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Yorodumi- PDB-1cid: CRYSTAL STRUCTURE OF DOMAINS 3 & 4 OF RAT CD4 AND THEIR RELATIONS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cid | |||||||||
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Title | CRYSTAL STRUCTURE OF DOMAINS 3 & 4 OF RAT CD4 AND THEIR RELATIONSHIP TO THE NH2-TERMINAL DOMAINS | |||||||||
Components | T CELL SURFACE GLYCOPROTEIN CD4 | |||||||||
Keywords | T-CELL SURFACE GLYCOPROTEIN | |||||||||
Function / homology | Function and homology information Translocation of ZAP-70 to Immunological synapse / : / PD-1 signaling / Phosphorylation of CD3 and TCR zeta chains / cytokine production / Downstream TCR signaling / Generation of second messenger molecules / Alpha-defensins / Other interleukin signaling / helper T cell enhancement of adaptive immune response ...Translocation of ZAP-70 to Immunological synapse / : / PD-1 signaling / Phosphorylation of CD3 and TCR zeta chains / cytokine production / Downstream TCR signaling / Generation of second messenger molecules / Alpha-defensins / Other interleukin signaling / helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / maintenance of protein location in cell / T cell selection / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / MHC class II protein binding / response to vitamin D / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway / positive regulation of monocyte differentiation / positive regulation of kinase activity / regulation of T cell activation / positive regulation of calcium ion transport into cytosol / plasma membrane => GO:0005886 / immunoglobulin binding / regulation of calcium ion transport / macrophage differentiation / T cell differentiation / positive regulation of protein kinase activity / coreceptor activity / positive regulation of T cell proliferation / positive regulation of calcium-mediated signaling / T cell activation / protein tyrosine kinase binding / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of T cell activation / response to estradiol / defense response to Gram-negative bacterium / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / positive regulation of viral entry into host cell / cell surface receptor signaling pathway / cell adhesion / positive regulation of protein phosphorylation / membrane raft / endoplasmic reticulum lumen / external side of plasma membrane / signaling receptor binding / endoplasmic reticulum membrane / protein kinase binding / positive regulation of DNA-templated transcription / enzyme binding / cell surface / signal transduction / protein homodimerization activity / zinc ion binding / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.8 Å | |||||||||
Authors | Brady, R.L. / Dodson, E.J. / Lange, G. | |||||||||
Citation | Journal: Science / Year: 1993 Title: Crystal structure of domains 3 and 4 of rat CD4: relation to the NH2-terminal domains. Authors: Brady, R.L. / Dodson, E.J. / Dodson, G.G. / Lange, G. / Davis, S.J. / Williams, A.F. / Barclay, A.N. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cid.cif.gz | 48.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cid.ent.gz | 33.7 KB | Display | PDB format |
PDBx/mmJSON format | 1cid.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cid_validation.pdf.gz | 375.4 KB | Display | wwPDB validaton report |
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Full document | 1cid_full_validation.pdf.gz | 407.2 KB | Display | |
Data in XML | 1cid_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 1cid_validation.cif.gz | 12 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/1cid ftp://data.pdbj.org/pub/pdb/validation_reports/ci/1cid | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: SULFATE OXYGENS ARE NOT VISIBLE IN ELECTRON DENSITY MAP. / 2: RESIDUES PRO 62 AND PRO 71 ARE CIS PROLINES. |
-Components
#1: Protein | Mass: 19706.373 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: OVARY / References: UniProt: P05540 |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.66 Å3/Da / Density % sol: 66.35 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.8 Å / Num. obs: 7274 / % possible obs: 99.1 % / Redundancy: 5.7 % / Num. measured all: 41516 / Rmerge(I) obs: 0.065 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||
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Refinement | Resolution: 2.8→10 Å / Rfactor all: 0.233 | ||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→10 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 10 Å / Num. reflection obs: 7133 / Rfactor obs: 0.233 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |