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Yorodumi- PDB-1ckl: N-TERMINAL TWO DOMAINS OF HUMAN CD46 (MEMBRANE COFACTOR PROTEIN, MCP) -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ckl | |||||||||
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Title | N-TERMINAL TWO DOMAINS OF HUMAN CD46 (MEMBRANE COFACTOR PROTEIN, MCP) | |||||||||
Components | PROTEIN (CD46) | |||||||||
Keywords | GLYCOPROTEIN / VIRUS RECEPTOR / COMPLEMENT COFACTOR / SHORT CONSENSUS REPEAT / SCR / MEASLES VIRUS | |||||||||
Function / homology | Function and homology information sequestering of extracellular ligand from receptor / inner acrosomal membrane / negative regulation of complement activation, classical pathway / T cell mediated immunity / regulation of Notch signaling pathway / positive regulation of transforming growth factor beta production / positive regulation of memory T cell differentiation / positive regulation of regulatory T cell differentiation / single fertilization / positive regulation of interleukin-10 production ...sequestering of extracellular ligand from receptor / inner acrosomal membrane / negative regulation of complement activation, classical pathway / T cell mediated immunity / regulation of Notch signaling pathway / positive regulation of transforming growth factor beta production / positive regulation of memory T cell differentiation / positive regulation of regulatory T cell differentiation / single fertilization / positive regulation of interleukin-10 production / complement activation, classical pathway / positive regulation of T cell proliferation / Regulation of Complement cascade / virus receptor activity / signaling receptor activity / adaptive immune response / cadherin binding / negative regulation of gene expression / focal adhesion / innate immune response / positive regulation of gene expression / cell surface / extracellular space / extracellular exosome / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.1 Å | |||||||||
Authors | Casasnovas, J. / Larvie, M. / Stehle, T. | |||||||||
Citation | Journal: EMBO J. / Year: 1999 Title: Crystal structure of two CD46 domains reveals an extended measles virus-binding surface. Authors: Casasnovas, J.M. / Larvie, M. / Stehle, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ckl.cif.gz | 177.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ckl.ent.gz | 146.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ckl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ck/1ckl ftp://data.pdbj.org/pub/pdb/validation_reports/ck/1ckl | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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5 |
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6 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given / Matrix: (1),Details | THE ASYMMETRIC UNIT CONTAINS SIX INDEPENDENT COPIES OF THE CRYSTALLIZED FRAGMENT (RESIDUES 1-126). THE QUALITY OF THE ELECTRON DENSITY IS BEST FOR CHAINS B AND F, AND EITHER OF THESE MAY BE BEST USED AS REPRESENTATIVE MODELS. | |
-Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 14517.551 Da / Num. of mol.: 6 / Fragment: N-TERMINAL TWO SCR DOMAINS Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Description: EXPRESSED IN CHO LEC 3.2.8.1 CELLS (P. STANLEY, 1989, MOL. CELL. BIOL. 9:377) Cell (production host): OVARY / Cell line (production host): CHO LEC 3.2.8.1 / Cellular location (production host): SECRETED / Gene (production host): HUMAN CD46 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P15529 |
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-Sugars , 7 types, 12 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||||||
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#3: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||||||
#4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Polysaccharide | Source method: isolated from a genetically manipulated source #7: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #8: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source |
-Non-polymers , 3 types, 23 molecules
#9: Chemical | ChemComp-CA / #10: Chemical | ChemComp-CL / #11: Water | ChemComp-HOH / | |
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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: 3.27 Å3/Da / Density % sol: 53 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: 16% PEG 8000, 40 MM CACL2, 100 MM NA-CACODYLATE PH 6.5, 7 MG/ML PROTEIN, 20C, pH 6.50 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging dropDetails: drop consists of equal volume of protein and reservoir solutions | ||||||||||||||||||||||||||||||
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: NSLS / Beamline: X12B / Wavelength: 1.069 |
Detector | Type: ADSC QUANTUM / Detector: CCD / Date: Jun 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.069 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→20 Å / Num. obs: 19873 / % possible obs: 92.6 % / Observed criterion σ(I): -1.5 / Redundancy: 3 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 3.1→3.3 Å / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3.1 / % possible all: 68.1 |
Reflection | *PLUS % possible obs: 92.6 % / Redundancy: 3 % |
Reflection shell | *PLUS Highest resolution: 3.1 Å / Lowest resolution: 3.3 Å / % possible obs: 68.1 % / Mean I/σ(I) obs: 3.1 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 3.1→20 Å / Cross valid method: RFREE THROUGHOUT / σ(F): 0 / Details: ENGH & HUBER PARAMETER FILES
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Refinement step | Cycle: LAST / Resolution: 3.1→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |