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- PDB-4nup: Crystal structure of mouse N-cadherin EC1-2 with AA insertion bet... -

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Basic information

Entry
Database: PDB / ID: 4nup
TitleCrystal structure of mouse N-cadherin EC1-2 with AA insertion between residues 2 and 3
ComponentsN-CADHERIN EC1-2
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 / gamma-catenin binding / neural crest cell development / glial cell differentiation / telencephalon development / neuroepithelial cell differentiation / type B pancreatic cell development / cell-cell adhesion mediated by cadherin / 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 / intercalated disc / homeostasis of number of cells / regulation of signal transduction / presynaptic active zone membrane / regulation of synaptic transmission, glutamatergic / T-tubule / synapse assembly / striated muscle cell differentiation / protein tyrosine kinase binding / protein localization to plasma membrane / adherens junction / sarcolemma / brain development / modulation of chemical synaptic transmission / cell morphogenesis / negative regulation of canonical Wnt signaling pathway / cerebral cortex development / cell-cell adhesion / beta-catenin binding / regulation of protein localization / cell migration / cell-cell junction / apical part of cell / cell junction / lamellipodium / basolateral plasma membrane / protein phosphatase binding / positive regulation of MAPK cascade / postsynaptic density / membrane => GO:0016020 / cell adhesion / neuron projection / cadherin binding / apical plasma membrane / synapse / glutamatergic 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
N-cadherin / 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 ...N-cadherin / 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
Cadherin-2 / Cadherin-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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_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_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: N-CADHERIN EC1-2
B: N-CADHERIN EC1-2
C: N-CADHERIN EC1-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,68013
Polymers71,2793
Non-polymers40110
Water10,377576
1
A: N-CADHERIN EC1-2
B: N-CADHERIN EC1-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7608
Polymers47,5192
Non-polymers2406
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-52 kcal/mol
Surface area21320 Å2
MethodPISA
2
C: N-CADHERIN EC1-2
hetero molecules

C: N-CADHERIN EC1-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,84010
Polymers47,5192
Non-polymers3218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area3700 Å2
ΔGint-66 kcal/mol
Surface area21480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.504, 65.791, 102.505
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein N-CADHERIN EC1-2


Mass: 23759.646 Da / Num. of mol.: 3 / Fragment: unp residues 160-374
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: Q3UIC2, UniProt: P15116*PLUS
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 576 / 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: 4.15 Å3/Da / Density % sol: 70.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.3M magnesium formate, 0.1M HEPES, pH 7.5, 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: 2.7→20 Å / Num. all: 34109 / Num. obs: 33779 / % possible obs: 99 % / 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: 2.7→19.963 Å / SU ML: 0.3 / σ(F): 1.34 / Phase error: 22.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2288 1665 5.05 %random
Rwork0.1722 ---
obs0.175 33678 98.98 %-
all-33779 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→19.963 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5010 0 10 576 5596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095151
X-RAY DIFFRACTIONf_angle_d1.267059
X-RAY DIFFRACTIONf_dihedral_angle_d14.2621943
X-RAY DIFFRACTIONf_chiral_restr0.059820
X-RAY DIFFRACTIONf_plane_restr0.007952
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6806-2.75930.31211340.23792326X-RAY DIFFRACTION88
2.7593-2.84810.28861350.22912661X-RAY DIFFRACTION100
2.8481-2.94960.30561500.21392618X-RAY DIFFRACTION100
2.9496-3.06730.25381250.21062679X-RAY DIFFRACTION100
3.0673-3.20640.27131300.20042664X-RAY DIFFRACTION100
3.2064-3.37470.24051430.18732672X-RAY DIFFRACTION100
3.3747-3.58490.24131410.17152674X-RAY DIFFRACTION100
3.5849-3.85990.21871560.15722672X-RAY DIFFRACTION100
3.8599-4.2450.20871350.14012704X-RAY DIFFRACTION100
4.245-4.85150.15551390.12262720X-RAY DIFFRACTION100
4.8515-6.08360.19451420.14892754X-RAY DIFFRACTION100
6.0836-19.9640.22611720.18642832X-RAY DIFFRACTION100

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