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- PDB-4nuq: Crystal structure of mouse N-cadherin EC1-2 W2F -

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Basic information

Entry
Database: PDB / ID: 4nuq
TitleCrystal structure of mouse N-cadherin EC1-2 W2F
ComponentsCadherin-2
KeywordsCELL ADHESION / cell adhesion molecule
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 / Resolution: 2.116 Å
AuthorsJin, X.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural and energetic determinants of adhesive binding specificity in type I cadherins.
Authors: Vendome, J. / Felsovalyi, K. / Song, H. / Yang, Z. / Jin, X. / Brasch, J. / Harrison, O.J. / Ahlsen, G. / Bahna, F. / Kaczynska, A. / Katsamba, P.S. / Edmond, D. / Hubbell, W.L. / Shapiro, L. / Honig, B.
History
DepositionDec 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_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.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_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_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_ref_seq_dif.details / _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: Cadherin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6994
Polymers23,5781
Non-polymers1203
Water2,864159
1
A: Cadherin-2
hetero molecules

A: Cadherin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3978
Polymers47,1572
Non-polymers2406
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area1850 Å2
ΔGint-41 kcal/mol
Surface area23000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.587, 86.245, 46.722
Angle α, β, γ (deg.)90.00, 98.52, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-552-

HOH

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Components

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


Mass: 23578.457 Da / Num. of mol.: 1 / Fragment: unp residues 160-374 / Mutation: W2F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdh2 / Production host: Escherichia coli (E. coli) / 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.: 159 / 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: 4.93 Å3/Da / Density % sol: 75.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 4% PEG4000, 0.2M magnesium chloride, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 9, 2010
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 26109 / Num. obs: 25222 / % possible obs: 96.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.116→19.912 Å / SU ML: 0.27 / σ(F): 1.39 / Phase error: 33.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2531 1281 5.06 %random
Rwork0.2116 ---
all0.254 25222 --
obs0.2137 25075 96.45 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.116→19.912 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1648 0 3 159 1810
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081694
X-RAY DIFFRACTIONf_angle_d1.082322
X-RAY DIFFRACTIONf_dihedral_angle_d12.374635
X-RAY DIFFRACTIONf_chiral_restr0.075271
X-RAY DIFFRACTIONf_plane_restr0.005315
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1162-2.20090.3311120.27972105X-RAY DIFFRACTION77
2.2009-2.30090.30921080.27242570X-RAY DIFFRACTION94
2.3009-2.4220.3311340.262748X-RAY DIFFRACTION99
2.422-2.57350.33571590.25492735X-RAY DIFFRACTION100
2.5735-2.77170.33171470.25112746X-RAY DIFFRACTION100
2.7717-3.04970.27961450.23752739X-RAY DIFFRACTION100
3.0497-3.4890.26431520.2132739X-RAY DIFFRACTION100
3.489-4.3880.21471670.18432725X-RAY DIFFRACTION100
4.388-19.91290.2161510.18392800X-RAY DIFFRACTION99

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