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Yorodumi- PDB-1ojv: Decay accelerating factor (CD55): the structure of an intact huma... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ojv | ||||||
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Title | Decay accelerating factor (CD55): the structure of an intact human complement regulator. | ||||||
Components | COMPLEMENT DECAY-ACCELERATING FACTOR | ||||||
Keywords | REGULATOR OF COMPLEMENT PATHWAY / REGULATOR OF COMPLEMENT / DECAY ACCELERATION OF C3/C5 CONVERTASES / PATHOGEN RECEPTOR / SHORT CONSENSUS REPEAT DOMAINS | ||||||
Function / homology | Function and homology information regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of complement activation / regulation of complement-dependent cytotoxicity / regulation of complement activation / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell activation / positive regulation of CD4-positive, alpha-beta T cell proliferation / Class B/2 (Secretin family receptors) / ficolin-1-rich granule membrane / side of membrane ...regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of complement activation / regulation of complement-dependent cytotoxicity / regulation of complement activation / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell activation / positive regulation of CD4-positive, alpha-beta T cell proliferation / Class B/2 (Secretin family receptors) / ficolin-1-rich granule membrane / side of membrane / COPI-mediated anterograde transport / transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / complement activation, classical pathway / secretory granule membrane / Regulation of Complement cascade / positive regulation of T cell cytokine production / virus receptor activity / positive regulation of cytosolic calcium ion concentration / membrane raft / Golgi membrane / innate immune response / lipid binding / Neutrophil degranulation / cell surface / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Lukacik, P. / Roversi, P. / White, J. / Esser, D. / Smith, G.P. / Billington, J. / Williams, P.A. / Rudd, P.M. / Wormald, M.R. / Crispin, M.D.M. ...Lukacik, P. / Roversi, P. / White, J. / Esser, D. / Smith, G.P. / Billington, J. / Williams, P.A. / Rudd, P.M. / Wormald, M.R. / Crispin, M.D.M. / Radcliffe, C.M. / Dwek, C.M. / Evans, D.J. / Morgan, B.P. / Smith, R.A.G. / Lea, S.M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2004 Title: Complement Regulation at the Molecular Level: The Structure of Decay-Accelerating Factor Authors: Lukacik, P. / Roversi, P. / White, J. / Esser, D. / Smith, G.P. / Billington, J. / Williams, P.A. / Rudd, P.M. / Wormald, M.R. / Harvey, D.J. / Crispin, M.D.M. / Radcliffe, C.M. / Dwek, R.A. ...Authors: Lukacik, P. / Roversi, P. / White, J. / Esser, D. / Smith, G.P. / Billington, J. / Williams, P.A. / Rudd, P.M. / Wormald, M.R. / Harvey, D.J. / Crispin, M.D.M. / Radcliffe, C.M. / Dwek, R.A. / Evans, D.J. / Morgan, B.P. / Smith, R.A.G. / Lea, S.M. #1: Journal: Protein Sci. / Year: 2004 Title: Biological Activity, Membrane-Targeting Modification, and Crystallization of Soluble Human Decay Accelerating Factor Expressed in E. Coli Authors: White, J. / Lukacik, P. / Esser, D. / Steward, M. / Giddings, N. / Bright, J.R. / Fritchley, S. / Morgan, B.P. / Lea, S.M. / Smith, G.P. / Smith, R.A.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ojv.cif.gz | 117.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ojv.ent.gz | 91.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ojv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ojv_validation.pdf.gz | 436.4 KB | Display | wwPDB validaton report |
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Full document | 1ojv_full_validation.pdf.gz | 459.1 KB | Display | |
Data in XML | 1ojv_validation.xml.gz | 21.3 KB | Display | |
Data in CIF | 1ojv_validation.cif.gz | 31.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oj/1ojv ftp://data.pdbj.org/pub/pdb/validation_reports/oj/1ojv | HTTPS FTP |
-Related structure data
Related structure data | 1ojwC 1ojyC 1ok1C 1ok2C 1ok3C 1ok9C 1h03S S: Starting model for refinement 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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Unit cell |
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-Components
#1: Protein | Mass: 28174.666 Da / Num. of mol.: 2 / Fragment: FOUR EXTRACELLULAR SCR DOMAINS RESIDUES 35-285 Source method: isolated from a genetically manipulated source Details: MODELLED GLYCEROLS, ACETATES AND SULPHATES FROM CRYSTALLISATION BUFFER Source: (gene. exp.) HOMO SAPIENS (human) / Description: HUMAN SEQUENCE EXPRESSED IN E.COLI. / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P08174 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Sequence details | RESIDUES A48 AND B48 MAP ONTO RESIDUE 80 OF SWISSPROT ENTRY P08174. RESIDUE 80 IN THE SWISSPROT ...RESIDUES A48 AND B48 MAP ONTO RESIDUE 80 OF SWISSPROT ENTRY P08174. RESIDUE 80 IN THE SWISSPROT ENTRY IS GIVEN AS THR, BUT SOME REFERENCES | |
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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: 2.53 Å3/Da / Density % sol: 42 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.6 Details: 0.2 M AMMONIUM SULPHATE, 20% M-PEG 5K, 0.1M SODIUM ACETATE PH 4.6, 16% GLYCEROL | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 4.6 / Method: unknown | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→16 Å / Num. obs: 23315 / % possible obs: 94.4 % / Redundancy: 31 % / Biso Wilson estimate: 0.874 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 2.3→2.42 Å / Rmerge(I) obs: 0.164 / Mean I/σ(I) obs: 4 / % possible all: 92 |
Reflection | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 17 Å / Num. obs: 29985 / % possible obs: 93.8 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.084 |
Reflection shell | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 2.2 Å / % possible obs: 90.6 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 2.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H03 Resolution: 2.3→16 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT PROTGEO / Details: BUSTER-TNT MAXIMUM LIKELIHOOD REFINEMENT
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Solvent computation | Solvent model: BABINET SCALING / Bsol: 57 Å2 / ksol: 0.44 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→16 Å
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Refine LS restraints |
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Refinement | *PLUS Num. reflection Rfree: 1197 / % reflection Rfree: 5 % / Rfactor Rfree: 0.252 / Rfactor Rwork: 0.207 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 2.37 Å / Rfactor Rfree: 0.267 / Rfactor Rwork: 0.227 |