+Open data
-Basic information
Entry | Database: PDB / ID: 1uot | ||||||
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Title | HUMAN CD55 DOMAINS 3 & 4 | ||||||
Components | COMPLEMENT DECAY-ACCELERATING FACTOR | ||||||
Keywords | REGULATOR OF COMPLEMENT PATHWAY / 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 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 | Williams, P. / Chaudhry, Y. / Goodfellow, I.G. / 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.G. / Billington, J. / Powell, R. / Spiller, O.B. / 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 | 1uot.cif.gz | 36.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uot.ent.gz | 24 KB | Display | PDB format |
PDBx/mmJSON format | 1uot.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1uot_validation.pdf.gz | 428 KB | Display | wwPDB validaton report |
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Full document | 1uot_full_validation.pdf.gz | 431.8 KB | Display | |
Data in XML | 1uot_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | 1uot_validation.cif.gz | 8.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uo/1uot ftp://data.pdbj.org/pub/pdb/validation_reports/uo/1uot | HTTPS FTP |
-Related structure data
Related structure data | 1h03SC 1h04C 1h2pC 1h2qC 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: 13586.049 Da / Num. of mol.: 1 / 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 |
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#2: Water | ChemComp-HOH / |
Compound details | FUNCTION: THIS PROTEIN RECOGNIZES C4B AND C3B FRAGMENTS THAT CONDENSE WITH CELL-SURFACE HYDROXYL OR ...FUNCTION: THIS PROTEIN RECOGNIZES |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 45 % |
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Crystal grow | pH: 5.6 / Details: pH 5.60 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 3→40 Å / Num. obs: 2432 / % possible obs: 88 % / Redundancy: 4.8 % / Biso Wilson estimate: 4.123 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 2.3 |
Reflection shell | Resolution: 3→3.1 Å / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 1 / % possible all: 82 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H03 Resolution: 3→18.5 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT PROTGEO Details: DRIVEN BY BUSTER MAXIMUM LIKELIHOOD. THIS IS A NEW REFINEMENT OF PDB ENTRY 1H2Q
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Solvent computation | Solvent model: BABINET SCALING / Bsol: 28 Å2 / ksol: 1.14 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→18.5 Å
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Refine LS restraints |
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