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Yorodumi- PDB-1kac: KNOB DOMAIN FROM ADENOVIRUS SEROTYPE 12 IN COMPLEX WITH DOMAIN 1 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kac | ||||||
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Title | KNOB DOMAIN FROM ADENOVIRUS SEROTYPE 12 IN COMPLEX WITH DOMAIN 1 OF ITS CELLULAR RECEPTOR CAR | ||||||
Components |
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Keywords | Viral protein/receptor / ADHESION PROTEIN RECEPTOR COMPLEX / 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 / regulation of AV node cell action potential / gamma-delta T cell activation / germ cell migration / apicolateral plasma membrane / transepithelial transport ...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 / regulation of AV node cell action potential / gamma-delta T cell activation / germ cell migration / apicolateral plasma membrane / transepithelial transport / cell-cell junction organization / connexin binding / adhesion receptor-mediated virion attachment to host cell / cardiac muscle cell development / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / intercalated disc / bicellular tight junction / cell adhesion molecule binding / neutrophil chemotaxis / acrosomal vesicle / mitochondrion organization / filopodium / PDZ domain binding / Cell surface interactions at the vascular wall / adherens junction / neuromuscular junction / beta-catenin binding / integrin binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cell junction / viral capsid / cell-cell junction / virus receptor activity / heart development / basolateral plasma membrane / cell body / growth cone / actin cytoskeleton organization / 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 12 Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.6 Å | ||||||
Authors | Bewley, M.C. / Springer, K. / Zhang, Y.B. / Freimuth, P. / Flanagan, J.M. | ||||||
Citation | 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kac.cif.gz | 72.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kac.ent.gz | 54.6 KB | Display | PDB format |
PDBx/mmJSON format | 1kac.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kac_validation.pdf.gz | 376.5 KB | Display | wwPDB validaton report |
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Full document | 1kac_full_validation.pdf.gz | 386.5 KB | Display | |
Data in XML | 1kac_validation.xml.gz | 9 KB | Display | |
Data in CIF | 1kac_validation.cif.gz | 13.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ka/1kac ftp://data.pdbj.org/pub/pdb/validation_reports/ka/1kac | HTTPS FTP |
-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: 19944.477 Da / Num. of mol.: 1 / Fragment: KNOB Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human adenovirus 12 / Genus: Mastadenovirus / Species: Human adenovirus A / Variant: SEROTYPE 12 / Cell line (production host): BL21(DE3) / Production host: Escherichia coli (E. coli) / Variant (production host): T7 / References: UniProt: P36711 |
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#2: Protein | Mass: 13640.500 Da / Num. of mol.: 1 / Fragment: DOMAIN 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P78310 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.6 Å3/Da / Density % sol: 78 % | ||||||||||||||||||
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Crystal grow | pH: 6.2 / Details: 900MM AMMONIUM SULPHATE ON 100MM MES, PH 6.2 | ||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 99 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→40 Å / Num. obs: 24636 / % possible obs: 100 % / Redundancy: 14.2 % / Rmerge(I) obs: 0.7 |
Reflection shell | Resolution: 2.6→2.7 Å / Rmerge(I) obs: 0.35 / % possible all: 100 |
Reflection shell | *PLUS % possible obs: 100 % / Mean I/σ(I) obs: 6 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 2.6→20 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Bsol: 61 Å2 / ksol: 0.43 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.9 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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Refine LS restraints |
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 2.9 % / Rfactor obs: 0.22 / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.22 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 44.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.7 |