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Yorodumi- PDB-1p6a: STRUCTURAL BASIS FOR VARIATION IN ADENOVIRUS AFFINITY FOR THE CEL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1p6a | ||||||
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Title | STRUCTURAL BASIS FOR VARIATION IN ADENOVIRUS AFFINITY FOR THE CELLULAR RECEPTOR CAR (S489Y MUTANT) | ||||||
Components |
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Keywords | Viral protein/receptor / VIRUS / VIRAL PROTEIN / Viral protein-receptor COMPLEX | ||||||
Function / homology | Function and homology information AV node cell-bundle of His cell adhesion involved in cell communication / cell adhesive protein binding involved in AV node cell-bundle of His cell communication / homotypic cell-cell adhesion / AV node cell to bundle of His cell communication / epithelial structure maintenance / gamma-delta T cell activation / regulation of AV node cell action potential / germ cell migration / apicolateral plasma membrane / cell-cell junction organization ...AV node cell-bundle of His cell adhesion involved in cell communication / cell adhesive protein binding involved in AV node cell-bundle of His cell communication / homotypic cell-cell adhesion / AV node cell to bundle of His cell communication / epithelial structure maintenance / gamma-delta T cell activation / regulation of AV node cell action potential / germ cell migration / apicolateral plasma membrane / cell-cell junction organization / transepithelial transport / connexin binding / adhesion receptor-mediated virion attachment to host cell / cardiac muscle cell development / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / bicellular tight junction / intercalated disc / mitochondrion organization / cell adhesion molecule binding / neutrophil chemotaxis / acrosomal vesicle / filopodium / PDZ domain binding / Cell surface interactions at the vascular wall / adherens junction / neuromuscular junction / beta-catenin binding / viral capsid / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cell-cell junction / integrin binding / virus receptor activity / cell junction / cell body / heart development / growth cone / actin cytoskeleton organization / basolateral plasma membrane / defense response to virus / cell adhesion / neuron projection / symbiont entry into host cell / membrane raft / signaling receptor binding / host cell nucleus / protein-containing complex / extracellular space / extracellular region / nucleoplasm / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Human adenovirus A serotype 12 Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.9 Å | ||||||
Authors | Howitt, J. / Bewley, M.C. / Graziano, V. / Flanagan, J.M. / Freimuth, P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Structural basis for variation in adenovirus affinity for the cellular coxsackievirus and adenovirus receptor. Authors: Howitt, J. / Bewley, M.C. / Graziano, V. / Flanagan, J.M. / Freimuth, P. #1: Journal: Science / Year: 1999 Title: Structural analysis of the mechanism of adenovirus binding to its human cellular receptor, CAR Authors: Bewley, M.C. / Springer, K. / Zhang, Y.B. / Freimuth, P. / Flanagan, J.M. #2: Journal: J.Virol. / Year: 1999 Title: Coxsackievirus and adenovirus receptor amino-terminal immunoglobulin V-related domain binds adenovirus type 2 and fiber knob from adenovirus type 12 Authors: Freimuth, P. / Springer, K. / Berard, C. / Hainfeld, J. / Bewley, M.C. / Flanagan, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1p6a.cif.gz | 66.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p6a.ent.gz | 53.5 KB | Display | PDB format |
PDBx/mmJSON format | 1p6a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p6/1p6a ftp://data.pdbj.org/pub/pdb/validation_reports/p6/1p6a | HTTPS FTP |
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-Related 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: 20020.572 Da / Num. of mol.: 1 / Fragment: knob domain (UNP residues 403-587) / Mutation: Y489S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human adenovirus A serotype 12 / Genus: Mastadenovirus / Species: Human adenovirus A / Gene: L5 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P36711 |
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#2: Protein | Mass: 13640.500 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CXADR, CAR / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P78310 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 5.97 Å3/Da / Density % sol: 79.39 % |
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Crystal grow | Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 99 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→20 Å |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.9→20 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber /
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Refinement step | Cycle: LAST / Resolution: 2.9→20 Å
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