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- EMDB-1991: Structure of complement component complex, sC5b9. -

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Basic information

Entry
Database: EMDB / ID: EMD-1991
TitleStructure of complement component complex, sC5b9.
Map dataThis is an image of a surface rendered view of the sC5b9 complex
Sample
  • Sample: sC5b9
  • Protein or peptide: C5b
  • Protein or peptide: C6
  • Protein or peptide: C7
  • Protein or peptide: C8
  • Protein or peptide: C9
  • Protein or peptide: Clusterin
  • Protein or peptide: vibronectin
Keywordscomplement terminal pathway / humoral immune pore / MACPF domain
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 24.0 Å
AuthorsBubeck D / Roversi P / Hakabyan S / Morgan BP / Lea SM / Llorca O
CitationJournal: Cell Rep / Year: 2012
Title: Assembly and regulation of the membrane attack complex based on structures of C5b6 and sC5b9.
Authors: Michael A Hadders / Doryen Bubeck / Pietro Roversi / Svetlana Hakobyan / Federico Forneris / B Paul Morgan / Michael K Pangburn / Oscar Llorca / Susan M Lea / Piet Gros /
Abstract: Activation of the complement system results in formation of membrane attack complexes (MACs), pores that disrupt lipid bilayers and lyse bacteria and other pathogens. Here, we present the crystal ...Activation of the complement system results in formation of membrane attack complexes (MACs), pores that disrupt lipid bilayers and lyse bacteria and other pathogens. Here, we present the crystal structure of the first assembly intermediate, C5b6, together with a cryo-electron microscopy reconstruction of a soluble, regulated form of the pore, sC5b9. Cleavage of C5 to C5b results in marked conformational changes, distinct from those observed in the homologous C3-to-C3b transition. C6 captures this conformation, which is preserved in the larger sC5b9 assembly. Together with antibody labeling, these structures reveal that complement components associate through sideways alignment of the central MAC-perforin (MACPF) domains, resulting in a C5b6-C7-C8β-C8α-C9 arc. Soluble regulatory proteins below the arc indicate a potential dual mechanism in protection from pore formation. These results provide a structural framework for understanding MAC pore formation and regulation, processes important for fighting infections and preventing complement-mediated tissue damage.
History
DepositionNov 17, 2011-
Header (metadata) releaseJan 27, 2012-
Map releaseFeb 24, 2012-
UpdateAug 29, 2012-
Current statusAug 29, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0122
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0122
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

image.png

Downloads & links

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Map

FileDownload / File: emd_1991.map.gz / Format: CCP4 / Size: 12.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is an image of a surface rendered view of the sC5b9 complex
Voxel sizeX=Y=Z: 2.76 Å
Density
Contour LevelBy AUTHOR: 0.0122 / Movie #1: 0.0122
Minimum - Maximum-0.02482872 - 0.09138546
Average (Standard dev.)0.00034994 (±0.00500717)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions150150150
Spacing150150150
CellA=B=C: 414.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.762.762.76
M x/y/z150150150
origin x/y/z0.0000.0000.000
length x/y/z414.000414.000414.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS150150150
D min/max/mean-0.0250.0910.000

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Supplemental data

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Sample components

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Entire : sC5b9

EntireName: sC5b9
Components
  • Sample: sC5b9
  • Protein or peptide: C5b
  • Protein or peptide: C6
  • Protein or peptide: C7
  • Protein or peptide: C8
  • Protein or peptide: C9
  • Protein or peptide: Clusterin
  • Protein or peptide: vibronectin

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Supramolecule #1000: sC5b9

SupramoleculeName: sC5b9 / type: sample / ID: 1000 / Details: The sample was monodisperse
Oligomeric state: 7, C8, and C9. In addition it contains clusterin and vitronectin with an unknown stoichiometry.
Number unique components: 7

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Macromolecule #1: C5b

MacromoleculeName: C5b / type: protein_or_peptide / ID: 1 / Name.synonym: sC5b9, or sMAC / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Tissue: Plasma

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Macromolecule #2: C6

MacromoleculeName: C6 / type: protein_or_peptide / ID: 2 / Name.synonym: sC5b9, or sMAC / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Tissue: Plasma

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Macromolecule #3: C7

MacromoleculeName: C7 / type: protein_or_peptide / ID: 3 / Name.synonym: sC5b9, or sMAC / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Tissue: Plasma

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Macromolecule #4: C8

MacromoleculeName: C8 / type: protein_or_peptide / ID: 4 / Name.synonym: sC5b9, or sMAC / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Tissue: Plasma

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Macromolecule #5: C9

MacromoleculeName: C9 / type: protein_or_peptide / ID: 5 / Name.synonym: sC5b9, or sMAC / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Tissue: Plasma

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Macromolecule #6: Clusterin

MacromoleculeName: Clusterin / type: protein_or_peptide / ID: 6 / Name.synonym: sC5b9, or sMAC / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Tissue: Plasma

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Macromolecule #7: vibronectin

MacromoleculeName: vibronectin / type: protein_or_peptide / ID: 7 / Name.synonym: sC5b9, or sMAC / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Tissue: Plasma

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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

Concentration0.1 mg/mL
BufferpH: 7.5 / Details: 150mM NaCl, 50mM Tris, 1mM CaCl2, and 1mM MgCl2
GridDetails: quantifoil holey carbon grids
VitrificationCryogen name: ETHANE / Instrument: OTHER / Details: Vitrification instrument: FEI Vitrobot

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Electron microscopy

MicroscopeJEOL 2200FS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 54400
Specialist opticsEnergy filter - Name: OMEGA
Sample stageSpecimen holder: single-tilt cryo holder / Specimen holder model: GATAN LIQUID NITROGEN
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 405 / Average electron dose: 10 e/Å2

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Image processing

CTF correctionDetails: Bsoft, phase flip on each particle
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 24.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN2, XMIPP / Number images used: 18983

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Atomic model buiding 1

Initial modelPDB ID:

3ojy


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C
SoftwareName: Chimera
DetailsPDBEntryID_givenInChain. Protocol: Rigid Body
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation Coefficient

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