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- PDB-5fmw: The poly-C9 component of the Complement Membrane Attack Complex -

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Basic information

Entry
Database: PDB / ID: 5fmw
TitleThe poly-C9 component of the Complement Membrane Attack Complex
ComponentsPOLYC9
KeywordsSTRUCTURAL PROTEIN / PORE-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, alternative pathway / complement activation / complement activation, classical pathway / Regulation of Complement cascade / protein homooligomerization / positive regulation of immune response ...cell killing / Terminal pathway of complement / membrane attack complex / other organism cell membrane / complement activation, alternative pathway / complement activation / 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 / Membrane attack complex/perforin (MACPF) domain profile. / MAC/Perforin domain / Membrane attack complex component/perforin (MACPF) domain / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. ...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 / Membrane attack complex/perforin (MACPF) domain profile. / MAC/Perforin domain / Membrane attack complex component/perforin (MACPF) domain / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.7 Å
Model type detailsCA ATOMS ONLY, CHAIN A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V
AuthorsDudkina, N.V. / Spicer, B.A. / Reboul, C.F. / Conroy, P.J. / Lukoyanova, N. / Elmlund, H. / Law, R.H.P. / Ekkel, S.M. / Kondos, S.C. / Goode, R.J.A. ...Dudkina, N.V. / Spicer, B.A. / Reboul, C.F. / Conroy, P.J. / Lukoyanova, N. / Elmlund, H. / Law, R.H.P. / Ekkel, S.M. / Kondos, S.C. / Goode, R.J.A. / Ramm, G. / Whisstock, J.C. / Saibil, H.R. / Dunstone, M.A.
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 10, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-3235
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Structure viewerMolecule:
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Assembly

Deposited unit
A: POLYC9
B: POLYC9
C: POLYC9
D: POLYC9
E: POLYC9
F: POLYC9
G: POLYC9
H: POLYC9
I: POLYC9
J: POLYC9
K: POLYC9
L: POLYC9
M: POLYC9
N: POLYC9
O: POLYC9
P: POLYC9
Q: POLYC9
R: POLYC9
S: POLYC9
T: POLYC9
U: POLYC9
V: POLYC9


Theoretical massNumber of molelcules
Total (without water)1,266,82322
Polymers1,266,82322
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
POLYC9 / Coordinate model: Cα atoms only


Mass: 57582.871 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Tissue: BLOOD / References: UniProt: P02748

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: POLYC9 / Type: COMPLEX
Buffer solutionName: 10 MM TRIS, 50 MM NACL / pH: 8 / Details: 10 MM TRIS, 50 MM NACL
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Details: LIQUID ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300 / Date: Dec 15, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 77000 X / Calibrated magnification: 36232 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1500 nm / Cs: 2.3 mm
Specimen holderTemperature: 85 K
Image recordingElectron dose: 25 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansNum. digital images: 1385

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Processing

EM software
IDNameVersionCategory
1CTFFIND3CTF correction
2IMAGIC3D reconstruction
3RELION3D reconstruction
CTF correctionDetails: EACH MICROGRAPH
SymmetryPoint symmetry: C22 (22 fold cyclic)
3D reconstructionResolution: 6.7 Å / Num. of particles: 5000 / Nominal pixel size: 2.76 Å / Actual pixel size: 2.76 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3235. (DEPOSITION ID: 13993).
Symmetry type: POINT
RefinementHighest resolution: 6.7 Å
Refinement stepCycle: LAST / Highest resolution: 6.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10582 0 0 0 10582

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