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Yorodumi- PDB-1ok9: Decay accelerating factor (CD55): The structure of an intact huma... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ok9 | ||||||
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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 / IMMUNE SYSTEM PROTEIN | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 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, R.A. / 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 | 1ok9.cif.gz | 113.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ok9.ent.gz | 87.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ok9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ok9_validation.pdf.gz | 480 KB | Display | wwPDB validaton report |
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Full document | 1ok9_full_validation.pdf.gz | 514.1 KB | Display | |
Data in XML | 1ok9_validation.xml.gz | 24.7 KB | Display | |
Data in CIF | 1ok9_validation.cif.gz | 31.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ok/1ok9 ftp://data.pdbj.org/pub/pdb/validation_reports/ok/1ok9 | HTTPS FTP |
-Related structure data
Related structure data | 1ojvSC 1ojwC 1ojyC 1ok1C 1ok2C 1ok3C 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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-Protein , 1 types, 2 molecules AB
#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: SOAKED IN 2MM K2PTCL4 FOR 6 DAYS 2 PT(II) BINDING SITES GLYCEROLS, ACETATES AND SULPHATES FROM CRYSTALLISATION BUFFER Source: (gene. exp.) HOMO SAPIENS (human) / Description: HUMAN SEQUENCE EXPRESSED IN E.COLI. / Production host: ESCHERICHIA COLI B (bacteria) / Variant (production host): B834(DE3) / References: UniProt: P08174 |
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-Non-polymers , 6 types, 23 molecules
#2: Chemical | ChemComp-ACT / #3: Chemical | #4: Chemical | ChemComp-CL / #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | MET AND GLN ADDED AT N-TERMINUS, CYS ADDED AT C-TERMINUS RESIDUES A48 B48 MAP TO RESIDUE 80 OF ...MET AND GLN ADDED AT N-TERMINUS, CYS ADDED AT C-TERMINUS RESIDUES A48 B48 MAP TO 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: 2.55 Å3/Da / Density % sol: 50 % Description: PT SITES FOUND WITH MOLREP PHASES FROM PDB ENTRY 1H03 | ||||||||||||||||||||||||||||||
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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 THEN SOAKED IN 2 MM K2PTCL4 FOR 6 DAYS | ||||||||||||||||||||||||||||||
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: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.96 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 18, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96 Å / Relative weight: 1 |
Reflection | Resolution: 3→41.9 Å / Num. obs: 10372 / % possible obs: 93 % / Redundancy: 3.8 % / Biso Wilson estimate: 2.1 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 3→3.16 Å / Rmerge(I) obs: 0.114 / Mean I/σ(I) obs: 5.8 / % possible all: 92.7 |
Reflection | *PLUS Highest resolution: 3 Å / Lowest resolution: 20 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.053 |
Reflection shell | *PLUS Highest resolution: 3 Å / Lowest resolution: 3.1 Å / % possible obs: 92.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.114 / Mean I/σ(I) obs: 5.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OJV Resolution: 3→20 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT PROTGEO Details: BUSTER-TNT MAXIMUM LIKELIHOOD REFINEMENT BETA11:-6.3 BETA12:4.0 BETA13:1.6 BETA22:11.2 BETA23:5.9 BETA33:-4.5
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Solvent computation | Solvent model: BABINET SCALING / Bsol: 71 Å2 / ksol: 0.38 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→20 Å
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Refine LS restraints |
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Refinement | *PLUS Num. reflection Rfree: 499 / % reflection Rfree: 5 % / Rfactor Rfree: 0.274 / Rfactor Rwork: 0.238 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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