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Yorodumi- PDB-1vca: CRYSTAL STRUCTURE OF AN INTEGRIN-BINDING FRAGMENT OF VASCULAR CEL... -
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-Basic information
Entry | Database: PDB / ID: 1vca | ||||||
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Title | CRYSTAL STRUCTURE OF AN INTEGRIN-BINDING FRAGMENT OF VASCULAR CELL ADHESION MOLECULE-1 AT 1.8 ANGSTROMS RESOLUTION | ||||||
Components | HUMAN VASCULAR CELL ADHESION MOLECULE-1 | ||||||
Keywords | CELL ADHESION PROTEIN / IMMUNOGLOBULIN SUPERFAMILY / INTEGRIN-BINDING | ||||||
Function / homology | Function and homology information cardiac neuron differentiation / alpha9-beta1 integrin-vascular cell adhesion molecule-1 complex / cell adhesion mediator activity / cell-cell adhesion mediated by integrin / chronic inflammatory response / membrane to membrane docking / leukocyte tethering or rolling / innervation / primary methylamine oxidase activity / amine metabolic process ...cardiac neuron differentiation / alpha9-beta1 integrin-vascular cell adhesion molecule-1 complex / cell adhesion mediator activity / cell-cell adhesion mediated by integrin / chronic inflammatory response / membrane to membrane docking / leukocyte tethering or rolling / innervation / primary methylamine oxidase activity / amine metabolic process / podosome / heterotypic cell-cell adhesion / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / response to ionizing radiation / response to zinc ion / microvillus / cellular response to vascular endothelial growth factor stimulus / Integrin cell surface interactions / response to nutrient / positive regulation of T cell proliferation / cell adhesion molecule binding / B cell differentiation / cell chemotaxis / cell-matrix adhesion / filopodium / response to nicotine / sarcolemma / integrin binding / cellular response to amyloid-beta / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / apical part of cell / cellular response to tumor necrosis factor / Interleukin-4 and Interleukin-13 signaling / response to ethanol / response to lipopolysaccharide / early endosome / response to hypoxia / cell adhesion / inflammatory response / external side of plasma membrane / cell surface / Golgi apparatus / endoplasmic reticulum / extracellular space / extracellular exosome / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å | ||||||
Authors | Jones, E.Y. / Harlos, K. / Bottomley, M.J. / Robinson, R.C. / Driscoll, P.C. / Edwards, R.M. / Clements, J.M. / Dudgeon, T.J. / Stuart, D.I. | ||||||
Citation | Journal: Nature / Year: 1995 Title: Crystal structure of an integrin-binding fragment of vascular cell adhesion molecule-1 at 1.8 A resolution. Authors: Jones, E.Y. / Harlos, K. / Bottomley, M.J. / Robinson, R.C. / Driscoll, P.C. / Edwards, R.M. / Clements, J.M. / Dudgeon, T.J. / Stuart, D.I. #1: Journal: J.Mol.Biol. / Year: 1994 Title: Crystallization and Preliminary X-Ray Diffraction Characterisation of Both a Native and Selenomethionyl Vla-4 Binding Fragment of Vcam-1 Authors: Bottomley, M.J. / Robinson, R.C. / Driscoll, P.C. / Harlos, K. / Stuart, D.I. / Aplin, R.T. / Clements, J.M. / Jones, E.Y. / Dudgeon, T.J. #2: Journal: Eur.J.Biochem. / Year: 1994 Title: Expression and Characterisation of a Very-Late Antigen-4 (Alpha4Beta1) Integrin Binding Fragment of Vascular Cell-Adhesion Molecule-1 Authors: Dudgeon, T.J. / Bottomley, M.J. / Driscoll, P.C. / Humphries, M.J. / Mould, A.P. / Wingfield, G.I. / Clements, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vca.cif.gz | 89.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vca.ent.gz | 73 KB | Display | PDB format |
PDBx/mmJSON format | 1vca.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vca_validation.pdf.gz | 374.1 KB | Display | wwPDB validaton report |
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Full document | 1vca_full_validation.pdf.gz | 378.8 KB | Display | |
Data in XML | 1vca_validation.xml.gz | 9.2 KB | Display | |
Data in CIF | 1vca_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vc/1vca ftp://data.pdbj.org/pub/pdb/validation_reports/vc/1vca | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO A 7 / 2: CIS PROLINE - PRO A 60 / 3: CIS PROLINE - PRO A 120 / 4: CIS PROLINE - PRO B 7 / 5: CIS PROLINE - PRO B 60 / 6: CIS PROLINE - PRO B 120 |
-Components
#1: Protein | Mass: 22535.574 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Strain: HW1110 / Production host: Escherichia coli (E. coli) / References: UniProt: P19320 #2: Water | ChemComp-HOH / | |
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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: 2.2 Å3/Da / Density % sol: 44.07 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Method: vapor diffusion, sitting drop / Details: Bottomley, M.J., (1994) J.Mol.Biol., 244, 464. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.97 Å |
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Detector | Type: FUJI / Detector: IMAGE PLATE / Date: 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Num. obs: 32077 / % possible obs: 85 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.067 |
Reflection | *PLUS Highest resolution: 1.8 Å / Rmerge(I) obs: 0.087 |
-Processing
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Refinement | Resolution: 1.8→15 Å / σ(F): 0 /
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Refinement step | Cycle: LAST / Resolution: 1.8→15 Å
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Refine LS restraints |
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