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- PDB-1vca: CRYSTAL STRUCTURE OF AN INTEGRIN-BINDING FRAGMENT OF VASCULAR CEL... -

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Basic information

Entry
Database: PDB / ID: 1vca
TitleCRYSTAL STRUCTURE OF AN INTEGRIN-BINDING FRAGMENT OF VASCULAR CELL ADHESION MOLECULE-1 AT 1.8 ANGSTROMS RESOLUTION
ComponentsHUMAN VASCULAR CELL ADHESION MOLECULE-1
KeywordsCELL ADHESION PROTEIN / IMMUNOGLOBULIN SUPERFAMILY / INTEGRIN-BINDING
Function / homology
Function and homology information


cardiac neuron differentiation / alpha9-beta1 integrin-vascular cell adhesion molecule-1 complex / chronic inflammatory response / cell-cell adhesion mediated by integrin / cell adhesion mediator activity / membrane to membrane docking / primary methylamine oxidase activity / leukocyte tethering or rolling / amine metabolic process / innervation ...cardiac neuron differentiation / alpha9-beta1 integrin-vascular cell adhesion molecule-1 complex / chronic inflammatory response / cell-cell adhesion mediated by integrin / cell adhesion mediator activity / membrane to membrane docking / primary methylamine oxidase activity / leukocyte tethering or rolling / amine metabolic process / innervation / heterophilic cell-cell adhesion / podosome / heterotypic cell-cell adhesion / leukocyte cell-cell adhesion / response to zinc ion / response to ionizing radiation / microvillus / cellular response to vascular endothelial growth factor stimulus / Integrin cell surface interactions / cell adhesion molecule binding / positive regulation of T cell proliferation / response to nutrient / B cell differentiation / cell-matrix adhesion / cell chemotaxis / response to nicotine / filopodium / sarcolemma / integrin binding / cellular response to amyloid-beta / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / apical part of cell / cellular response to tumor necrosis factor / response to ethanol / Interleukin-4 and Interleukin-13 signaling / response to lipopolysaccharide / early endosome / response to hypoxia / cell adhesion / inflammatory response / external side of plasma membrane / cell surface / endoplasmic reticulum / Golgi apparatus / extracellular space / extracellular exosome / plasma membrane
Similarity search - Function
Vascular cell adhesion molecule-1 / Intercellular adhesion molecule/vascular cell adhesion molecule, N-terminal / : / Immunoglobulin C2-set / Immunoglobulin C2-set domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain ...Vascular cell adhesion molecule-1 / Intercellular adhesion molecule/vascular cell adhesion molecule, N-terminal / : / Immunoglobulin C2-set / Immunoglobulin C2-set domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Vascular cell adhesion protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsJones, 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
DepositionMar 21, 1995Processing site: BNL
Revision 1.0Sep 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HUMAN VASCULAR CELL ADHESION MOLECULE-1
B: HUMAN VASCULAR CELL ADHESION MOLECULE-1


Theoretical massNumber of molelcules
Total (without water)45,0712
Polymers45,0712
Non-polymers00
Water4,576254
1
A: HUMAN VASCULAR CELL ADHESION MOLECULE-1


Theoretical massNumber of molelcules
Total (without water)22,5361
Polymers22,5361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HUMAN VASCULAR CELL ADHESION MOLECULE-1


Theoretical massNumber of molelcules
Total (without water)22,5361
Polymers22,5361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.700, 66.500, 113.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: 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

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Components

#1: Protein HUMAN VASCULAR CELL ADHESION MOLECULE-1 / VCAM-D1 / 2


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 / water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.07 %
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop / Details: Bottomley, M.J., (1994) J.Mol.Biol., 244, 464.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
113 mg/mlprotein1drop
20.14 Mlithium sulphate monohydrate1reservoir
30.1 MTris-HCl1reservoir
420-22 %(w/v)PEG40001reservoir
51reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.97 Å
DetectorType: FUJI / Detector: IMAGE PLATE / Date: 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionNum. 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

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Processing

Software
NameVersionClassification
DENZOdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementResolution: 1.8→15 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.202 -
obs0.202 32030
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3108 0 0 254 3362
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.99
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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