[English] 日本語
Yorodumi
- EMDB-15779: CryoEM structure of C5b8-CD59 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-15779
TitleCryoEM structure of C5b8-CD59
Map dataCryoEM reconstruction of C5b8-CD59.
Sample
  • Complex: C5b8-CD59
    • Complex: Complement components C5, C6, C7 and C8
      • Protein or peptide: Complement C5
      • Protein or peptide: Complement component C6
      • Protein or peptide: Complement component C7
      • Protein or peptide: Complement component C8 beta chain
      • Protein or peptide: Complement component C8 alpha chain
      • Protein or peptide: Complement component C8 gamma chain
    • Complex: CD59 glycoprotein
      • Protein or peptide: CD59 glycoprotein
  • Ligand: CALCIUM ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


negative regulation of activation of membrane attack complex / Terminal pathway of complement / membrane attack complex / complement binding / regulation of complement-dependent cytotoxicity / regulation of complement activation / Activation of C3 and C5 / negative regulation of macrophage chemotaxis / Cargo concentration in the ER / complement activation ...negative regulation of activation of membrane attack complex / Terminal pathway of complement / membrane attack complex / complement binding / regulation of complement-dependent cytotoxicity / regulation of complement activation / Activation of C3 and C5 / negative regulation of macrophage chemotaxis / Cargo concentration in the ER / complement activation / complement activation, alternative pathway / chemokine activity / COPII-mediated vesicle transport / retinol binding / endopeptidase inhibitor activity / tertiary granule membrane / positive regulation of vascular endothelial growth factor production / COPI-mediated anterograde transport / specific granule membrane / 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 / chemotaxis / positive regulation of immune response / blood coagulation / extracellular vesicle / G alpha (i) signalling events / in utero embryonic development / vesicle / blood microparticle / killing of cells of another organism / cell surface receptor signaling pathway / inflammatory response / immune response / G protein-coupled receptor signaling pathway / Golgi membrane / external side of plasma membrane / innate immune response / signaling receptor binding / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / protein-containing complex binding / 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 / MAC/Perforin domain / Membrane attack complex/perforin (MACPF) domain profile. / 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, complement system / Anaphylatoxin/fibulin / 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. / 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 / Tissue inhibitor of metalloproteinases-like, OB-fold / Thrombospondin type 1 domain / Low-density lipoprotein receptor domain class A / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / Lipocalin family conserved site / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Snake toxin-like superfamily / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Lipocalin/cytosolic fatty-acid binding domain / Lipocalin / cytosolic fatty-acid binding protein family / Calycin / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / Lipocalin signature. / Immunoglobulin-like fold
Similarity search - Domain/homology
Complement C5 / 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) / Escherichia coli (E. coli) / human (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsBubeck D / Couves EC / Gardner S
Funding supportEuropean Union, United Kingdom, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)864751European Union
Cancer Research UKC24523/A26234 United Kingdom
Citation
Journal: 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.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2018
Title: Real-space refinement in PHENIX for cryo-EM and crystallography
Authors: Afonine PV / Poon BK / Read RJ / Sobolev OV / Terwilliger TC / Urzhumtsev A / Adams PD
History
DepositionSep 7, 2022-
Header (metadata) releaseFeb 22, 2023-
Map releaseFeb 22, 2023-
UpdateMar 1, 2023-
Current statusMar 1, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_15779.png

Downloads & links

-
Map

FileDownload / File: emd_15779.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM reconstruction of C5b8-CD59.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.17 Å/pix.
x 448 pix.
= 524.608 Å		1.17 Å/pix.
x 448 pix.
= 524.608 Å		1.17 Å/pix.
x 448 pix.
= 524.608 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.171 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.75
Minimum - Maximum-4.269096 - 9.492268
Average (Standard dev.)0.00413231 (±0.12551086)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 524.60803 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_15779_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: CryoEM reconstruction of C5b8-CD59.

Fileemd_15779_half_map_1.map
AnnotationCryoEM reconstruction of C5b8-CD59.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: CryoEM reconstruction of C5b8-CD59.

Fileemd_15779_half_map_2.map
AnnotationCryoEM reconstruction of C5b8-CD59.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : C5b8-CD59

EntireName: C5b8-CD59
Components
  • Complex: C5b8-CD59
    • Complex: Complement components C5, C6, C7 and C8
      • Protein or peptide: Complement C5
      • Protein or peptide: Complement component C6
      • Protein or peptide: Complement component C7
      • Protein or peptide: Complement component C8 beta chain
      • Protein or peptide: Complement component C8 alpha chain
      • Protein or peptide: Complement component C8 gamma chain
    • Complex: CD59 glycoprotein
      • Protein or peptide: CD59 glycoprotein
  • Ligand: CALCIUM ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

+
Supramolecule #1: C5b8-CD59

SupramoleculeName: C5b8-CD59 / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#7 / Details: Inhibited complement membrane attack complex

+
Supramolecule #2: Complement components C5, C6, C7 and C8

SupramoleculeName: Complement components C5, C6, C7 and C8 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)

+
Supramolecule #3: CD59 glycoprotein

SupramoleculeName: CD59 glycoprotein / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #7
Source (natural)Organism: Escherichia coli (E. coli)

+
Macromolecule #1: Complement C5

MacromoleculeName: Complement C5 / type: protein_or_peptide / ID: 1 / 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

+
Macromolecule #2: Complement component C6

MacromoleculeName: Complement component C6 / type: protein_or_peptide / ID: 2 / 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

+
Macromolecule #3: Complement component C7

MacromoleculeName: Complement component C7 / type: protein_or_peptide / ID: 3 / 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

+
Macromolecule #4: Complement component C8 beta chain

MacromoleculeName: Complement component C8 beta chain / type: protein_or_peptide / ID: 4 / 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

+
Macromolecule #5: Complement component C8 alpha chain

MacromoleculeName: Complement component C8 alpha chain / type: protein_or_peptide / ID: 5 / 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

+
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: 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

+
Macromolecule #7: CD59 glycoprotein

MacromoleculeName: CD59 glycoprotein / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 13.35533 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGIQGGSVLF GLLLVLAVFC HSGHSLQCYN CPNPTADCKT AVNCSSDFDA CLITKAGLQV YNKCWKFEHC NFNDVTTRLR ENELTYYCC KKDLCNFNEQ LENGGTSLSE KTVLLLVTPF L

+
Macromolecule #10: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 10 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

+
Macromolecule #11: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 11 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: NITROGEN
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 294 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 2 / Number real images: 12805 / Average exposure time: 9.8 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.9 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 1138825
Details: CrYOLO neural network based particle picking, standard model, low threshold (0.01).
Startup modelType of model: INSILICO MODEL
In silico model: An initial model was generated using ab-inito reconstruction in cryoSPARC.
Final reconstructionNumber classes used: 2 / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 206782
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final 3D classificationNumber classes: 4 / Avg.num./class: 51965 / Software - Name: RELION (ver. 3.1)
Details: 3D Classification was used to remove junk particles and particles with graphene oxide edges.
FSC plot (resolution estimation)

-
Atomic model buiding 1

DetailsInitial 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.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 87
Output model

PDB-8b0f:
CryoEM structure of C5b8-CD59

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more