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- PDB-2qvi: Crystal structure of N-cadherin domains EC12 -

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Basic information

Entry
Database: PDB / ID: 2qvi
TitleCrystal structure of N-cadherin domains EC12
ComponentsCadherin-2
KeywordsCELL ADHESION / beta barrel / strand swap / domain swap / Calcium / Cleavage on pair of basic residues / Glycoprotein / Membrane / Phosphoprotein / Transmembrane
Function / homology
Function and homology information


mesenchymal cell migration / regulation of oligodendrocyte progenitor proliferation / regulation of postsynaptic density protein 95 clustering / radial glial cell differentiation / neuroligin clustering involved in postsynaptic membrane assembly / positive regulation of synaptic vesicle clustering / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / Adherens junctions interactions / desmosome ...mesenchymal cell migration / regulation of oligodendrocyte progenitor proliferation / regulation of postsynaptic density protein 95 clustering / radial glial cell differentiation / neuroligin clustering involved in postsynaptic membrane assembly / positive regulation of synaptic vesicle clustering / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / Adherens junctions interactions / desmosome / synaptic vesicle clustering / neural crest cell development / gamma-catenin binding / glial cell differentiation / cell-cell adhesion mediated by cadherin / telencephalon development / neuroepithelial cell differentiation / type B pancreatic cell development / neuronal stem cell population maintenance / alpha-catenin binding / fascia adherens / apicolateral plasma membrane / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / Myogenesis / regulation of Rho protein signal transduction / postsynaptic specialization membrane / brain morphogenesis / catenin complex / cell-cell junction assembly / adherens junction organization / blood vessel morphogenesis / regulation of myelination / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of axonogenesis / cortical actin cytoskeleton / nitric-oxide synthase binding / homophilic cell adhesion via plasma membrane adhesion molecules / plasma membrane raft / homeostasis of number of cells / intercalated disc / presynaptic active zone membrane / regulation of synaptic transmission, glutamatergic / synapse assembly / striated muscle cell differentiation / T-tubule / protein tyrosine kinase binding / protein localization to plasma membrane / adherens junction / brain development / negative regulation of canonical Wnt signaling pathway / sarcolemma / modulation of chemical synaptic transmission / cell morphogenesis / cell-cell adhesion / cerebral cortex development / beta-catenin binding / regulation of protein localization / cell-cell junction / cell migration / apical part of cell / lamellipodium / cell junction / basolateral plasma membrane / protein phosphatase binding / postsynaptic density / positive regulation of MAPK cascade / cell adhesion / neuron projection / cadherin binding / apical plasma membrane / glutamatergic synapse / synapse / calcium ion binding / protein-containing complex binding / protein kinase binding / enzyme binding / cell surface / protein-containing complex / RNA binding / membrane / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Cadherin prodomain like / Cadherin prodomain / Cadherin prodomain like / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Catenin binding domain superfamily / Cadherins / Cadherin / Cadherin conserved site / Cadherin domain signature. ...Cadherin prodomain like / Cadherin prodomain / Cadherin prodomain like / 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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.012 Å
AuthorsShapiro, L.S. / Carroll, K.J.
CitationJournal: To be Published
Title: Biophysical characterization of N-cadherin and E-cadherin homophilic and heterophilic interactions
Authors: Shapiro, L.S. / Carroll, K.J. / Honig, B.
History
DepositionAug 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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

Downloads & links

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Assembly

Deposited unit
A: Cadherin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7384
Polymers23,6171
Non-polymers1203
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.657, 86.902, 46.708
Angle α, β, γ (deg.)90.000, 97.730, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cadherin-2 / / Neural cadherin / N-cadherin / CD325 antigen


Mass: 23617.492 Da / Num. of mol.: 1 / Fragment: UNP residues 160-374
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdh2 / References: UniProt: P15116
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 108 / 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: 4.88 Å3/Da / Density % sol: 74.8 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 7566 / % possible obs: 83.8 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.105 / Χ2: 1.001 / Net I/σ(I): 10.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3-3.111.50.2784091.00844.9
3.11-3.231.90.2395300.99961.6
3.23-3.382.10.246691.00573.4
3.38-3.552.40.18774185.6
3.55-3.782.50.152813191.7
3.78-4.062.70.1138601.00194.8
4.06-4.472.70.097873195.6
4.47-5.112.70.08875196.6
5.11-6.42.70.084872197
6.4-202.70.061891196

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT3data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.012→19.96 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.299 383 4.2 %
Rwork0.254 --
obs-7560 83.5 %
Solvent computationBsol: 50.64 Å2
Displacement parametersBiso mean: 35.992 Å2
Baniso -1Baniso -2Baniso -3
1-10.041 Å20 Å2-4.411 Å2
2---17.312 Å20 Å2
3---7.271 Å2
Refinement stepCycle: LAST / Resolution: 3.012→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1654 0 3 108 1765
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:ion.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param

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