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- EMDB-12651: cryoEM structure of 2C9-sMAC -

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Basic information

Entry
Database: EMDB / ID: EMD-12651
TitlecryoEM structure of 2C9-sMAC
Map dataLocally sharpened 2C9-sMAC map, resolution 3.27 A
Sample
  • Complex: 2C9-sMAC
    • Protein or peptide: x 7 types
  • Ligand: x 4 types
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 / complement activation, classical pathway / positive regulation of chemokine production / Peptide ligand-binding receptors / Regulation of Complement cascade / protein homooligomerization / extracellular vesicle / chemotaxis / positive regulation of immune response / G alpha (i) signalling events / blood microparticle / killing of cells of another organism / in utero embryonic development / cell surface receptor signaling pathway / immune response / inflammatory response / G protein-coupled receptor signaling pathway / signaling receptor binding / innate immune response / protein-containing complex binding / 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 / Membrane attack complex component/perforin domain, conserved site / Membrane attack complex/perforin (MACPF) domain signature. / : / 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. / Netrin domain / NTR 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 / 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. / LDL-receptor class A (LDLRA) domain profile. / Thrombospondin type 1 domain / 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. / 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
Similarity search - Component
Biological speciesHomo sapiens (human) / Human (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsMenny A / Couves EC / Bubeck D
Funding supportEuropean Union, United Kingdom, 3 items
OrganizationGrant numberCountry
European Research Council (ERC)No. 864751European Union
Cancer Research UKC24523/A26234 United Kingdom
Engineering and Physical Sciences Research CouncilEP/L015498/1 United Kingdom
CitationJournal: 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
DepositionMar 22, 2021-
Header (metadata) releaseOct 6, 2021-
Map releaseOct 6, 2021-
UpdateNov 17, 2021-
Current statusNov 17, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7nyd
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12651.png

Downloads & links

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Map

FileDownload / File: emd_12651.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocally sharpened 2C9-sMAC map, resolution 3.27 A
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 400 pix.
= 418.8 Å		1.05 Å/pix.
x 400 pix.
= 418.8 Å		1.05 Å/pix.
x 400 pix.
= 418.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.047 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.0017913133 - 2.0983205
Average (Standard dev.)0.0010500759 (±0.022683728)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 418.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0471.0471.047
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z418.800418.800418.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0022.0980.001

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Supplemental data

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Half map: Half map 2 from the 3D auto-refinement of 2C9-sMAC

Fileemd_12651_half_map_1.map
AnnotationHalf map 2 from the 3D auto-refinement of 2C9-sMAC
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 from the 3D auto-refinement of 2C9-sMAC

Fileemd_12651_half_map_2.map
AnnotationHalf map 1 from the 3D auto-refinement of 2C9-sMAC
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-sMAC

EntireName: 2C9-sMAC
Components
  • Complex: 2C9-sMAC
    • Protein or peptide: Complement component C8 beta chain
    • Protein or peptide: Complement component C8 alpha chain
    • Protein or peptide: Complement component C9
    • Protein or peptide: Complement component C7
    • Protein or peptide: Complement component C6
    • Protein or peptide: Complement component C8 gamma chain
    • Protein or peptide: Complement C5Complement component 5
  • Ligand: beta-D-mannopyranose
  • Ligand: CALCIUM IONCalcium
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: alpha-L-fucopyranose

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Supramolecule #1: 2C9-sMAC

SupramoleculeName: 2C9-sMAC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Details: This sMAC oligomer contains one copy of C5b8 and 2 copies of C9, as well as multiple copies of the chaperones vitronectin and clusterin
Source (natural)Organism: Homo sapiens (human)
Molecular weightExperimental: 1 MDa

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Macromolecule #1: Complement component C8 beta chain

MacromoleculeName: Complement component C8 beta chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 61.122852 KDa
SequenceString: SVDVTLMPID CELSSWSSWT TCDPCQKKRY RYAYLLQPSQ FHGEPCNFSD KEVEDCVTNR PCRSQVRCEG FVCAQTGRCV NRRLLCNGD NDCGDQSDEA NCRRIYKKCQ HEMDQYWGIG SLASGINLFT NSFEGPVLDH RYYAGGCSPH YILNTRFRKP Y NVESYTPQ ...String:
SVDVTLMPID CELSSWSSWT TCDPCQKKRY RYAYLLQPSQ FHGEPCNFSD KEVEDCVTNR PCRSQVRCEG FVCAQTGRCV NRRLLCNGD NDCGDQSDEA NCRRIYKKCQ HEMDQYWGIG SLASGINLFT NSFEGPVLDH RYYAGGCSPH YILNTRFRKP Y NVESYTPQ TQGKYEFILK EYESYSDFER NVTEKMASKS GFSFGFKIPG IFELGISSQS DRGKHYIRRT KRFSHTKSVF LH ARSDLEV AHYKLKPRSL MLHYEFLQRV KRLPLEYSYG EYRDLFRDFG THYITEAVLG GIYEYTLVMN KEAMERGDYT LNN VHACAK NDFKIGGAIE EVYVSLGVSV GKCRGILNEI KDRNKRDTMV EDLVVLVRGG ASEHITTLAY QELPTADLMQ EWGD AVQYN PAIIKVKVEP LYELVTATDF AYSSTVRQNM KQALEEFQKE VSSCHCAPCQ GNGVPVLKGS RCDCICPVGS QGLAC EVSY RKNTPIDGKW NCWSNWSSCS GRRKTRQRQC NNPPPQNGGS PCSGPASETL DCS

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Macromolecule #2: Complement component C8 alpha chain

MacromoleculeName: Complement component C8 alpha chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 61.782992 KDa
SequenceString: AATPAAVTCQ LSNWSEWTDC FPCQDKKYRH RSLLQPNKFG GTICSGDIWD QASCSSSTTC VRQAQCGQDF QCKETGRCLK RHLVCNGDQ DCLDGSDEDD CEDVRAIDED CSQYEPIPGS QKAALGYNIL TQEDAQSVYD ASYYGGQCET VYNGEWRELR Y DSTCERLY ...String:
AATPAAVTCQ LSNWSEWTDC FPCQDKKYRH RSLLQPNKFG GTICSGDIWD QASCSSSTTC VRQAQCGQDF QCKETGRCLK RHLVCNGDQ DCLDGSDEDD CEDVRAIDED CSQYEPIPGS QKAALGYNIL TQEDAQSVYD ASYYGGQCET VYNGEWRELR Y DSTCERLY YGDDEKYFRK PYNFLKYHFE ALADTGISSE FYDNANDLLS KVKKDKSDSF GVTIGIGPAG SPLLVGVGVS HS QDTSFLN ELNKYNEKKF IFTRIFTKVQ TAHFKMRKDD IMLDEGMLQS LMELPDQYNY GMYAKFINDY GTHYITSGSM GGI YEYILV IDKAKMESLG ITSRDITTCF GGSLGIQYED KINVGGGLSG DHCKKFGGGK TERARKAMAV EDIISRVRGG SSGW SGGLA QNRSTITYRS WGRSLKYNPV VIDFEMQPIH EVLRHTSLGP LEAKRQNLRR ALDQYLMEFN ACRCGPCFNN GVPIL EGTS CRCQCRLGSL GAACEQTQTE GAKADGSWSC WSSWSVCRAG IQERRRECDN PAPQNGGASC PGRKVQTQAC

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Macromolecule #3: Complement component C9

MacromoleculeName: Complement component C9 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 61.056594 KDa
SequenceString: QYTTSYDPEL TESSGSASHI DCRMSPWSEW SQCDPCLRQM FRSRSIEVFG QFNGKRCTDA VGDRRQCVPT EPCEDAEDDC GNDFQCSTG RCIKMRLRCN GDNDCGDFSD EDDCESEPRP PCRDRVVEES ELARTAGYGI NILGMDPLST PFDNEFYNGL C NRDRDGNT ...String:
QYTTSYDPEL TESSGSASHI DCRMSPWSEW SQCDPCLRQM FRSRSIEVFG QFNGKRCTDA VGDRRQCVPT EPCEDAEDDC GNDFQCSTG RCIKMRLRCN GDNDCGDFSD EDDCESEPRP PCRDRVVEES ELARTAGYGI NILGMDPLST PFDNEFYNGL C NRDRDGNT LTYYRRPWNV ASLIYETKGE KNFRTEHYEE QIEAFKSIIQ EKTSNFNAAI SLKFTPTETN KAEQCCEETA SS ISLHGKG SFRFSYSKNE TYQLFLSYSS KKEKMFLHVK GEIHLGRFVM RNRDVVLTTT FVDDIKALPT TYEKGEYFAF LET YGTHYS SSGSLGGLYE LIYVLDKASM KRKGVELKDI KRCLGYHLDV SLAFSEISVG AEFNKDDCVK RGEGRAVNIT SENL IDDVV SLIRGGTRKY AFELKEKLLR GTVIDVTDFV NWASSINDAP VLISQKLSPI YNLVPVKMKN AHLKKQNLER AIEDY INEF SVRKCHTCQN GGTVILMDGK CLCACPFKFE GIACEISKQK ISEGLPALEF PNEK

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Macromolecule #4: Complement component C7

MacromoleculeName: Complement component C7 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 91.221484 KDa
SequenceString: SSPVNCQWDF YAPWSECNGC TKTQTRRRSV AVYGQYGGQP CVGNAFETQS CEPTRGCPTE EGCGERFRCF SGQCISKSLV CNGDSDCDE DSADEDRCED SERRPSCDID KPPPNIELTG NGYNELTGQF RNRVINTKSF GGQCRKVFSG DGKDFYRLSG N VLSYTFQV ...String:
SSPVNCQWDF YAPWSECNGC TKTQTRRRSV AVYGQYGGQP CVGNAFETQS CEPTRGCPTE EGCGERFRCF SGQCISKSLV CNGDSDCDE DSADEDRCED SERRPSCDID KPPPNIELTG NGYNELTGQF RNRVINTKSF GGQCRKVFSG DGKDFYRLSG N VLSYTFQV KINNDFNYEF YNSTWSYVKH TSTEHTSSSR KRSFFRSSSS SSRSYTSHTN EIHKGKSYQL LVVENTVEVA QF INNNPEF LQLAEPFWKE LSHLPSLYDY SAYRRLIDQY GTHYLQSGSL GGEYRVLFYV DSEKLKQNDF NSVEEKKCKS SGW HFVVKF SSHGCKELEN ALKAASGTQN NVLRGEPFIR GGGAGFISGL SYLELDNPAG NKRRYSAWAE SVTNLPQVIK QKLT PLYEL VKEVPCASVK KLYLKWALEE YLDEFDPCHC RPCQNGGLAT VEGTHCLCHC KPYTFGAACE QGVLVGNQAG GVDGG WSCW SSWSPCVQGK KTRSRECNNP PPSGGGRSCV GETTESTQCE DEELEHLRLL EPHCFPLSLV PTEFCPSPPA LKDGFV QDE GTMFPVGKNV VYTCNEGYSL IGNPVARCGE DLRWLVGEMH CQKIACVLPV LMDGIQSHPQ KPFYTVGEKV TVSCSGG MS LEGPSAFLCG SSLKWSPEMK NARCVQKENP LTQAVPKCQR WEKLQNSRCV CKMPYECGPS LDVCAQDERS KRILPLTV C KMHVLHCQGR NYTLTGRDSC TLPASAEKAC GACPLWGKCD AESSKCVCRE ASECEEEGFS ICVEVNGKEQ TMSECEAGA LRCRGQSISV TSIRPCAAET Q

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Macromolecule #5: Complement component C6

MacromoleculeName: Complement component C6 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 102.541312 KDa
SequenceString: CFCDHYAWTQ WTSCSKTCNS GTQSRHRQIV VDKYYQENFC EQICSKQETR ECNWQRCPIN CLLGDFGPWS DCDPCIEKQS KVRSVLRPS QFGGQPCTAP LVAFQPCIPS KLCKIEEADC KNKFRCDSGR CIARKLECNG ENDCGDNSDE RDCGRTKAVC T RKYNPIPS ...String:
CFCDHYAWTQ WTSCSKTCNS GTQSRHRQIV VDKYYQENFC EQICSKQETR ECNWQRCPIN CLLGDFGPWS DCDPCIEKQS KVRSVLRPS QFGGQPCTAP LVAFQPCIPS KLCKIEEADC KNKFRCDSGR CIARKLECNG ENDCGDNSDE RDCGRTKAVC T RKYNPIPS VQLMGNGFHF LAGEPRGEVL DNSFTGGICK TVKSSRTSNP YRVPANLENV GFEVQTAEDD LKTDFYKDLT SL GHNENQQ GSFSSQGGSS FSVPIFYSSK RSENINHNSA FKQAIQASHK KDSSFIRIHK VMKVLNFTTK AKDLHLSDVF LKA LNHLPL EYNSALYSRI FDDFGTHYFT SGSLGGVYDL LYQFSSEELK NSGLTEEEAK HCVRIETKKR VLFAKKTKVE HRCT TNKLS EKHEGSFIQG AEKSISLIRG GRSEYGAALA WEKGSSGLEE KTFSEWLESV KENPAVIDFE LAPIVDLVRN IPCAV TKRN NLRKALQEYA AKFDPCQCAP CPNNGRPTLS GTECLCVCQS GTYGENCEKQ SPDYKSNAVD GQWGCWSSWS TCDATY KRS RTRECNNPAP QRGGKRCEGE KRQEEDCTFS IMENNGQPCI NDDEEMKEVD LPEIEADSGC PQPVPPENGF IRNEKQL YL VGEDVEISCL TGFETVGYQY FRCLPDGTWR QGDVECQRTE CIKPVVQEVL TITPFQRLYR IGESIELTCP KGFVVAGP S RYTCQGNSWT PPISNSLTCE KDTLTKLKGH CQLGQKQSGS ECICMSPEED CSHHSEDLCV FDTDSNDYFT SPACKFLAE KCLNNQQLHF LHIGSCQDGR QLEWGLERTR LSSNSTKKES CGYDTCYDWE KCSASTSKCV CLLPPQCFKG GNQLYCVKMG SSTSEKTLN ICEVGTIRCA NRKMEILHPG KCLA

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Macromolecule #6: Complement component C8 gamma chain

MacromoleculeName: Complement component C8 gamma chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 20.410105 KDa
SequenceString:
QKPQRPRRPA SPISTIQPKA NFDAQQFAGT WLLVAVGSAC RFLQEQGHRA EATTLHVAPQ GTAMAVSTFR KLDGICWQVR QLYGDTGVL GRFLLQARDA RGAVHVVVAE TDYQSFAVLY LERAGQLSVK LYARSLPVSD SVLSGFEQRV QEAHLTEDQI F YFPKYGFC EAADQFHVLD EVRR

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Macromolecule #7: Complement C5

MacromoleculeName: Complement C5 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 186.546656 KDa
SequenceString: QEQTYVISAP KIFRVGASEN IVIQVYGYTE AFDATISIKS YPDKKFSYSS GHVHLSSENK FQNSAILTIQ PKQLPGGQNP VSYVYLEVV SKHFSKSKRM PITYDNGFLF IHTDKPVYTP DQSVKVRVYS LNDDLKPAKR ETVLTFIDPE GSEVDMVEEI D HIGIISFP ...String:
QEQTYVISAP KIFRVGASEN IVIQVYGYTE AFDATISIKS YPDKKFSYSS GHVHLSSENK FQNSAILTIQ PKQLPGGQNP VSYVYLEVV SKHFSKSKRM PITYDNGFLF IHTDKPVYTP DQSVKVRVYS LNDDLKPAKR ETVLTFIDPE GSEVDMVEEI D HIGIISFP DFKIPSNPRY GMWTIKAKYK EDFSTTGTAY FEVKEYVLPH FSVSIEPEYN FIGYKNFKNF EITIKARYFY NK VVTEADV YITFGIREDL KDDQKEMMQT AMQNTMLING IAQVTFDSET AVKELSYYSL EDLNNKYLYI AVTVIESTGG FSE EAEIPG IKYVLSPYKL NLVATPLFLK PGIPYPIKVQ VKDSLDQLVG GVPVTLNAQT IDVNQETSDL DPSKSVTRVD DGVA SFVLN LPSGVTVLEF NVKTDAPDLP EENQAREGYR AIAYSSLSQS YLYIDWTDNH KALLVGEHLN IIVTPKSPYI DKITH YNYL ILSKGKIIHF GTREKFSDAS YQSINIPVTQ NMVPSSRLLV YYIVTGEQTA ELVSDSVWLN IEEKCGNQLQ VHLSPD ADA YSPGQTVSLN MATGMDSWVA LAAVDSAVYG VQRGAKKPLE RVFQFLEKSD LGCGAGGGLN NANVFHLAGL TFLTNAN AD DSQENDEPCK EILRPRRTLQ KKIEEIAAKY KHSVVKKCCY DGACVNNDET CEQRAARISL GPRCIKAFTE CCVVASQL R ANISHKDMQL GRLHMKTLLP VSKPEIRSYF PESWLWEVHL VPRRKQLQFA LPDSLTTWEI QGVGISNTGI CVADTVKAK VFKDVFLEMN IPYSVVRGEQ IQLKGTVYNY RTSGMQFCVK MSAVEGICTS ESPVIDHQGT KSSKCVRQKV EGSSSHLVTF TVLPLEIGL HNINFSLETW FGKEILVKTL RVVPEGVKRE SYSGVTLDPR GIYGTISRRK EFPYRIPLDL VPKTEIKRIL S VKGLLVGE ILSAVLSQEG INILTHLPKG SAEAELMSVV PVFYVFHYLE TGNHWNIFHS DPLIEKQKLK KKLKEGMLSI MS YRNADYS YSVWKGGSAS TWLTAFALRV LGQVNKYVEQ NQNSICNSLL WLVENYQLDN GSFKENSQYQ PIKLQGTLPV EAR ENSLYL TAFTVIGIRK AFDICPLVKI DTALIKADNF LLENTLPAQS TFTLAISAYA LSLGDKTHPQ FRSIVSALKR EALV KGNPP IYRFWKDNLQ HKDSSVPNTG TARMVETTAY ALLTSLNLKD INYVNPVIKW LSEEQRYGGG FYSTQDTINA IEGLT EYSL LVKQLRLSMD IDVSYKHKGA LHNYKMTDKN FLGRPVEVLL NDDLIVSTGF GSGLATVHVT TVVHKTSTSE EVCSFY LKI DTQDIEASHY RGYGNSDYKR IVACASYKPS REESSSGSSH AVMDISLPTG ISANEEDLKA LVEGVDQLFT DYQIKDG HV ILQLNSIPSS DFLCVRFRIF ELFEVGFLSP ATFTVYEYHR PDKQCTMFYS TSNIKIQKVC EGAACKCVEA DCGQMQEE L DLTISAETRK QTACKPEIAY AYKVSITSIT VENVFVKYKA TLLDIYKTGE AVAEKDSEIT FIKKVTCTNA ELVKGRQYL IMGKEALQIK YNFSFRYIYP LDSLTWIEYW PRDTTCSSCQ AFLANLDEFA EDIFLNGC

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Macromolecule #11: beta-D-mannopyranose

MacromoleculeName: beta-D-mannopyranose / type: ligand / ID: 11 / Number of copies: 6 / Formula: BMA
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-BMA:
beta-D-mannopyranose / Mannose

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Macromolecule #12: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 12 / Number of copies: 4 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #13: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 13 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Macromolecule #14: alpha-L-fucopyranose

MacromoleculeName: alpha-L-fucopyranose / type: ligand / ID: 14 / Number of copies: 1 / Formula: FUC
Molecular weightTheoretical: 164.156 Da
Chemical component information

ChemComp-FUC:
alpha-L-fucopyranose / Fucose

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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

Concentration0.065 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4-1)
Startup modelType of model: INSILICO MODEL
In silico model: The initial model was generated in Relion 3.1
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 142499

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Atomic model buiding 1

Initial model(PDB ID:

6h03

,

6h04

,

4a5w

,

2wcy

,

6cxo

)
RefinementProtocol: RIGID BODY FIT
Output model

PDB-7nyd:
cryoEM structure of 2C9-sMAC

+
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