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Yorodumi- PDB-4d9r: Inhibiting Alternative Pathway Complement Activation by Targeting... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4d9r | ||||||
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Title | Inhibiting Alternative Pathway Complement Activation by Targeting the Exosite on Factor D | ||||||
Components |
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Keywords | HYDROLASE/IMMUNE SYSTEM / Factor D / complement / antibody / exosite / Fab / chymotrypsin / protease / HYDROLASE-IMMUNE SYSTEM complex | ||||||
Function / homology | Function and homology information complement factor D / IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / Alternative complement activation / Fc-gamma receptor I complex binding / CD22 mediated BCR regulation / complement-dependent cytotoxicity / complement activation, alternative pathway ...complement factor D / IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / Alternative complement activation / Fc-gamma receptor I complex binding / CD22 mediated BCR regulation / complement-dependent cytotoxicity / complement activation, alternative pathway / IgG immunoglobulin complex / complement activation / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / immunoglobulin mediated immune response / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / immunoglobulin complex, circulating / immunoglobulin receptor binding / serine-type peptidase activity / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / platelet alpha granule lumen / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / complement activation, classical pathway / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / antigen binding / response to bacterium / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Platelet degranulation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / secretory granule lumen / adaptive immune response / ficolin-1-rich granule lumen / Potential therapeutics for SARS / blood microparticle / immune response / serine-type endopeptidase activity / Neutrophil degranulation / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å | ||||||
Authors | Murray, J.M. / Wiesmann, C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Inhibiting alternative pathway complement activation by targeting the factor d exosite. Authors: Katschke, K.J. / Wu, P. / Ganesan, R. / Kelley, R.F. / Mathieu, M.A. / Hass, P.E. / Murray, J. / Kirchhofer, D. / Wiesmann, C. / van Lookeren Campagne, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4d9r.cif.gz | 264.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4d9r.ent.gz | 210.8 KB | Display | PDB format |
PDBx/mmJSON format | 4d9r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4d9r_validation.pdf.gz | 473.2 KB | Display | wwPDB validaton report |
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Full document | 4d9r_full_validation.pdf.gz | 491.1 KB | Display | |
Data in XML | 4d9r_validation.xml.gz | 49.1 KB | Display | |
Data in CIF | 4d9r_validation.cif.gz | 70.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d9/4d9r ftp://data.pdbj.org/pub/pdb/validation_reports/d9/4d9r | HTTPS FTP |
-Related structure data
Related structure data | 4d9qC 1hfdS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 24438.807 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CFD, DF, Factor D, PFD / Production host: Escherichia coli (E. coli) / References: UniProt: P00746, complement factor D #2: Antibody | Mass: 23235.719 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IGKC / Production host: Escherichia coli (E. coli) / References: UniProt: P01834 #3: Antibody | Mass: 23189.896 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01857 #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.64 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris-HCl, 0.02 M NH4PO4, MPD 50.0% v/v, 0.01 M hexamine cobalt (III) chloride, pH 8.5, vapor diffusion, hanging drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 11, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.42→25 Å / Num. all: 61198 / Num. obs: 60502 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 55.38 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 9.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HFD Resolution: 2.42→19.84 Å / Cor.coef. Fo:Fc: 0.9379 / Cor.coef. Fo:Fc free: 0.9174 / Occupancy max: 1 / Occupancy min: 0.3 / SU R Cruickshank DPI: 0.363 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 53.25 Å2
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Refine analyze | Luzzati coordinate error obs: 0.331 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.42→19.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.42→2.48 Å / Total num. of bins used: 20
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