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- PDB-1nci: STRUCTURAL BASIS OF CELL-CELL ADHESION BY CADHERINS -

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Basic information

Entry
Database: PDB / ID: 1nci
TitleSTRUCTURAL BASIS OF CELL-CELL ADHESION BY CADHERINS
ComponentsN-CADHERINCadherin-2
KeywordsCELL ADHESION PROTEIN / CADHERIN
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
URANYL (VI) ION / Cadherin-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsShapiro, L. / Fannon, A.M. / Kwong, P.D. / Thompson, A. / Lehmann, M.S. / Grubel, G. / Legrand, J.-F. / Als-Nielsen, J. / Colman, D.R. / Hendrickson, W.A.
CitationJournal: Nature / Year: 1995
Title: Structural basis of cell-cell adhesion by cadherins.
Authors: Shapiro, L. / Fannon, A.M. / Kwong, P.D. / Thompson, A. / Lehmann, M.S. / Grubel, G. / Legrand, J.F. / Als-Nielsen, J. / Colman, D.R. / Hendrickson, W.A.
History
DepositionMar 23, 1995Processing site: BNL
Revision 1.0Jul 10, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_special_symmetry / 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_database_status.process_site / _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
B: N-CADHERIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7603
Polymers24,4902
Non-polymers2701
Water5,675315
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-13 kcal/mol
Surface area10790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.200, 57.500, 52.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Atom site foot note1: CIS PROLINE - PRO A 16 / 2: CIS PROLINE - PRO A 18 / 3: CIS PROLINE - PRO A 47 / 4: CIS PROLINE - PRO B 16 / 5: CIS PROLINE - PRO B 18 / 6: CIS PROLINE - PRO B 47
Components on special symmetry positions
IDModelComponents
11A-440-

HOH

21A-463-

HOH

31B-244-

HOH

41B-251-

HOH

DetailsTHE ASYMMETRIC UNIT (MOLECULES A AND B) COMPRISE A CADHERIN STRAND DIMER. AN ADHESION DIMER IS FORMED, FOR EXAMPLE, BETWEEN MOLECULE A AND THE (X + 1/2, 3/2 - Y, -1 -Z) SYMMETRY MATE OF MOLECULE B. SYMMETRY THE CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS PRESENTED BELOW GENERATE THE SUBUNITS OF THE POLYMERIC MOLECULE. APPLIED TO RESIDUES: B 1 .. 100 ADHESION DIMER MATE OF MOLECULE A IS A SYMMETRY-MATE OF MOLECULE B, AND CAN BE GENERATED BY THE FOLLOWING TRANSFORMATION: SYMMETRY1 1 1.000000 0.000000 0.000000 37.60000 SYMMETRY2 1 0.000000 1.500000 0.000000 86.25000 SYMMETRY3 1 0.000000 0.000000 1.000000 -52.50000

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Components

#1: Protein N-CADHERIN / Cadherin-2


Mass: 12244.817 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / References: UniProt: P15116
#2: Chemical ChemComp-IUM / URANYL (VI) ION / Uranyl


Mass: 270.028 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2U
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE MODEL INCLUDES ONE URANYL ION (UO2 2+) BOUND AT THE PUTATIVE CALCIUM BINDING SITE.
Sequence detailsRESIDUE NUMBERING IS FOR THE MATURE PROTEIN.

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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: 2.32 Å3/Da / Density % sol: 46.87 %
Description: 5 WAVELENGTH MAD EXPERIMENT; DATA COLLECTED NEAR URANIUM L(III) EDGE
Crystal grow
*PLUS
Temperature: 19.5 ℃ / pH: 4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
135 mg/mlprotein1drop
20.5-0.6 Maqueous sodium sulfate1reservoir
30.1 MNa acetate1reservoir
45 mMUO2 acetate1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.7217 - 0.7263
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Aug 1, 1994
RadiationScattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.72171
20.72631
ReflectionNum. obs: 33075 / % possible obs: 95.7 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.038
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 15 Å / Rmerge(I) obs: 0.038

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
X-PLORphasing
RefinementResolution: 2.1→5 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.253 --
Rwork0.195 --
obs0.195 31010 96.2 %
Displacement parametersBiso mean: 17.1 Å2
Refinement stepCycle: LAST / Resolution: 2.1→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1557 0 3 315 1875
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.81
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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