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

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Basic information

Entry
Database: PDB / ID: 1nch
TitleSTRUCTURAL BASIS OF CELL-CELL ADHESION BY CADHERINS
ComponentsN-CADHERIN
KeywordsCELL ADHESION PROTEIN / CADHERIN
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 / gamma-catenin binding ...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 / gamma-catenin binding / synaptic vesicle clustering / 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 / catenin complex / brain morphogenesis / 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 / intercalated disc / homeostasis of number of cells / 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 / beta-catenin binding / cell-cell adhesion / 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
YTTERBIUM (III) 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: Derived calculations / Version format compliance
Revision 1.3Nov 20, 2019Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_conn_angle ...pdbx_database_status / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_ref_seq_dif
Item: _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)24,8364
Polymers24,4902
Non-polymers3462
Water4,161231
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: N-CADHERIN
hetero molecules

A: N-CADHERIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8364
Polymers24,4902
Non-polymers3462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area2430 Å2
ΔGint-25 kcal/mol
Surface area10570 Å2
MethodPISA, PQS
3
B: N-CADHERIN
hetero molecules

B: N-CADHERIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8364
Polymers24,4902
Non-polymers3462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)79.730, 79.730, 74.960
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
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
DetailsTHE ASYMMETRIC UNIT (MOLECULES A AND B) COMPRISE A CADHERIN ADHESION DIMER. A STRAND DIMER IS FORMED, FOR EXAMPLE, BETWEEN MOLECULE A AND ITS (Y, X, -Z) SYMMETRY MATE. NOTE THAT THIS TRANSFORMATION IS IN THE NON-ORTHOGONAL TRIGONAL LATTICE.

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Components

#1: Protein N-CADHERIN


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-YB / YTTERBIUM (III) ION


Mass: 173.040 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Yb
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE MODEL INCLUDES TWO YTTERBIUM IONS (YB 3+) BOUND AT A PUTATIVE CALCIUM BINDING SITE FOR EACH ...THE MODEL INCLUDES TWO YTTERBIUM IONS (YB 3+) BOUND AT A PUTATIVE CALCIUM BINDING SITE FOR EACH MOLECULE OF THE ASYMMETRIC UNIT.
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: 2.81 Å3/Da / Density % sol: 56.16 %
Description: 5 WAVELENGTH MAD EXPERIMENT TAKEN NEAR URANIUM L(III) EDGE. INITIAL PHASING WAS OBTAINED FROM TWO MULTI-WAVELENGTH ANOMALOUS DIFFRACTION (MAD) EXPERIMENTS (ONE 4 WAVELENGTHS AND ONE FIVE ...Description: 5 WAVELENGTH MAD EXPERIMENT TAKEN NEAR URANIUM L(III) EDGE. INITIAL PHASING WAS OBTAINED FROM TWO MULTI-WAVELENGTH ANOMALOUS DIFFRACTION (MAD) EXPERIMENTS (ONE 4 WAVELENGTHS AND ONE FIVE WAVELENGTHS) PERFORMED USING RADIATION NEAR THE YTTERBIUM LIII ABSORPTION EDGE PRODUCED BY AN UNDULATOR AT THE EUROPEAN SYNCHROTRON RADIATION FACILITY. HIGH RESOLUTION REFINEMENT WAS COMPLETED STARTING FROM A MODEL PRODUCED FROM ANOTHER MAD EXPERIMENT ON THE TYPE C CRYSTAL OF THIS MOLECULE
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
20.8 M1reservoirLi2SO4
30.1 Msodium acetate1reservoir
420 mMYb acetate1reservoir
1protein solution1drop0.002-0.003ml

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.98 Å
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Aug 1, 1994
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionNum. obs: 15198 / % possible obs: 93.2 % / Rmerge(I) obs: 0.047
Reflection
*PLUS
Rmerge(I) obs: 0.047

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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
Rfree0.309 --
Rwork0.224 --
obs0.224 13950 92 %
Displacement parametersBiso mean: 32.6 Å2
Refinement stepCycle: LAST / Resolution: 2.1→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1528 0 2 231 1761
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg2.13
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

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