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- PDB-2w9l: CANINE ADENOVIRUS TYPE 2 FIBRE HEAD IN COMPLEX WITH CAR DOMAIN D1... -
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Open data
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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 | |||||||||||||||
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![]() | 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 | ![]() 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 / mitochondrion organization / neutrophil chemotaxis / acrosomal vesicle / filopodium / PDZ domain binding / Cell surface interactions at the vascular wall / adherens junction / neuromuscular junction / beta-catenin binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / viral capsid / cell-cell junction / integrin binding / cell junction / virus receptor activity / heart development / cell body / growth cone / actin cytoskeleton organization / basolateral plasma membrane / defense response to virus / cell adhesion / symbiont entry into host cell / neuron projection / 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 | ![]() ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | 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. | |||||||||||||||
![]() | ![]() 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 681.2 KB | Display | ![]() |
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PDB format | ![]() | 563.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.3 MB | Display | ![]() |
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Full document | ![]() | 4.4 MB | Display | |
Data in XML | ![]() | 119.4 KB | Display | |
Data in CIF | ![]() | 164.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2wbvC ![]() 2wbwC ![]() 2j1kS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() #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.) ![]() ![]() ![]() #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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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