+Open data
-Basic information
Entry | Database: PDB / ID: 5fmw | ||||||
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Title | The poly-C9 component of the Complement Membrane Attack Complex | ||||||
Components | POLYC9 | ||||||
Keywords | STRUCTURAL 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 / killing of cells of another organism / blood microparticle / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.7 Å | ||||||
Model type details | CA 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 | ||||||
Authors | 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. ...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. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5fmw.cif.gz | 286.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fmw.ent.gz | 192.8 KB | Display | PDB format |
PDBx/mmJSON format | 5fmw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fmw_validation.pdf.gz | 672.7 KB | Display | wwPDB validaton report |
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Full document | 5fmw_full_validation.pdf.gz | 672.3 KB | Display | |
Data in XML | 5fmw_validation.xml.gz | 110.1 KB | Display | |
Data in CIF | 5fmw_validation.cif.gz | 173.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fm/5fmw ftp://data.pdbj.org/pub/pdb/validation_reports/fm/5fmw | HTTPS FTP |
-Related structure data
Related structure data | 3235MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | 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
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: POLYC9 / Type: COMPLEX |
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Buffer solution | Name: 10 MM TRIS, 50 MM NACL / pH: 8 / Details: 10 MM TRIS, 50 MM NACL |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Details: LIQUID ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 / Date: Dec 15, 2014 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 77000 X / Calibrated magnification: 36232 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1500 nm / Cs: 2.3 mm |
Specimen holder | Temperature: 85 K |
Image recording | Electron dose: 25 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Num. digital images: 1385 |
-Processing
EM software |
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CTF correction | Details: EACH MICROGRAPH | ||||||||||||||||
Symmetry | Point symmetry: C22 (22 fold cyclic) | ||||||||||||||||
3D reconstruction | Resolution: 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 | ||||||||||||||||
Refinement | Highest resolution: 6.7 Å | ||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 6.7 Å
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