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- PDB-1ok2: Decay accelerating factor (CD55): the structure of an intact huma... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ok2 | ||||||
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Title | Decay accelerating factor (CD55): the structure of an intact human complement regulator. | ||||||
![]() | COMPLEMENT DECAY-ACCELERATING FACTOR | ||||||
![]() | REGULATOR OF COMPLEMENT PATHWAY / REGULATOR OF COMPLEMENT / DECAY ACCELERATION OF C3/C5 CONVERTASES / PATHOGEN RECEPTOR / SHORT CONSENSUS REPEAT DOMAINS | ||||||
Function / homology | ![]() regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of complement activation / negative regulation of complement activation, classical pathway / regulation of complement-dependent cytotoxicity / regulation of complement activation / T cell mediated immunity / 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) ...regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of complement activation / negative regulation of complement activation, classical pathway / regulation of complement-dependent cytotoxicity / regulation of complement activation / T cell mediated immunity / 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 / secretory granule membrane / complement activation, classical pathway / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 120.1 KB | Display | ![]() |
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PDB format | ![]() | 93.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.2 KB | Display | ![]() |
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Full document | ![]() | 457.6 KB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 23.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ojvC ![]() 1ojwC ![]() 1ojyC ![]() 1ok1C ![]() 1ok3C ![]() 1ok9C ![]() 1h03S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() #2: Chemical | ChemComp-ACT / #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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||||||||||||
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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, 10% 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: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 15, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 2.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→19 Å / Num. obs: 18310 / % possible obs: 99 % / Redundancy: 7 % / Biso Wilson estimate: 0.239 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.4 |
Reflection shell | Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 11.9 / % possible all: 98 |
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 19 Å / Rmerge(I) obs: 0.07 |
Reflection shell | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 2.6 Å / % possible obs: 98 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 11.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1H03 Resolution: 2.5→19 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT PROTGEO Details: BUSTER-TNT MAXIMUM LIKELIHOOD REFINEMENT. ANISOTROPIC SCALING BETAIJS: BETA11:-11.4 BETA12:- 3.8 BETA13:5.4 BETA22:6.6 BETA23:-2.2 BETA33:-0.8
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Solvent computation | Solvent model: BABINET SCALING / Bsol: 64 Å2 / ksol: 0.41 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→19 Å
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Refine LS restraints |
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Refinement | *PLUS Num. reflection Rfree: 931 / % reflection Rfree: 5 % / Rfactor Rfree: 0.274 / Rfactor Rwork: 0.227 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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