+Open data
-Basic information
Entry | Database: PDB / ID: 1h03 | ||||||
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Title | Human CD55 domains 3 & 4 | ||||||
Components | COMPLEMENT DECAY-ACCELERATING FACTOR | ||||||
Keywords | IMMUNE SYSTEM PROTEIN / COMPLEMENT DECAY ACCELERATING FACTOR / ENTEROVIRAL RECEPTOR / BACTERIAL RECEPTOR / LIGAND FOR CD97 / COMPLEMENT PATHWAY / ALTERNATIVE SPLICING / GPI-ANCHOR | ||||||
Function / homology | Function and homology information negative regulation of complement activation / regulation of lipopolysaccharide-mediated signaling pathway / 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 / COPI-mediated anterograde transport ...negative regulation of complement activation / regulation of lipopolysaccharide-mediated signaling pathway / 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 / COPI-mediated anterograde transport / side of membrane / complement activation, classical pathway / transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / 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 / MIRAS / Resolution: 1.7 Å | ||||||
Authors | Williams, P. / Chaudhry, Y. / Goodfellow, I. / Billington, J. / Spiller, B. / Evans, D.J. / Lea, S.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Mapping Cd55 Function. The Structure of Two Pathogen-Binding Domains at 1.7 A Authors: Williams, P. / Chaudhry, Y. / Goodfellow, I. / Billington, J. / Powell, R. / Spiller, O. / Evans, D.J. / Lea, S.M. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Crystallization and Preliminary X-Ray Diffraction Analysis of a Biologically Active Fragment of Cd55 Authors: Lea, S.M. / Powell, R. / Evans, D.J. #2: Journal: J.Biol.Chem. / Year: 1998 Title: Determination of the Affinity and Kinetic Constants for the Interaction between the Human Virus Echovirus 11 and its Cellular Receptor, Cd55 Authors: Lea, S.M. / Powell, R. / Mckee, T. / Evans, D.J. / Brown, D.J. / Stuart, D.I. / Van Der Merwe, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h03.cif.gz | 58.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h03.ent.gz | 45.7 KB | Display | PDB format |
PDBx/mmJSON format | 1h03.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h0/1h03 ftp://data.pdbj.org/pub/pdb/validation_reports/h0/1h03 | HTTPS FTP |
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-Related 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: 13586.049 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR SCR DOMAINS 3 & 4, RESIDUES 161-285 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: PICHIA PASTORIS (fungus) / References: UniProt: P08174 #2: Water | ChemComp-HOH / | Compound details | RECOGNIZES C4B AND C3B FRAGMENTS GENERATED DURING C4 AND C3 ACTIVATION. PART OF THE COMPLEMENT ...RECOGNIZES | |
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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: 2.14 Å3/Da / Density % sol: 42.52 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.6 / Details: pH 5.60 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 4.6 / Method: vapor diffusion, sitting dropDetails: Lea, S.M., (1999) Acta Crystallogr.,Sect.D, D55, 1198. | ||||||||||||||||||||||||||||||
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: PX14.1 / Wavelength: 1.488 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. obs: 44162 / % possible obs: 100 % / Redundancy: 15.5 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 1.7→1.75 Å / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 1.5 / % possible all: 92 |
Reflection | *PLUS Num. measured all: 685390 |
Reflection shell | *PLUS % possible obs: 92 % / Rmerge(I) obs: 0.35 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 1.7→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 30 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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Xplor file |
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Refinement | *PLUS Rfactor Rfree: 0.241 / Rfactor Rwork: 0.196 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |