: Complement component C8 beta chain
      • Protein or peptide: Complement component C8 gamma chain
      • Protein or peptide: Complement component C8 alpha chain
      • Protein or peptide: Complement C5Complement component 5
      • Protein or peptide: Complement component C7
      • Protein or peptide: Complement component C6
      • Protein or peptide: Complement component C9

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Supramolecule #1: 2C9, CD59 inhibited MAC Complex

SupramoleculeName: 2C9, CD59 inhibited MAC Complex / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Details: Solved in a DOPC, MSP2N2 nanodisc with a myristolated cytotopic CD59.

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Supramolecule #2: CD59 glycoprotein

SupramoleculeName: CD59 glycoprotein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human) / Location in cell: Serum

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Supramolecule #3: Complement components C5, C6, C7, C8 and C9

SupramoleculeName: Complement components C5, C6, C7, C8 and C9 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#8
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: CD59 glycoprotein

MacromoleculeName: CD59 glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.234388 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MGIQGGSVLF GLLLVLAVFC HSGHMLQCYN CPNPTADCKT AVNCSSDFDA CLITKAGLQV YNKCWKFEHC NFNDVTTRLR ENELTYYCC KKDLCNFNEQ LENGGTSLSE KTVLLLVTPF LAAAWSLHP

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Macromolecule #2: Complement component C8 beta chain

MacromoleculeName: Complement component C8 beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: human (human)
Molecular weightTheoretical: 67.136891 KDa
SequenceString: MKNSRTWAWR APVELFLLCA ALGCLSLPGS RGERPHSFGS NAVNKSFAKS RQMRSVDVTL MPIDCELSSW SSWTTCDPCQ KKRYRYAYL LQPSQFHGEP CNFSDKEVED CVTNRPCRSQ VRCEGFVCAQ TGRCVNRRLL CNGDNDCGDQ SDEANCRRIY K KCQHEMDQ ...String:
MKNSRTWAWR APVELFLLCA ALGCLSLPGS RGERPHSFGS NAVNKSFAKS RQMRSVDVTL MPIDCELSSW SSWTTCDPCQ KKRYRYAYL LQPSQFHGEP CNFSDKEVED CVTNRPCRSQ VRCEGFVCAQ TGRCVNRRLL CNGDNDCGDQ SDEANCRRIY K KCQHEMDQ YWGIGSLASG INLFTNSFEG PVLDHRYYAG GCSPHYILNT RFRKPYNVES YTPQTQGKYE FILKEYESYS DF ERNVTEK MASKSGFSFG FKIPGIFELG ISSQSDRGKH YIRRTKRFSH TKSVFLHARS DLEVAHYKLK PRSLMLHYEF LQR VKRLPL EYSYGEYRDL FRDFGTHYIT EAVLGGIYEY TLVMNKEAME RGDYTLNNVH ACAKNDFKIG GAIEEVYVSL GVSV GKCRG ILNEIKDRNK RDTMVEDLVV LVRGGASEHI TTLAYQELPT ADLMQEWGDA VQYNPAIIKV KVEPLYELVT ATDFA YSST VRQNMKQALE EFQKEVSSCH CAPCQGNGVP VLKGSRCDCI CPVGSQGLAC EVSYRKNTPI DGKWNCWSNW SSCSGR RKT RQRQCNNPPP QNGGSPCSGP ASETLDCS

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Macromolecule #3: Complement component C8 gamma chain

MacromoleculeName: Complement component C8 gamma chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: human (human)
Molecular weightTheoretical: 22.302424 KDa
SequenceString: MLPPGTATLL TLLLAAGSLG QKPQRPRRPA SPISTIQPKA NFDAQQFAGT WLLVAVGSAC RFLQEQGHRA EATTLHVAPQ GTAMAVSTF RKLDGICWQV RQLYGDTGVL GRFLLQARDA RGAVHVVVAE TDYQSFAVLY LERAGQLSVK LYARSLPVSD S VLSGFEQR ...String:
MLPPGTATLL TLLLAAGSLG QKPQRPRRPA SPISTIQPKA NFDAQQFAGT WLLVAVGSAC RFLQEQGHRA EATTLHVAPQ GTAMAVSTF RKLDGICWQV RQLYGDTGVL GRFLLQARDA RGAVHVVVAE TDYQSFAVLY LERAGQLSVK LYARSLPVSD S VLSGFEQR VQEAHLTEDQ IFYFPKYGFC EAADQFHVLD EVRR

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Macromolecule #4: Complement component C8 alpha chain

MacromoleculeName: Complement component C8 alpha chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: human (human)
Molecular weightTheoretical: 65.239152 KDa
SequenceString: MFAVVFFILS LMTCQPGVTA QEKVNQRVRR AATPAAVTCQ LSNWSEWTDC FPCQDKKYRH RSLLQPNKFG GTICSGDIWD QASCSSSTT CVRQAQCGQD FQCKETGRCL KRHLVCNGDQ DCLDGSDEDD CEDVRAIDED CSQYEPIPGS QKAALGYNIL T QEDAQSVY ...String:
MFAVVFFILS LMTCQPGVTA QEKVNQRVRR AATPAAVTCQ LSNWSEWTDC FPCQDKKYRH RSLLQPNKFG GTICSGDIWD QASCSSSTT CVRQAQCGQD FQCKETGRCL KRHLVCNGDQ DCLDGSDEDD CEDVRAIDED CSQYEPIPGS QKAALGYNIL T QEDAQSVY DASYYGGQCE TVYNGEWREL RYDSTCERLY YGDDEKYFRK PYNFLKYHFE ALADTGISSE FYDNANDLLS KV KKDKSDS FGVTIGIGPA GSPLLVGVGV SHSQDTSFLN ELNKYNEKKF IFTRIFTKVQ TAHFKMRKDD IMLDEGMLQS LME LPDQYN YGMYAKFIND YGTHYITSGS MGGIYEYILV IDKAKMESLG ITSRDITTCF GGSLGIQYED KINVGGGLSG DHCK KFGGG KTERARKAMA VEDIISRVRG GSSGWSGGLA QNRSTITYRS WGRSLKYNPV VIDFEMQPIH EVLRHTSLGP LEAKR QNLR RALDQYLMEF NACRCGPCFN NGVPILEGTS CRCQCRLGSL GAACEQTQTE GAKADGSWSC WSSWSVCRAG IQERRR ECD NPAPQNGGAS CPGRKVQTQA C

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Macromolecule #5: Complement C5

MacromoleculeName: Complement C5 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: human (human)
Molecular weightTheoretical: 188.512094 KDa
SequenceString: MGLLGILCFL IFLGKTWGQE QTYVISAPKI FRVGASENIV IQVYGYTEAF DATISIKSYP DKKFSYSSGH VHLSSENKFQ NSAILTIQP KQLPGGQNPV SYVYLEVVSK HFSKSKRMPI TYDNGFLFIH TDKPVYTPDQ SVKVRVYSLN DDLKPAKRET V LTFIDPEG ...String:
MGLLGILCFL IFLGKTWGQE QTYVISAPKI FRVGASENIV IQVYGYTEAF DATISIKSYP DKKFSYSSGH VHLSSENKFQ NSAILTIQP KQLPGGQNPV SYVYLEVVSK HFSKSKRMPI TYDNGFLFIH TDKPVYTPDQ SVKVRVYSLN DDLKPAKRET V LTFIDPEG SEVDMVEEID HIGIISFPDF KIPSNPRYGM WTIKAKYKED FSTTGTAYFE VKEYVLPHFS VSIEPEYNFI GY KNFKNFE ITIKARYFYN KVVTEADVYI TFGIREDLKD DQKEMMQTAM QNTMLINGIA QVTFDSETAV KELSYYSLED LNN KYLYIA VTVIESTGGF SEEAEIPGIK YVLSPYKLNL VATPLFLKPG IPYPIKVQVK DSLDQLVGGV PVTLNAQTID VNQE TSDLD PSKSVTRVDD GVASFVLNLP SGVTVLEFNV KTDAPDLPEE NQAREGYRAI AYSSLSQSYL YIDWTDNHKA LLVGE HLNI IVTPKSPYID KITHYNYLIL SKGKIIHFGT REKFSDASYQ SINIPVTQNM VPSSRLLVYY IVTGEQTAEL VSDSVW LNI EEKCGNQLQV HLSPDADAYS PGQTVSLNMA TGMDSWVALA AVDSAVYGVQ RGAKKPLERV FQFLEKSDLG CGAGGGL NN ANVFHLAGLT FLTNANADDS QENDEPCKEI LRPRRTLQKK IEEIAAKYKH SVVKKCCYDG ACVNNDETCE QRAARISL G PRCIKAFTEC CVVASQLRAN ISHKDMQLGR LHMKTLLPVS KPEIRSYFPE SWLWEVHLVP RRKQLQFALP DSLTTWEIQ GVGISNTGIC VADTVKAKVF KDVFLEMNIP YSVVRGEQIQ LKGTVYNYRT SGMQFCVKMS AVEGICTSES PVIDHQGTKS SKCVRQKVE GSSSHLVTFT VLPLEIGLHN INFSLETWFG KEILVKTLRV VPEGVKRESY SGVTLDPRGI YGTISRRKEF P YRIPLDLV PKTEIKRILS VKGLLVGEIL SAVLSQEGIN ILTHLPKGSA EAELMSVVPV FYVFHYLETG NHWNIFHSDP LI EKQKLKK KLKEGMLSIM SYRNADYSYS VWKGGSASTW LTAFALRVLG QVNKYVEQNQ NSICNSLLWL VENYQLDNGS FKE NSQYQP IKLQGTLPVE ARENSLYLTA FTVIGIRKAF DICPLVKIDT ALIKADNFLL ENTLPAQSTF TLAISAYALS LGDK THPQF RSIVSALKRE ALVKGNPPIY RFWKDNLQHK DSSVPNTGTA RMVETTAYAL LTSLNLKDIN YVNPVIKWLS EEQRY GGGF YSTQDTINAI EGLTEYSLLV KQLRLSMDID VSYKHKGALH NYKMTDKNFL GRPVEVLLND DLIVSTGFGS GLATVH VTT VVHKTSTSEE VCSFYLKIDT QDIEASHYRG YGNSDYKRIV ACASYKPSRE ESSSGSSHAV MDISLPTGIS ANEEDLK AL VEGVDQLFTD YQIKDGHVIL QLNSIPSSDF LCVRFRIFEL FEVGFLSPAT FTVYEYHRPD KQCTMFYSTS NIKIQKVC E GAACKCVEAD CGQMQEELDL TISAETRKQT ACKPEIAYAY KVSITSITVE NVFVKYKATL LDIYKTGEAV AEKDSEITF IKKVTCTNAE LVKGRQYLIM GKEALQIKYN FSFRYIYPLD SLTWIEYWPR DTTCSSCQAF LANLDEFAED IFLNGC

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Macromolecule #6: Complement component C7

MacromoleculeName: Complement component C7 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: human (human)
Molecular weightTheoretical: 93.625328 KDa
SequenceString: MKVISLFILV GFIGEFQSFS SASSPVNCQW DFYAPWSECN GCTKTQTRRR SVAVYGQYGG QPCVGNAFET QSCEPTRGCP TEEGCGERF RCFSGQCISK SLVCNGDSDC DEDSADEDRC EDSERRPSCD IDKPPPNIEL TGNGYNELTG QFRNRVINTK S FGGQCRKV ...String:
MKVISLFILV GFIGEFQSFS SASSPVNCQW DFYAPWSECN GCTKTQTRRR SVAVYGQYGG QPCVGNAFET QSCEPTRGCP TEEGCGERF RCFSGQCISK SLVCNGDSDC DEDSADEDRC EDSERRPSCD IDKPPPNIEL TGNGYNELTG QFRNRVINTK S FGGQCRKV FSGDGKDFYR LSGNVLSYTF QVKINNDFNY EFYNSTWSYV KHTSTEHTSS SRKRSFFRSS SSSSRSYTSH TN EIHKGKS YQLLVVENTV EVAQFINNNP EFLQLAEPFW KELSHLPSLY DYSAYRRLID QYGTHYLQSG SLGGEYRVLF YVD SEKLKQ NDFNSVEEKK CKSSGWHFVV KFSSHGCKEL ENALKAASGT QNNVLRGEPF IRGGGAGFIS GLSYLELDNP AGNK RRYSA WAESVTNLPQ VIKQKLTPLY ELVKEVPCAS VKKLYLKWAL EEYLDEFDPC HCRPCQNGGL ATVEGTHCLC HCKPY TFGA ACEQGVLVGN QAGGVDGGWS CWSSWSPCVQ GKKTRSRECN NPPPSGGGRS CVGETTESTQ CEDEELEHLR LLEPHC FPL SLVPTEFCPS PPALKDGFVQ DEGTMFPVGK NVVYTCNEGY SLIGNPVARC GEDLRWLVGE MHCQKIACVL PVLMDGI QS HPQKPFYTVG EKVTVSCSGG MSLEGPSAFL CGSSLKWSPE MKNARCVQKE NPLTQAVPKC QRWEKLQNSR CVCKMPYE C GPSLDVCAQD ERSKRILPLT VCKMHVLHCQ GRNYTLTGRD SCTLPASAEK ACGACPLWGK CDAESSKCVC REASECEEE GFSICVEVNG KEQTMSECEA GALRCRGQSI SVTSIRPCAA ETQ

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Macromolecule #7: Complement component C6

MacromoleculeName: Complement component C6 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: human (human)
Molecular weightTheoretical: 104.91818 KDa
SequenceString: MARRSVLYFI LLNALINKGQ ACFCDHYAWT QWTSCSKTCN SGTQSRHRQI VVDKYYQENF CEQICSKQET RECNWQRCPI NCLLGDFGP WSDCDPCIEK QSKVRSVLRP SQFGGQPCTA PLVAFQPCIP SKLCKIEEAD CKNKFRCDSG RCIARKLECN G ENDCGDNS ...String:
MARRSVLYFI LLNALINKGQ ACFCDHYAWT QWTSCSKTCN SGTQSRHRQI VVDKYYQENF CEQICSKQET RECNWQRCPI NCLLGDFGP WSDCDPCIEK QSKVRSVLRP SQFGGQPCTA PLVAFQPCIP SKLCKIEEAD CKNKFRCDSG RCIARKLECN G ENDCGDNS DERDCGRTKA VCTRKYNPIP SVQLMGNGFH FLAGEPRGEV LDNSFTGGIC KTVKSSRTSN PYRVPANLEN VG FEVQTAE DDLKTDFYKD LTSLGHNENQ QGSFSSQGGS SFSVPIFYSS KRSENINHNS AFKQAIQASH KKDSSFIRIH KVM KVLNFT TKAKDLHLSD VFLKALNHLP LEYNSALYSR IFDDFGTHYF TSGSLGGVYD LLYQFSSEEL KNSGLTEEEA KHCV RIETK KRVLFAKKTK VEHRCTTNKL SEKHEGSFIQ GAEKSISLIR GGRSEYGAAL AWEKGSSGLE EKTFSEWLES VKENP AVID FELAPIVDLV RNIPCAVTKR NNLRKALQEY AAKFDPCQCA PCPNNGRPTL SGTECLCVCQ SGTYGENCEK QSPDYK SNA VDGQWGCWSS WSTCDATYKR SRTRECNNPA PQRGGKRCEG EKRQEEDCTF SIMENNGQPC INDDEEMKEV DLPEIEA DS GCPQPVPPEN GFIRNEKQLY LVGEDVEISC LTGFETVGYQ YFRCLPDGTW RQGDVECQRT ECIKPVVQEV LTITPFQR L YRIGESIELT CPKGFVVAGP SRYTCQGNSW TPPISNSLTC EKDTLTKLKG HCQLGQKQSG SECICMSPEE DCSHHSEDL CVFDTDSNDY FTSPACKFLA EKCLNNQQLH FLHIGSCQDG RQLEWGLERT RLSSNSTKKE SCGYDTCYDW EKCSASTSKC VCLLPPQCF KGGNQLYCVK MGSSTSEKTL NICEVGTIRC ANRKMEILHP GKCLA

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Macromolecule #8: Complement component C9

MacromoleculeName: Complement component C9 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: human (human)
Molecular weightTheoretical: 63.252301 KDa
SequenceString: MSACRSFAVA ICILEISILT AQYTTSYDPE LTESSGSASH IDCRMSPWSE WSQCDPCLRQ MFRSRSIEVF GQFNGKRCTD AVGDRRQCV PTEPCEDAED DCGNDFQCST GRCIKMRLRC NGDNDCGDFS DEDDCESEPR PPCRDRVVEE SELARTAGYG I NILGMDPL ...String:
MSACRSFAVA ICILEISILT AQYTTSYDPE LTESSGSASH IDCRMSPWSE WSQCDPCLRQ MFRSRSIEVF GQFNGKRCTD AVGDRRQCV PTEPCEDAED DCGNDFQCST GRCIKMRLRC NGDNDCGDFS DEDDCESEPR PPCRDRVVEE SELARTAGYG I NILGMDPL STPFDNEFYN GLCNRDRDGN TLTYYRRPWN VASLIYETKG EKNFRTEHYE EQIEAFKSII QEKTSNFNAA IS LKFTPTE TNKAEQCCEE TASSISLHGK GSFRFSYSKN ETYQLFLSYS SKKEKMFLHV KGEIHLGRFV MRNRDVVLTT TFV DDIKAL PTTYEKGEYF AFLETYGTHY SSSGSLGGLY ELIYVLDKAS MKRKGVELKD IKRCLGYHLD VSLAFSEISV GAEF NKDDC VKRGEGRAVN ITSENLIDDV VSLIRGGTRK YAFELKEKLL RGTVIDVTDF VNWASSINDA PVLISQKLSP IYNLV PVKM KNAHLKKQNL ERAIEDYINE FSVRKCHTCQ NGGTVILMDG KCLCACPFKF EGIACEISKQ KISEGLPALE FPNEK

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
120.0 mMNaClSodium chloridesodium chloride

Details: 20 mM HEPES pH 7.4, 120 mM NaCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 4.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 9.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 4 / Number real images: 52838 / Average exposure time: 2.0 sec. / Average electron dose: 50.0 e/Å2 / Details: Collected over 4 separate data collections
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionDetails: Dataset 1: 737,138 Dataset 2: 1,058,026 Dataset 3: 1,330,232 Dataset 4: 722,870
Startup modelType of model: INSILICO MODEL / In silico model: Ab initio model generated by CryoSPARC
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 47244
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model(PDB ID:

7nyd

,

2j8b

)
DetailsInitial fitting was done in ISODLE, final refinements were done in ISOLDE
Output model

PDB-8b0h:
2C9, C5b9-CD59 cryoEM structure

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