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

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Open data


ID or keywords:

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no data

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Basic information

Entry
Database: EMDB / ID: 0112
TitleHinge region of the Membrane Attack Complex in the open conformation
Map data
SampleMembrane Attack ComplexComplement membrane attack complex:
C5b / C6 / C7 / C8 alpha / C8 beta / C8 gamma / C9
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 4.9 Å resolution
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
DateDeposition: Jul 6, 2018 / Header (metadata) release: Aug 22, 2018 / Map release: Dec 19, 2018 / Last update: Dec 26, 2018

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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
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_0112.map.gz (map file in CCP4 format, 186625 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
360 pix
1.38 Å/pix.
= 498.24 Å
360 pix
1.38 Å/pix.
= 498.24 Å
360 pix
1.38 Å/pix.
= 498.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.384 Å
Density
Contour Level:0.09 (by author), 0.09 (movie #1):
Minimum - Maximum-0.23835017 - 0.4409761
Average (Standard dev.)-0.00092138455 (0.0075461976)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions360360360
Origin0.00.00.0
Limit359.0359.0359.0
Spacing360360360
CellA=B=C: 498.24 Å
α=β=γ: 90.0 deg.

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
start NX/NY/NZ
NX/NY/NZ
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 Complex
Details: Protein complex was assembled on liposomes and detergent solubilized
Number of components: 8

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Component #1: protein, Membrane Attack Complex

ProteinName: Membrane Attack ComplexComplement membrane attack complex
Details: Protein complex was assembled on liposomes and detergent solubilized
Recombinant expression: No
MassTheoretical: 69 kDa
SourceSpecies: Homo sapiens (human)

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Component #2: protein, C5b

ProteinName: C5b / Details: Component of the Membrane Attack Complex / Recombinant expression: No
SourceSpecies: Homo sapiens (human)

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Component #3: protein, C6

ProteinName: C6 / Details: Component of the Membrane Attack Complex / Recombinant expression: No
SourceSpecies: Homo sapiens (human)

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Component #4: protein, C7

ProteinName: C7 / Details: Component of the Membrane Attack Complex / Recombinant expression: No
SourceSpecies: Homo sapiens (human)

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Component #5: protein, C8 alpha

ProteinName: C8 alpha / Details: Component of the Membrane Attack Complex / Recombinant expression: No
SourceSpecies: Homo sapiens (human)

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Component #6: protein, C8 beta

ProteinName: C8 beta / Details: Component of the Membrane Attack Complex / Recombinant expression: No
SourceSpecies: Homo sapiens (human)

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Component #7: protein, C8 gamma

ProteinName: C8 gamma / Details: Component of the Membrane Attack Complex / Recombinant expression: No
SourceSpecies: Homo sapiens (human)

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Component #8: protein, C9

ProteinName: C9 / Details: Component of the Membrane Attack Complex / Recombinant expression: No
SourceSpecies: Homo sapiens (human)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 5 e/Å2 / Illumination mode: SPOT SCAN
LensMagnification: 59000.0 X (nominal) / Imaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 13009

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 81968
3D reconstructionSoftware: RELION / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF

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