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- EMDB-0107: Closed conformation of the Membrane Attack Complex -

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Basic information

Entry
Database: EMDB / ID: 0107
TitleClosed conformation of the Membrane Attack Complex
Map data
SampleMembrane Attack ComplexComplement membrane attack complex:
C5b / C6 / C7 / C8 alpha / C8 beta / C8 gamma / C9 / (Complement component ...) x 6 / Complement C5,Complement C5 / ligand
Function / homologyCalycin / Immunoglobulin-like fold / LDL receptor-like superfamily / Sushi/SCR/CCP superfamily / Low-density lipoprotein (LDL) receptor class A, conserved site / Lipocalin family conserved site / Membrane attack complex component/perforin (MACPF) domain / Membrane attack complex component/perforin domain, conserved site / Netrin module, non-TIMP type / Anaphylatoxin, complement system ...Calycin / Immunoglobulin-like fold / LDL receptor-like superfamily / Sushi/SCR/CCP superfamily / Low-density lipoprotein (LDL) receptor class A, conserved site / Lipocalin family conserved site / Membrane attack complex component/perforin (MACPF) domain / Membrane attack complex component/perforin domain, conserved site / Netrin module, non-TIMP type / Anaphylatoxin, complement system / Alpha-macroglobulin, TED domain / Alpha-macroglobulin, receptor-binding domain superfamily / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin, receptor-binding / Growth factor receptor cysteine-rich domain superfamily / Tissue inhibitor of metalloproteinases-like, OB-fold / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Factor I / membrane attack complex / Alpha-1-microglobulin / Macroglobulin domain / Thrombospondin type-1 (TSP1) repeat superfamily / Complement C5 / Lipocalin / UNC-6/NTR/C345C module / EGF-like domain signature 1. / Kazal-type serine protease inhibitor domain / Alpha-2-macroglobulin bait region domain / A-macroglobulin TED domain / A-macroglobulin receptor binding domain / MG2 domain / MAC/Perforin domain / Anaphylotoxin-like domain / Alpha-2-macroglobulin family / Complement component C6 / Thrombospondin type 1 domain / Sushi repeat (SCR repeat) / Lipocalin / cytosolic fatty-acid binding protein family / Low-density lipoprotein receptor domain class A / Kazal-type serine protease inhibitor domain / Complement component C9 / Complement component C8 beta chain / Complement component C8 alpha chain / Complement component C7 / Kazal domain / Low-density lipoprotein (LDL) receptor class A repeat / Membrane attack complex/perforin (MACPF) domain signature. / EGF-like domain signature 2. / Regulation of Complement cascade / G alpha (i) signalling events / Peptide ligand-binding receptors / Activation of C3 and C5 / Terminal pathway of complement / Kazal domain profile. / Membrane attack complex/perforin (MACPF) domain profile. / Sushi/CCP/SCR domain profile. / NTR domain profile. / Membrane attack complex component/perforin/complement C9 / Thrombospondin type-1 (TSP1) repeat profile. / LDL-receptor class A (LDLRA) domain profile. / LDL-receptor class A (LDLRA) domain signature. / Lipocalin signature. / Anaphylatoxin/fibulin / Sushi/SCR/CCP domain / Anaphylatoxin domain profile. / Anaphylatoxin, complement system domain / Anaphylatoxin domain signature. / Alpha-2-macroglobulin / Netrin domain / Thrombospondin type-1 (TSP1) repeat / Lipocalin/cytosolic fatty-acid binding domain / cell killing / membrane attack complex / complement binding / positive regulation of activation of membrane attack complex / cellular sodium ion homeostasis / positive regulation of chemokine secretion / negative regulation of macrophage chemotaxis / complement activation, alternative pathway / chemokine activity / endopeptidase inhibitor activity / other organism cell membrane / retinol binding / extracellular vesicle / positive regulation of vascular endothelial growth factor production / complement activation / regulation of complement activation / complement activation, classical pathway / positive regulation of angiogenesis / in utero embryonic development / chemotaxis / protein homooligomerization / activation of MAPK activity / cytolysis / cell surface receptor signaling pathway / blood microparticle / immune response / protein-containing complex binding / inflammatory response / G protein-coupled receptor signaling pathway / innate immune response
Function and homology information
SourceHomo sapiens (human) / Human (human)
Methodsingle particle reconstruction / cryo EM / 5.6 Å resolution
AuthorsMenny A / Serna M / Boyd CM / Gardner 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
Validation ReportPDB-ID: 6h04

SummaryFull reportAbout validation report
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: 0.06
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6h04
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_0107.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:0.06 (by author), 0.06 (movie #1):
Minimum - Maximum-0.15325686 - 0.34172073
Average (Standard dev.)0.000082104794 (0.011335653)
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-0.1530.3420.000

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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: 16

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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 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)

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Component #3: protein, C6

ProteinName: C6 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)

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Component #4: protein, C7

ProteinName: C7 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)

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Component #5: protein, C8 alpha

ProteinName: C8 alpha / Recombinant expression: No
SourceSpecies: Homo sapiens (human)

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Component #6: protein, C8 beta

ProteinName: C8 beta / Recombinant expression: No
SourceSpecies: Homo sapiens (human)

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Component #7: protein, C8 gamma

ProteinName: C8 gamma / Recombinant expression: No
SourceSpecies: Homo sapiens (human)

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Component #8: protein, C9

ProteinName: C9 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)

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Component #9: protein, Complement component C9

ProteinName: Complement component C9 / Number of Copies: 18 / Recombinant expression: No
MassTheoretical: 61.056594 kDa
SourceSpecies: Human (human)

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Component #10: protein, Complement C5,Complement C5

ProteinName: Complement C5,Complement C5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 177.707391 kDa
SourceSpecies: Human (human)

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Component #11: protein, Complement component C8 beta chain

ProteinName: Complement component C8 beta chain / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 61.122852 kDa
SourceSpecies: Human (human)

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Component #12: protein, Complement component C7

ProteinName: Complement component C7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 91.221484 kDa
SourceSpecies: Human (human)

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Component #13: protein, Complement component C8 gamma chain

ProteinName: Complement component C8 gamma chain / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.410105 kDa
SourceSpecies: Human (human)

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Component #14: protein, Complement component C8 alpha chain

ProteinName: Complement component C8 alpha chain / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 61.782992 kDa
SourceSpecies: Human (human)

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Component #15: protein, Complement component C6

ProteinName: Complement component C6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 102.541312 kDa
SourceSpecies: Human (human)

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Component #16: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 76 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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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: 53167
3D reconstructionSoftware: RELION / Resolution: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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