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- EMDB-1805: Structure of human complement C8, a precursor to membrane attack. -

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Basic information

Entry
Database: EMDB / ID: EMD-1805
TitleStructure of human complement C8, a precursor to membrane attack.
Map dataThis is the EM reconstruction of human C8
Sample
  • Sample: Human complement C8
  • Protein or peptide: Human complement C8 alpha subunit
  • Protein or peptide: Human complement C8 beta subunit
  • Protein or peptide: Human complement C8 gamma subunit
KeywordsC8 / complement / membrane attack complex / MAC / terminal pathway
Function / homologyMembrane attack complex component/perforin/complement C9 / Thrombospondin type-1 (TSP1) repeat / complement activation, alternative pathway / complement activation, classical pathway / Lipocalin/cytosolic fatty-acid binding domain
Function and homology information
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 25.0 Å
AuthorsBubeck D / Roversi P / Donev R / Morgan BP / Llorca O / Lea SM
CitationJournal: J Mol Biol / Year: 2011
Title: Structure of human complement C8, a precursor to membrane attack.
Authors: Doryen Bubeck / Pietro Roversi / Rossen Donev / B Paul Morgan / Oscar Llorca / Susan M Lea /
Abstract: Complement component C8 plays a pivotal role in the formation of the membrane attack complex (MAC), an important antibacterial immune effector. C8 initiates membrane penetration and coordinates MAC ...Complement component C8 plays a pivotal role in the formation of the membrane attack complex (MAC), an important antibacterial immune effector. C8 initiates membrane penetration and coordinates MAC pore formation. High-resolution structures of C8 subunits have provided some insight into the function of the C8 heterotrimer; however, there is no structural information describing how the intersubunit organization facilitates MAC assembly. We have determined the structure of C8 by electron microscopy and fitted the C8α-MACPF (membrane attack complex/perforin)-C8γ co-crystal structure and a homology model for C8β-MACPF into the density. Here, we demonstrate that both the C8γ protrusion and the C8α-MACPF region that inserts into the membrane upon activation are accessible.
History
DepositionOct 12, 2010-
Header (metadata) releaseOct 13, 2010-
Map releaseOct 20, 2010-
UpdateSep 9, 2011-
Current statusSep 9, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 3.6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1805.jpg

Downloads & links

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Map

FileDownload / File: emd_1805.map.gz / Format: CCP4 / Size: 422.9 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the EM reconstruction of human C8
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.7 Å/pix.
x 48 pix.
= 225.6 Å		4.7 Å/pix.
x 48 pix.
= 225.6 Å		4.7 Å/pix.
x 48 pix.
= 225.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.7 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.6 / Movie #1: 3.6
Minimum - Maximum-5.21946 - 13.638299999999999
Average (Standard dev.)-0.00000000476728 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-24-24-24
Dimensions484848
Spacing484848
CellA=B=C: 225.6 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.74.74.7
M x/y/z484848
origin x/y/z0.0000.0000.000
length x/y/z225.600225.600225.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-150-150-149
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS-24-24-24
NC/NR/NS484848
D min/max/mean-5.21913.638-0.000

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Supplemental data

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Sample components

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Entire : Human complement C8

EntireName: Human complement C8
Components
  • Sample: Human complement C8
  • Protein or peptide: Human complement C8 alpha subunit
  • Protein or peptide: Human complement C8 beta subunit
  • Protein or peptide: Human complement C8 gamma subunit

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Supramolecule #1000: Human complement C8

SupramoleculeName: Human complement C8 / type: sample / ID: 1000
Details: The sample was purified by size exclusion chromatography and the purity checked by SDS-PAGE
Oligomeric state: Heterotrimer of C8alpha C8beta and C8gamma
Number unique components: 3
Molecular weightTheoretical: 150 KDa

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Macromolecule #1: Human complement C8 alpha subunit

MacromoleculeName: Human complement C8 alpha subunit / type: protein_or_peptide / ID: 1 / Name.synonym: C8 alpha / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Tissue: Serum / Location in cell: Extracellular
Molecular weightTheoretical: 65.163 KDa
SequenceGO: complement activation, alternative pathway / InterPro: Thrombospondin type-1 (TSP1) repeat

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Macromolecule #2: Human complement C8 beta subunit

MacromoleculeName: Human complement C8 beta subunit / type: protein_or_peptide / ID: 2 / Name.synonym: C8 beta / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Tissue: Serum / Location in cell: Extracellular
SequenceGO: complement activation, classical pathway
InterPro: Membrane attack complex component/perforin/complement C9

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Macromolecule #3: Human complement C8 gamma subunit

MacromoleculeName: Human complement C8 gamma subunit / type: protein_or_peptide / ID: 3 / Name.synonym: C8 gamma / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Tissue: Serum / Location in cell: Extracellular
SequenceGO: complement activation, alternative pathway / InterPro: Lipocalin/cytosolic fatty-acid binding domain

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.03 mg/mL
BufferpH: 7.4
Details: 100 mM NaCl, 0.15 mM CaCl2, 0.5 mM MgCl2, 5 mM Imidazole pH 7.4.
StainingType: NEGATIVE / Details: 0.75% uranyl formate using the two-drop method
GridDetails: Carbon-coated copper-palladium grid, which was glow-discharged for 10 seconds at 20 mA
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingDigitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Average electron dose: 10 e/Å2 / Bits/pixel: 4
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal magnification: 59000
Sample stageSpecimen holder: OTHER / Specimen holder model: OTHER
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

DetailsMicrographs were digitized using a SCAI scanner at a step size of 7 um and binned by a factor of 4 resulting in a pixel size of 4.74 A per pixel
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 5167
Final two d classificationNumber classes: 362

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Atomic model buiding 1

Initial modelPDB ID:

2rd7


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: C
SoftwareName: UCSF Chimera
DetailsPDBEntryID_givenInChain. Protocol: Real space rigid body. Fitted as a rigid body in real space
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: R-factor

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