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Yorodumi- PDB-2w9l: CANINE ADENOVIRUS TYPE 2 FIBRE HEAD IN COMPLEX WITH CAR DOMAIN D1... -
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-Basic information
Entry | Database: PDB / ID: 2w9l | |||||||||||||||
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Title | CANINE ADENOVIRUS TYPE 2 FIBRE HEAD IN COMPLEX WITH CAR DOMAIN D1 AND SIALIC ACID | |||||||||||||||
Components |
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Keywords | RECEPTOR / IMMUNOGLOBULIN DOMAIN / CAR / KNOB / FIBER / FIBRE / CAV-2 / CANINE / COMPLEX / ERYTHROCYTE / SIALIC ACID / GLYCOPROTEIN / FIBER HEAD / ADENOVIRUS / FIBRE HEAD / LIPOPROTEIN / FIBER PROTEIN / CELL JUNCTION / CELL ADHESION / RED BLOOD CELL / COXSACKIEVIRUS / PHOSPHOPROTEIN / MEMBRANE / SECRETED / PALMITATE / DOMAIN D1 / HOST-VIRUS INTERACTION / VIRUS-RECEPTOR COMPLEX / TRANSMEMBRANE / CELL MEMBRANE / SIALYL-LACTOSE / TIGHT JUNCTION / PHOSPHORYLATION / HEMAGGLUTINATION | |||||||||||||||
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 / cell adhesion molecule binding / mitochondrion organization / 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 | HOMO SAPIENS (human) CANINE ADENOVIRUS 2 | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å | |||||||||||||||
Authors | Seiradake, E. / Henaff, D. / Wodrich, H. / Billet, O. / Perreau, M. / Hippert, C. / Mennechet, F. / Schoehn, G. / Lortat-Jacob, H. / Dreja, H. ...Seiradake, E. / Henaff, D. / Wodrich, H. / Billet, O. / Perreau, M. / Hippert, C. / Mennechet, F. / Schoehn, G. / Lortat-Jacob, H. / Dreja, H. / Ibanes, S. / Kalatzis, V. / Wang, J.P. / Finberg, R.W. / Cusack, S. / Kremer, E.J. | |||||||||||||||
Citation | Journal: PLoS Pathog. / Year: 2009 Title: The cell adhesion molecule "CAR" and sialic acid on human erythrocytes influence adenovirus in vivo biodistribution. Authors: Seiradake, E. / Henaff, D. / Wodrich, H. / Billet, O. / Perreau, M. / Hippert, C. / Mennechet, F. / Schoehn, G. / Lortat-Jacob, H. / Dreja, H. / Ibanes, S. / Kalatzis, V. / Wang, J.P. / ...Authors: Seiradake, E. / Henaff, D. / Wodrich, H. / Billet, O. / Perreau, M. / Hippert, C. / Mennechet, F. / Schoehn, G. / Lortat-Jacob, H. / Dreja, H. / Ibanes, S. / Kalatzis, V. / Wang, J.P. / Finberg, R.W. / Cusack, S. / Kremer, E.J. | |||||||||||||||
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 | 2w9l.cif.gz | 681.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w9l.ent.gz | 563.9 KB | Display | PDB format |
PDBx/mmJSON format | 2w9l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w9/2w9l ftp://data.pdbj.org/pub/pdb/validation_reports/w9/2w9l | HTTPS FTP |
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-Related structure data
Related structure data | 2wbvC 2wbwC 2j1kS 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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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 13804.705 Da / Num. of mol.: 12 / Fragment: DOMAIN D1, RESIDUES 16-139 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / 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, RESIDUES 358-542 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CANINE ADENOVIRUS 2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): Star / References: UniProt: Q65914 #3: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Water | ChemComp-HOH / | Sequence details | CONTAINS POLY-HIS 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: 2.9 Å3/Da / Density % sol: 56 % / Description: NONE |
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Crystal grow | Details: 20% POLYETHYLENE GLYCOL MONOMETHYL-ETHER 550, 0.1 M BICINE, PH 9, 0.1 M NACL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93927 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 20, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93927 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→49.6 Å / Num. obs: 105112 / % possible obs: 98.3 % / Observed criterion σ(I): 1 / Redundancy: 8.18 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 14.18 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 8.37 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3.3 / % possible all: 93.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2J1K Resolution: 2.91→49.63 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.893 / SU B: 34.734 / SU ML: 0.299 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.389 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THERE ARE 24 NCS OPERATIONS, WHICH CAN BE PICKED UP EASILY WITH REGULAR CRYSTALLOGRAPHIC SOFTWARE.
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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: 33.92 Å2
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Refinement step | Cycle: LAST / Resolution: 2.91→49.63 Å
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Refine LS restraints |
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