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- PDB-3ppe: Crystal structure of chicken VE-cadherin EC1-2 -

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Basic information

Entry
Database: PDB / ID: 3ppe
TitleCrystal structure of chicken VE-cadherin EC1-2
ComponentsVascular endothelial cadherin
KeywordsCELL ADHESION / extracellular cadherin (EC) domain / beta barrel / Ig-domain like / domain swapped dimer interface / calcium dependent cell-cell adhesion / cell surface
Function / homology
Function and homology information


VEGFR2 mediated vascular permeability / Adherens junctions interactions / positive regulation of establishment of endothelial barrier / blood vessel maturation / blood vessel endothelial cell migration / cell-cell adhesion mediated by cadherin / cardiac epithelial to mesenchymal transition / protein localization to bicellular tight junction / regulation of vascular permeability / BMP receptor binding ...VEGFR2 mediated vascular permeability / Adherens junctions interactions / positive regulation of establishment of endothelial barrier / blood vessel maturation / blood vessel endothelial cell migration / cell-cell adhesion mediated by cadherin / cardiac epithelial to mesenchymal transition / protein localization to bicellular tight junction / regulation of vascular permeability / BMP receptor binding / cell-cell adhesion via plasma-membrane adhesion molecules / bicellular tight junction assembly / fibrinogen binding / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / vascular endothelial growth factor receptor 2 binding / positive regulation of BMP signaling pathway / vasculature development / catenin complex / regulation of establishment of cell polarity / cell-cell junction assembly / adherens junction organization / negative regulation of microtubule polymerization / homophilic cell adhesion via plasma membrane adhesion molecules / bicellular tight junction / negative regulation of endothelial cell apoptotic process / positive regulation of protein dephosphorylation / protein tyrosine kinase binding / transforming growth factor beta receptor signaling pathway / positive regulation of protein-containing complex assembly / adherens junction / regulation of protein phosphorylation / cell morphogenesis / beta-catenin binding / intracellular calcium ion homeostasis / negative regulation of inflammatory response / positive regulation of angiogenesis / protein phosphatase binding / nuclear membrane / transmembrane transporter binding / membrane => GO:0016020 / positive regulation of cell migration / cadherin binding / negative regulation of cell population proliferation / external side of plasma membrane / calcium ion binding / positive regulation of gene expression / nucleoplasm
Similarity search - Function
VE-cadherin / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Catenin binding domain superfamily / Cadherins / Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain ...VE-cadherin / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Catenin binding domain superfamily / Cadherins / Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBrasch, J. / Harrison, O.J. / Ahlsen, G. / Carnally, S.M. / Henderson, R.M. / Honig, B. / Shapiro, L.S.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structure and binding mechanism of vascular endothelial cadherin: a divergent classical cadherin.
Authors: Brasch, J. / Harrison, O.J. / Ahlsen, G. / Carnally, S.M. / Henderson, R.M. / Honig, B. / Shapiro, L.
History
DepositionNov 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vascular endothelial cadherin
B: Vascular endothelial cadherin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6278
Polymers45,3872
Non-polymers2406
Water10,575587
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-43 kcal/mol
Surface area21610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.973, 99.973, 105.987
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-267-

HOH

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Components

#1: Protein Vascular endothelial cadherin


Mass: 22693.367 Da / Num. of mol.: 2
Fragment: chicken VE-cadherin domains EC1-EC2, UNP residues 41-243
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: pSMT3 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2DE3 pLysS / References: UniProt: Q8AYD0
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 587 / Source method: isolated from a natural source / Formula: H2O

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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: 2.92 Å3/Da / Density % sol: 57.84 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18% (w/v) PEG 8,000, 200mM Calcium acetate, 100mM sodium cacodylate pH6.5., VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97885 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 9, 2009
RadiationMonochromator: Bent single Si(111) crystal (horizontal focusing and deflection)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97885 Å / Relative weight: 1
ReflectionResolution: 2.1→80 Å / Num. obs: 31991 / % possible obs: 100 % / Redundancy: 14.1 %
Reflection shellResolution: 2.1→2.18 Å / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0072refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A4E

2a4e


Resolution: 2.1→72.74 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.904 / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24189 1613 5.1 %RANDOM
Rwork0.18401 ---
obs0.18692 30319 99.96 %-
all-31937 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.211 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2---0.06 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.1→72.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3196 0 6 587 3789
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223317
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6661.9494514
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.9055423
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.16424.375160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.20115582
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0051524
X-RAY DIFFRACTIONr_chiral_restr0.1080.2517
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212526
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5981.52050
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.2723349
X-RAY DIFFRACTIONr_scbond_it2.81931267
X-RAY DIFFRACTIONr_scangle_it4.3454.51155
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.101→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 121 -
Rwork0.188 2190 -
obs--99.83 %

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