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Yorodumi- EMDB-7773: The X-ray crystal structure of Complement component-9 reveals tha... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7773 | |||||||||
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Title | The X-ray crystal structure of Complement component-9 reveals that the first trans-membrane region acts as a brake on self-assembly | |||||||||
Map data | Structure of the polyC9 component of the membrane attack complex. | |||||||||
Sample |
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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 | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Spicer BA / Law RHP / Pang S / Dunstone MA / Whisstock JC | |||||||||
Citation | Journal: Nat Commun / Year: 2018 Title: The first transmembrane region of complement component-9 acts as a brake on its self-assembly. Authors: Bradley A Spicer / Ruby H P Law / Tom T Caradoc-Davies / Sue M Ekkel / Charles Bayly-Jones / Siew-Siew Pang / Paul J Conroy / Georg Ramm / Mazdak Radjainia / Hariprasad Venugopal / James C ...Authors: Bradley A Spicer / Ruby H P Law / Tom T Caradoc-Davies / Sue M Ekkel / Charles Bayly-Jones / Siew-Siew Pang / Paul J Conroy / Georg Ramm / Mazdak Radjainia / Hariprasad Venugopal / James C Whisstock / Michelle A Dunstone / Abstract: Complement component 9 (C9) functions as the pore-forming component of the Membrane Attack Complex (MAC). During MAC assembly, multiple copies of C9 are sequentially recruited to membrane associated ...Complement component 9 (C9) functions as the pore-forming component of the Membrane Attack Complex (MAC). During MAC assembly, multiple copies of C9 are sequentially recruited to membrane associated C5b8 to form a pore. Here we determined the 2.2 Å crystal structure of monomeric murine C9 and the 3.9 Å resolution cryo EM structure of C9 in a polymeric assembly. Comparison with other MAC proteins reveals that the first transmembrane region (TMH1) in monomeric C9 is uniquely positioned and functions to inhibit its self-assembly in the absence of C5b8. We further show that following C9 recruitment to C5b8, a conformational change in TMH1 permits unidirectional and sequential binding of additional C9 monomers to the growing MAC. This mechanism of pore formation contrasts with related proteins, such as perforin and the cholesterol dependent cytolysins, where it is believed that pre-pore assembly occurs prior to the simultaneous release of the transmembrane regions. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_7773.map.gz | 17.3 MB | EMDB map data format | |
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Header (meta data) | emd-7773-v30.xml emd-7773.xml | 20.1 KB 20.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_7773_fsc.xml | 12.5 KB | Display | FSC data file |
Images | emd_7773.png | 193.7 KB | ||
Masks | emd_7773_msk_1.map | 163.6 MB | Mask map | |
Others | emd_7773_additional.map.gz emd_7773_half_map_1.map.gz emd_7773_half_map_2.map.gz | 124.7 MB 126.5 MB 126.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7773 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7773 | HTTPS FTP |
-Related structure data
Related structure data | 6dlwMC 6cxoC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_7773.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Structure of the polyC9 component of the membrane attack complex. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_7773_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Complement component-9, Combined unfiltered raw map.
File | emd_7773_additional.map | ||||||||||||
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Annotation | Complement component-9, Combined unfiltered raw map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Complement component-9, Unfiltered half map 2.
File | emd_7773_half_map_1.map | ||||||||||||
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Annotation | Complement component-9, Unfiltered half map 2. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Complement component-9, Unfiltered half map 1.
File | emd_7773_half_map_2.map | ||||||||||||
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Annotation | Complement component-9, Unfiltered half map 1. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : polyC9
Entire | Name: polyC9 |
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Components |
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-Supramolecule #1: polyC9
Supramolecule | Name: polyC9 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all / Details: polyC9 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 1342 kDa/nm |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: Expi293 / Recombinant plasmid: pSEctag2a |
-Macromolecule #1: human complement protein 9
Macromolecule | Name: human complement protein 9 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: msacrsfav a icileisi lt aqyttsy dpe ltessg sash idcrm spwse wsqc dpclrq mfr srsievf gq fngkrctd a vgdrrqcvp tepcedaedd cgndfqcst g rcikmrlr cn gdndcgd fsd eddces eprp pcrdr vvees elar ...String: msacrsfav a icileisi lt aqyttsy dpe ltessg sash idcrm spwse wsqc dpclrq mfr srsievf gq fngkrctd a vgdrrqcvp tepcedaedd cgndfqcst g rcikmrlr cn gdndcgd fsd eddces eprp pcrdr vvees elar tagygi nil gmdplst pf dnefyngl c nrdrdgntl tyyrrpwnva sliyetkge k nfrtehye eq ieafksi iqe ktsnfn aais lkftp tetnk aeqc ceetas sis lhgkgsf rf sysknety q lflsysskk ekmflhvkge ihlgrfvmr n rdvvlttt fv ddikalp tty ekgeyf afle tygth ysssg slgg lyeliy vld kasmkrk gv elkdikrc l gyhldvsla fseisvgaef nkddcvkrg e gravnits en liddvvs lir ggtrky afel kekll rgtvi dvtd fvnwas sin dapvlis qk lspiynlv p vkmknahlk kqnleraied yinefsvrk c htcqnggt vi lmdgkcl cac pfkfeg iace iskqk isegl pale fpnek |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.3 mg/mL | ||||||||
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Buffer | pH: 7.2 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER | ||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV Details: 2.5 uL sample applied to Quantifoil grid R1.2/1.3 x200 mesh. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Number grids imaged: 1 / Average exposure time: 8.0 sec. / Average electron dose: 46.4 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: RECIPROCAL / Protocol: BACKBONE TRACE |
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Output model | PDB-6dlw: |