+Open data
-Basic information
Entry | Database: PDB / ID: 2j1k | ||||||
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Title | CAV-2 fibre head in complex with CAR D1 | ||||||
Components |
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Keywords | VIRUS/RECEPTOR / VIRUS-RECEPTOR COMPLEX / COMPLEX / MEMBRANE / RECEPTOR / PALMITATE / DOMAIN D1 / IMMUNOGLOBULIN DOMAIN / HOST-VIRUS INTERACTION / GLYCOPROTEIN / FIBER PROTEIN / CELL ADHESION / PHOSPHORYLATION / TRANSMEMBRANE / TIGHT JUNCTION / COXSACKIEVIRUS / FIBER HEAD / ADENOVIRUS / FIBRE HEAD / LIPOPROTEIN / CAR / KNOB / FIBER / FIBRE / CAV-2 / CANINE | ||||||
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 | HOMO SAPIENS (human) CANINE ADENOVIRUS 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Seiradake, E. / Lortat-Jacob, H. / Billet, O. / Kremer, E.J. / Cusack, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Structural and Mutational Analysis of Human Ad37 and Canine Adenovirus 2 Fiber Heads in Complex with the D1 Domain of Coxsackie and Adenovirus Receptor. Authors: Seiradake, E. / Lortat-Jacob, H. / Billet, O. / Kremer, E.J. / Cusack, S. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2j1k.cif.gz | 719.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2j1k.ent.gz | 596.8 KB | Display | PDB format |
PDBx/mmJSON format | 2j1k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2j1k_validation.pdf.gz | 600.7 KB | Display | wwPDB validaton report |
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Full document | 2j1k_full_validation.pdf.gz | 646.3 KB | Display | |
Data in XML | 2j1k_validation.xml.gz | 139.4 KB | Display | |
Data in CIF | 2j1k_validation.cif.gz | 197.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j1/2j1k ftp://data.pdbj.org/pub/pdb/validation_reports/j1/2j1k | HTTPS FTP |
-Related structure data
Related structure data | 2j12C 2j2jC 1kacS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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-Components
#1: Protein | Mass: 14251.245 Da / Num. of mol.: 12 / Fragment: D1 DOMAIN, RESIDUES 15-140 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PAB3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL1 BLUE / References: UniProt: P78310 #2: Protein | Mass: 21685.541 Da / Num. of mol.: 12 / Fragment: FIBRE HEAD DOMAIN, RESIDUES 358-542 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CANINE ADENOVIRUS 2 / Plasmid: PQE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 / References: UniProt: Q65914 #3: Water | ChemComp-HOH / | Sequence details | CONTAINS N-TERMINAL 6XHIS TAG | |
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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: 2.8 Å3/Da / Density % sol: 56 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→47.7 Å / Num. obs: 200033 / % possible obs: 96 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 13.37 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 3.75 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.1 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KAC Resolution: 2.3→192.45 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / SU B: 10.615 / SU ML: 0.14 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.27 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.18 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→192.45 Å
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Refine LS restraints |
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