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- EMDB-0112: Hinge region of the Membrane Attack Complex in the open conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-0112
TitleHinge region of the Membrane Attack Complex in the open conformation
Map data
Sample
  • Complex: Membrane Attack ComplexComplement membrane attack complex
    • Complex: C5b
    • Complex: C6
    • Complex: C7
    • Complex: C8 alpha
    • Complex: C8 beta
    • Complex: C8 gamma
    • Complex: C9
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsMenny A / Serna M / Boyd CB / Gardener S / Joseph AP / Topf M / Bubeck D
CitationJournal: Nat Commun / Year: 2018
Title: CryoEM reveals how the complement membrane attack complex ruptures lipid bilayers.
Authors: Anaïs Menny / Marina Serna / Courtney M Boyd / Scott Gardner / Agnel Praveen Joseph / B Paul Morgan / Maya Topf / Nicholas J Brooks / Doryen Bubeck /
Abstract: The membrane attack complex (MAC) is one of the immune system's first responders. Complement proteins assemble on target membranes to form pores that lyse pathogens and impact tissue homeostasis of ...The membrane attack complex (MAC) is one of the immune system's first responders. Complement proteins assemble on target membranes to form pores that lyse pathogens and impact tissue homeostasis of self-cells. How MAC disrupts the membrane barrier remains unclear. Here we use electron cryo-microscopy and flicker spectroscopy to show that MAC interacts with lipid bilayers in two distinct ways. Whereas C6 and C7 associate with the outer leaflet and reduce the energy for membrane bending, C8 and C9 traverse the bilayer increasing membrane rigidity. CryoEM reconstructions reveal plasticity of the MAC pore and demonstrate how C5b6 acts as a platform, directing assembly of a giant β-barrel whose structure is supported by a glycan scaffold. Our work provides a structural basis for understanding how β-pore forming proteins breach the membrane and reveals a mechanism for how MAC kills pathogens and regulates cell functions.
History
DepositionJul 6, 2018-
Header (metadata) releaseAug 22, 2018-
Map releaseDec 19, 2018-
UpdateDec 26, 2018-
Current statusDec 26, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.09
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.09
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0112.png

Downloads & links

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Map

FileDownload / File: emd_0112.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.384 Å
Density
Contour LevelBy AUTHOR: 0.09 / Movie #1: 0.09
Minimum - Maximum-0.23835017 - 0.4409761
Average (Standard dev.)-0.00092138455 (±0.0075461976)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 498.24 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3841.3841.384
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z498.240498.240498.240
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.2380.441-0.001

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Supplemental data

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Sample components

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Entire : Membrane Attack Complex

EntireName: Membrane Attack ComplexComplement membrane attack complex
Components
  • Complex: Membrane Attack ComplexComplement membrane attack complex
    • Complex: C5b
    • Complex: C6
    • Complex: C7
    • Complex: C8 alpha
    • Complex: C8 beta
    • Complex: C8 gamma
    • Complex: C9

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Supramolecule #1: Membrane Attack Complex

SupramoleculeName: Membrane Attack Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Details: Protein complex was assembled on liposomes and detergent solubilized
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 69 KDa

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Supramolecule #2: C5b

SupramoleculeName: C5b / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 / Details: Component of the Membrane Attack Complex
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: C6

SupramoleculeName: C6 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 / Details: Component of the Membrane Attack Complex
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: C7

SupramoleculeName: C7 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #4 / Details: Component of the Membrane Attack Complex
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #5: C8 alpha

SupramoleculeName: C8 alpha / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #6 / Details: Component of the Membrane Attack Complex
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #6: C8 beta

SupramoleculeName: C8 beta / type: complex / ID: 6 / Parent: 1 / Macromolecule list: #3 / Details: Component of the Membrane Attack Complex
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #7: C8 gamma

SupramoleculeName: C8 gamma / type: complex / ID: 7 / Parent: 1 / Macromolecule list: #5 / Details: Component of the Membrane Attack Complex
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #8: C9

SupramoleculeName: C9 / type: complex / ID: 8 / Parent: 1 / Macromolecule list: #7 / Details: Component of the Membrane Attack Complex
Source (natural)Organism: Homo sapiens (human)

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 8 / Number real images: 13009 / Average exposure time: 2.0 sec. / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 288366
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Startup modelType of model: EMDB MAP
EMDB ID:

3134


Details: Low pass filtered to 60 A
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 81968

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