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- EMDB-3235: Structure of the poly-C9 component of the Complement Membrane Att... -

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Basic information

Entry
Database: EMDB / ID: EMD-3235
TitleStructure of the poly-C9 component of the Complement Membrane Attack Complex
Map dataReconstruction of the poly-C9 component of the Complement Membrane Attack Complex
Sample
  • Sample: C9 from human plasma
  • Protein or peptide: C9
Keywordspore-forming protein / complement / C9 / MACPF
Function / homology
Function and homology information


cell killing / Terminal pathway of complement / membrane attack complex / other organism cell membrane / complement activation / complement activation, alternative pathway / immune system process / complement activation, classical pathway / Regulation of Complement cascade / protein homooligomerization ...cell killing / Terminal pathway of complement / membrane attack complex / other organism cell membrane / complement activation / complement activation, alternative pathway / immune system process / complement activation, classical pathway / Regulation of Complement cascade / protein homooligomerization / positive regulation of immune response / blood microparticle / killing of cells of another organism / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Membrane attack complex component/perforin/complement C9 / Membrane attack complex component/perforin domain, conserved site / Membrane attack complex/perforin (MACPF) domain signature. / membrane-attack complex / perforin / MAC/Perforin domain / Membrane attack complex/perforin (MACPF) domain profile. / Membrane attack complex component/perforin (MACPF) domain / Thrombospondin type 1 domain / Low-density lipoprotein receptor domain class A / Thrombospondin type-1 (TSP1) repeat superfamily ...Membrane attack complex component/perforin/complement C9 / Membrane attack complex component/perforin domain, conserved site / Membrane attack complex/perforin (MACPF) domain signature. / membrane-attack complex / perforin / MAC/Perforin domain / Membrane attack complex/perforin (MACPF) domain profile. / Membrane attack complex component/perforin (MACPF) domain / Thrombospondin type 1 domain / Low-density lipoprotein receptor domain class A / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1.
Similarity search - Domain/homology
Complement component C9
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.7 Å
AuthorsDudkina NV / Spicer BA / Reboul CF / Conroy PJ / Lukoyanova N / Elmlund H / Law RHP / Ekkel SM / Kondos SC / Goode RJA ...Dudkina NV / Spicer BA / Reboul CF / Conroy PJ / Lukoyanova N / Elmlund H / Law RHP / Ekkel SM / Kondos SC / Goode RJA / Ramm G / Whisstock JC / Saibil HR / Dunstone MA
CitationJournal: Nat Commun / Year: 2016
Title: Structure of the poly-C9 component of the complement membrane attack complex.
Authors: Natalya V Dudkina / Bradley A Spicer / Cyril F Reboul / Paul J Conroy / Natalya Lukoyanova / Hans Elmlund / Ruby H P Law / Susan M Ekkel / Stephanie C Kondos / Robert J A Goode / Georg Ramm ...Authors: Natalya V Dudkina / Bradley A Spicer / Cyril F Reboul / Paul J Conroy / Natalya Lukoyanova / Hans Elmlund / Ruby H P Law / Susan M Ekkel / Stephanie C Kondos / Robert J A Goode / Georg Ramm / James C Whisstock / Helen R Saibil / Michelle A Dunstone /
Abstract: The membrane attack complex (MAC)/perforin-like protein complement component 9 (C9) is the major component of the MAC, a multi-protein complex that forms pores in the membrane of target pathogens. In ...The membrane attack complex (MAC)/perforin-like protein complement component 9 (C9) is the major component of the MAC, a multi-protein complex that forms pores in the membrane of target pathogens. In contrast to homologous proteins such as perforin and the cholesterol-dependent cytolysins (CDCs), all of which require the membrane for oligomerisation, C9 assembles directly onto the nascent MAC from solution. However, the molecular mechanism of MAC assembly remains to be understood. Here we present the 8 Å cryo-EM structure of a soluble form of the poly-C9 component of the MAC. These data reveal a 22-fold symmetrical arrangement of C9 molecules that yield an 88-strand pore-forming β-barrel. The N-terminal thrombospondin-1 (TSP1) domain forms an unexpectedly extensive part of the oligomerisation interface, thus likely facilitating solution-based assembly. These TSP1 interactions may also explain how additional C9 subunits can be recruited to the growing MAC subsequent to membrane insertion.
History
DepositionNov 9, 2015-
Header (metadata) releaseNov 18, 2015-
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: 0.09
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.09
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5fmw
  • Surface level: 0.09
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-3235_ima...

Downloads & links

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Map

FileDownload / File: emd_3235.map.gz / Format: CCP4 / Size: 58.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of the poly-C9 component of the Complement Membrane Attack Complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.76 Å/pix.
x 250 pix.
= 690. Å		2.76 Å/pix.
x 250 pix.
= 690. Å		2.76 Å/pix.
x 250 pix.
= 690. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.76 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09 / Movie #1: 0.09
Minimum - Maximum-0.053409 - 0.39757299
Average (Standard dev.)0.00102137 (±0.01166051)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-125-125-125
Dimensions250250250
Spacing250250250
CellA=B=C: 690.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.762.762.76
M x/y/z250250250
origin x/y/z0.0000.0000.000
length x/y/z690.000690.000690.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-125-125-125
NC/NR/NS250250250
D min/max/mean-0.0530.3980.001

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Supplemental data

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Sample components

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Entire : C9 from human plasma

EntireName: C9 from human plasma
Components
  • Sample: C9 from human plasma
  • Protein or peptide: C9

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Supramolecule #1000: C9 from human plasma

SupramoleculeName: C9 from human plasma / type: sample / ID: 1000 / Oligomeric state: 22 / Number unique components: 1
Molecular weightExperimental: 1.3 MDa

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Macromolecule #1: C9

MacromoleculeName: C9 / type: protein_or_peptide / ID: 1 / Name.synonym: complement component 9 / Number of copies: 1 / Oligomeric state: 22 / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Tissue: Blood
Molecular weightTheoretical: 1.3 MDa
SequenceUniProtKB: Complement component C9 / GO: immune system process

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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

Concentration1 mg/mL
BufferpH: 8 / Details: 10 mM Tris-HCl, 100 mM NaCl
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 91 K / Instrument: FEI VITROBOT MARK III / Method: Blot for 5s before plunging

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Electron microscopy

MicroscopeFEI POLARA 300
TemperatureMin: 80 K / Max: 90 K / Average: 85 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification
Specialist opticsEnergy filter - Name: GIF Quantum / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
DateDec 15, 2014
Image recordingCategory: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Digitization - Sampling interval: 5 µm / Number real images: 1385 / Average electron dose: 25 e/Å2
Details: IMOD was applied to 1385 frames grouped from the 70 recorded.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 36232 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.3 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 77000
Sample stageSpecimen holder model: GATAN HELIUM
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

DetailsThe particles were selected manually.
CTF correctionDetails: each micrograph
Final reconstructionApplied symmetry - Point group: C22 (22 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 6.7 Å / Resolution method: OTHER / Software - Name: CTFFIND3, RELION, IMAGIC / Number images used: 5000

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