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- PDB-3q2w: Crystal structure of mouse N-cadherin ectodomain -

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Basic information

Entry
Database: PDB / ID: 3q2w
TitleCrystal structure of mouse N-cadherin ectodomain
ComponentsCadherin-2
KeywordsCELL ADHESION / cadherin / calcium binding
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
alpha-D-mannopyranose / Cadherin-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsJin, X. / Shapiro, L.
CitationJournal: Structure / Year: 2011
Title: The extracellular architecture of adherens junctions revealed by crystal structures of type I cadherins.
Authors: Harrison, O.J. / Jin, X. / Hong, S. / Bahna, F. / Ahlsen, G. / Brasch, J. / Wu, Y. / Vendome, J. / Felsovalyi, K. / Hampton, C.M. / Troyanovsky, R.B. / Ben-Shaul, A. / Frank, J. / ...Authors: Harrison, O.J. / Jin, X. / Hong, S. / Bahna, F. / Ahlsen, G. / Brasch, J. / Wu, Y. / Vendome, J. / Felsovalyi, K. / Hampton, C.M. / Troyanovsky, R.B. / Ben-Shaul, A. / Frank, J. / Troyanovsky, S.M. / Shapiro, L. / Honig, B.
History
DepositionDec 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_chiral.details / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cadherin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,14427
Polymers61,5301
Non-polymers3,61526
Water1,09961
1
A: Cadherin-2
hetero molecules

A: Cadherin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,28954
Polymers123,0592
Non-polymers7,23052
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area10690 Å2
ΔGint-40 kcal/mol
Surface area62670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.372, 111.648, 262.107
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 61529.699 Da / Num. of mol.: 1 / Fragment: UNP residues 160-711
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdh2 / Cell (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P15116

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Sugars , 3 types, 14 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 73 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 5.44 Å3/Da / Density % sol: 77.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% PEG8000, 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 31, 2009
RadiationMonochromator: Si (111) crystal monochromator with vertical focusing mirror
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: 24506 / Num. obs: 21590 / % possible obs: 88.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.6_289)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→19.947 Å / SU ML: 0.4 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2672 1029 5.09 %random
Rwork0.2295 ---
all0.232 21590 --
obs0.2315 20206 89.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 0.796 Å2 / ksol: 0.236 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-17.3637 Å2-0 Å2-0 Å2
2---14.0322 Å2-0 Å2
3----3.3315 Å2
Refinement stepCycle: LAST / Resolution: 3.2→19.947 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4171 0 209 61 4441
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074473
X-RAY DIFFRACTIONf_angle_d1.1766137
X-RAY DIFFRACTIONf_dihedral_angle_d19.2191695
X-RAY DIFFRACTIONf_chiral_restr0.067749
X-RAY DIFFRACTIONf_plane_restr0.002796
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2001-3.3680.34921080.28842180X-RAY DIFFRACTION72
3.368-3.57790.321140.24742376X-RAY DIFFRACTION79
3.5779-3.85230.26661400.23822552X-RAY DIFFRACTION85
3.8523-4.23660.28281510.23272880X-RAY DIFFRACTION95
4.2366-4.8420.22891870.20282970X-RAY DIFFRACTION99
4.842-6.07180.24531700.2133047X-RAY DIFFRACTION100
6.0718-19.94760.23431590.213172X-RAY DIFFRACTION100

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