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Yorodumi- PDB-2qqh: Structure of C8a-MACPF reveals mechanism of membrane attack in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qqh | ||||||
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Title | Structure of C8a-MACPF reveals mechanism of membrane attack in complement immune defense | ||||||
Components | Complement component C8 alpha chain | ||||||
Keywords | IMMUNE SYSTEM / MEMBRANE PROTEIN / MACPF / MEMBRANE PERFORATION / Cleavage on pair of basic residues / Complement alternate pathway / Complement pathway / Cytolysis / EGF-like domain / Glycoprotein / Immune response / Innate immunity / Membrane attack complex / Polymorphism / Secreted | ||||||
Function / homology | Function and homology information Terminal pathway of complement / membrane attack complex / complement binding / complement activation, alternative pathway / complement activation / complement activation, classical pathway / Regulation of Complement cascade / positive regulation of immune response / blood microparticle / killing of cells of another organism ...Terminal pathway of complement / membrane attack complex / complement binding / complement activation, alternative pathway / complement activation / complement activation, classical pathway / Regulation of Complement cascade / positive regulation of immune response / blood microparticle / killing of cells of another organism / immune response / protein-containing complex binding / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS, MAD / Resolution: 2.5 Å | ||||||
Authors | Hadders, M.A. / Gros, P. | ||||||
Citation | Journal: Science / Year: 2007 Title: Structure of C8alpha-MACPF reveals mechanism of membrane attack in complement immune defense. Authors: Hadders, M.A. / Beringer, D.X. / Gros, P. | ||||||
History |
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Remark 999 | Sequence Residues 337 to 379 are identical to those of residues 367 to 409 in UniProt entry P07357, ...Sequence Residues 337 to 379 are identical to those of residues 367 to 409 in UniProt entry P07357, which are ITSRDITTCFGGSLGIQYEDKINVGGGLSGDHCKKFGGGKTER. However, only 12 residues were observed and the alignment between sequence and coordinates is unknown in this region. These 12 residues were originally modeled as ALA/GLY and have been changed to UNK during processing. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qqh.cif.gz | 70.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qqh.ent.gz | 56.4 KB | Display | PDB format |
PDBx/mmJSON format | 2qqh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/2qqh ftp://data.pdbj.org/pub/pdb/validation_reports/qq/2qqh | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 37543.215 Da / Num. of mol.: 1 / Mutation: C164S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: C8A / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): Origami / References: UniProt: P07357 | ||||
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#2: Chemical | #3: Chemical | ChemComp-NI / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.98 Å3/Da / Density % sol: 69.08 % |
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Crystal grow | Temperature: 303 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 1M LiSO4, 5mM NiCl2, 100mM Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 303K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.006 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 10, 2007 |
Radiation | Monochromator: Si 311 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.006 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→40 Å / Num. all: 21349 / Num. obs: 21349 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.1 % / Biso Wilson estimate: 63.3 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 3.2 / Num. unique all: 2888 / Rsym value: 0.513 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS, MAD / Resolution: 2.5→40 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.888 / SU B: 16.508 / SU ML: 0.198 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.315 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.487 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.64 Å / Total num. of bins used: 20
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