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- EMDB-3134: Electron cryo-microscopy of an immune pore -

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Basic information

Entry
Database: EMDB / ID: EMD-3134
TitleElectron cryo-microscopy of an immune pore
Map dataReconstruction of the membrane attack complex
Sample
  • Sample: Membrane attack complex
  • Protein or peptide: C5
  • Protein or peptide: C6
  • Protein or peptide: C7
  • Protein or peptide: C8 alpha
  • Protein or peptide: C8 beta
  • Protein or peptide: C8 gamma
  • Protein or peptide: C9
Keywordscryo-EM / single particles / membrane protein
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.5 Å
AuthorsSerna M / Bubeck D
CitationJournal: Nat Commun / Year: 2016
Title: Structural basis of complement membrane attack complex formation.
Authors: Marina Serna / Joanna L Giles / B Paul Morgan / Doryen Bubeck /
Abstract: In response to complement activation, the membrane attack complex (MAC) assembles from fluid-phase proteins to form pores in lipid bilayers. MAC directly lyses pathogens by a 'multi-hit' mechanism; ...In response to complement activation, the membrane attack complex (MAC) assembles from fluid-phase proteins to form pores in lipid bilayers. MAC directly lyses pathogens by a 'multi-hit' mechanism; however, sublytic MAC pores on host cells activate signalling pathways. Previous studies have described the structures of individual MAC components and subcomplexes; however, the molecular details of its assembly and mechanism of action remain unresolved. Here we report the electron cryo-microscopy structure of human MAC at subnanometre resolution. Structural analyses define the stoichiometry of the complete pore and identify a network of interaction interfaces that determine its assembly mechanism. MAC adopts a 'split-washer' configuration, in contrast to the predicted closed ring observed for perforin and cholesterol-dependent cytolysins. Assembly precursors partially penetrate the lipid bilayer, resulting in an irregular β-barrel pore. Our results demonstrate how differences in symmetric and asymmetric components of the MAC underpin a molecular basis for pore formation and suggest a mechanism of action that extends beyond membrane penetration.
History
DepositionAug 25, 2015-
Header (metadata) releaseJan 13, 2016-
Map releaseFeb 10, 2016-
UpdateFeb 17, 2016-
Current statusFeb 17, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.12
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.12
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD3134_imag...

Downloads & links

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Map

FileDownload / File: emd_3134.map.gz / Format: CCP4 / Size: 34.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of the membrane attack complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.8 Å/pix.
x 210 pix.
= 588. Å		2.8 Å/pix.
x 210 pix.
= 588. Å		2.8 Å/pix.
x 210 pix.
= 588. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12 / Movie #1: 0.12
Minimum - Maximum-0.33782661 - 0.64413261
Average (Standard dev.)0.00165011 (±0.01986981)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions210210210
Spacing210210210
CellA=B=C: 588.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.82.82.8
M x/y/z210210210
origin x/y/z0.0000.0000.000
length x/y/z588.000588.000588.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS210210210
D min/max/mean-0.3380.6440.002

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Supplemental data

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Sample components

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Entire : Membrane attack complex

EntireName: Membrane attack complex
Components
  • Sample: Membrane attack complex
  • Protein or peptide: C5
  • Protein or peptide: C6
  • Protein or peptide: C7
  • Protein or peptide: C8 alpha
  • Protein or peptide: C8 beta
  • Protein or peptide: C8 gamma
  • Protein or peptide: C9

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Supramolecule #1000: Membrane attack complex

SupramoleculeName: Membrane attack complex / type: sample / ID: 1000
Details: Protein complex was assembled on liposomes and detergent solubilized
Number unique components: 7
Molecular weightTheoretical: 1.8 MDa

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Macromolecule #1: C5

MacromoleculeName: C5 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Tissue: Plasma
Molecular weightTheoretical: 190 KDa

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Macromolecule #2: C6

MacromoleculeName: C6 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Tissue: Plasma
Molecular weightTheoretical: 120 KDa

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Macromolecule #3: C7

MacromoleculeName: C7 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Tissue: Plasma
Molecular weightTheoretical: 110 KDa

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Macromolecule #4: C8 alpha

MacromoleculeName: C8 alpha / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Tissue: Plasma
Molecular weightTheoretical: 152 KDa

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Macromolecule #5: C8 beta

MacromoleculeName: C8 beta / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Tissue: Plasma
Molecular weightTheoretical: 152 KDa

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Macromolecule #6: C8 gamma

MacromoleculeName: C8 gamma / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Tissue: Plasma
Molecular weightTheoretical: 152 KDa

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Macromolecule #7: C9

MacromoleculeName: C9 / type: protein_or_peptide / ID: 7 / Number of copies: 18 / Oligomeric state: eighteen-mer / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Tissue: Plasma
Molecular weightTheoretical: 69 KDa

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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 / Details: 20 mM HEPES-NaOH, 150 mM NaCl
GridDetails: 300 mesh quantifoil R1.2/1.3 grids with thin carbon support
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DateJul 2, 2015
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Digitization - Sampling interval: 14.0 µm / Number real images: 622 / Average electron dose: 45 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.00 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsParticles were manually selected.
CTF correctionDetails: CTFFIND3, phase flip on each particle
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.5 Å / Resolution method: OTHER / Software - Name: RELION, EMAN2 / Number images used: 41981

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Atomic model buiding 1

Initial modelPDB ID:

3ojy

SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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Atomic model buiding 2

Initial modelPDB ID:

4a5w

SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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