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- PDB-4num: Crystal structure of mouse N-cadherin EC1-2 A78SI92M -

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Basic information

Entry
Database: PDB / ID: 4num
TitleCrystal structure of mouse N-cadherin EC1-2 A78SI92M
ComponentsCadherin-2
KeywordsCELL ADHESION / cell adhesion molecule
Function / homology
Function and homology information


mesenchymal cell migration / regulation of oligodendrocyte progenitor proliferation / radial glial cell differentiation / neuroligin clustering involved in postsynaptic membrane assembly / regulation of postsynaptic density protein 95 clustering / 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 / synaptic vesicle clustering ...mesenchymal cell migration / regulation of oligodendrocyte progenitor proliferation / radial glial cell differentiation / neuroligin clustering involved in postsynaptic membrane assembly / regulation of postsynaptic density protein 95 clustering / 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 / synaptic vesicle clustering / gamma-catenin binding / neural crest cell development / telencephalon development / desmosome / glial cell differentiation / 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 / brain morphogenesis / catenin complex / cell-cell junction assembly / adherens junction organization / blood vessel morphogenesis / postsynaptic specialization membrane / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of myelination / 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 / striated muscle cell differentiation / synapse assembly / T-tubule / protein tyrosine kinase binding / protein localization to plasma membrane / adherens junction / modulation of chemical synaptic transmission / negative regulation of canonical Wnt signaling pathway / cell morphogenesis / sarcolemma / cerebral cortex development / cell-cell adhesion / beta-catenin binding / cell-cell junction / cell migration / apical part of cell / lamellipodium / regulation of protein localization / basolateral plasma membrane / protein phosphatase binding / positive regulation of MAPK cascade / postsynaptic density / cell adhesion / neuron projection / cadherin binding / apical plasma membrane / glutamatergic synapse / calcium ion binding / synapse / protein-containing complex binding / protein kinase binding / enzyme binding / cell surface / protein-containing complex / RNA binding / identical protein binding / membrane / 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 / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 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_seq_id / _struct_conn.ptnr2_label_asym_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

Downloads & links

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Assembly

Deposited unit
A: Cadherin-2
B: Cadherin-2
C: Cadherin-2
D: Cadherin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,08716
Polymers94,6064
Non-polymers48112
Water00
1
A: Cadherin-2
B: Cadherin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5448
Polymers47,3032
Non-polymers2406
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-33 kcal/mol
Surface area22500 Å2
MethodPISA
2
C: Cadherin-2
D: Cadherin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5448
Polymers47,3032
Non-polymers2406
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-34 kcal/mol
Surface area22540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.751, 221.152, 72.239
Angle α, β, γ (deg.)90.00, 103.85, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.357777, -0.35282, -0.864589), (-0.498966, -0.710386, 0.496371), (-0.789321, 0.608991, 0.078115)54.63142, 55.99346, 15.10757
3given(0.545494, 0.381725, 0.746139), (-0.715767, 0.675328, 0.177792), (-0.43602, -0.631046, 0.641613)-13.47838, -15.16053, 70.66274
4given(0.441286, 0.022909, -0.897074), (0.059476, -0.998223, 0.003765), (-0.895393, -0.055015, -0.441864)15.37048, 107.61206, 28.73595

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Components

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


Mass: 23651.531 Da / Num. of mol.: 4 / Fragment: unp residues 160-374 / Mutation: A78S, I92M
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.: 12 / Source method: obtained synthetically / Formula: Ca

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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: 4.9 Å3/Da / Density % sol: 74.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 15% PEG3350, 0.2M sodium chloride, 0.1M Tris, pH 8.5, 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: Jul 11, 2008
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: 3.2→20 Å / Num. all: 27180 / Num. obs: 25725 / % possible obs: 94.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→19.97 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.864 / SU B: 21.577 / SU ML: 0.331 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R Free: 0.453 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25284 1295 5 %RANDOM
Rwork0.21926 ---
all0.292 25551 --
obs0.22098 24430 94.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.826 Å2
Baniso -1Baniso -2Baniso -3
1-1.36 Å2-0 Å21.7 Å2
2---3.65 Å20 Å2
3---1.66 Å2
Refinement stepCycle: LAST / Resolution: 3.3→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6648 0 12 0 6660
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0196812
X-RAY DIFFRACTIONr_bond_other_d0.0010.026452
X-RAY DIFFRACTIONr_angle_refined_deg1.0711.9669328
X-RAY DIFFRACTIONr_angle_other_deg0.719314854
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7965860
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.45525.031318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.936151086
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.11548
X-RAY DIFFRACTIONr_chiral_restr0.0620.21078
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217864
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021476
LS refinement shellResolution: 3.3→3.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.433 75 -
Rwork0.349 1255 -
obs--66.73 %

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