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- PDB-2a62: Crystal structure of mouse cadherin-8 EC1-3 -

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Basic information

Entry
Database: PDB / ID: 2a62
TitleCrystal structure of mouse cadherin-8 EC1-3
ComponentsCadherin-8
KeywordsCELL ADHESION / cadherin / extracellular domain / homodimer / calcium binding
Function / homology
Function and homology information


Adherens junctions interactions / cell-cell adhesion mediated by cadherin / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / catenin complex / cell-cell junction assembly / adherens junction organization / regulation of synapse organization / homophilic cell adhesion via plasma membrane adhesion molecules / synaptic cleft / axon terminus ...Adherens junctions interactions / cell-cell adhesion mediated by cadherin / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / catenin complex / cell-cell junction assembly / adherens junction organization / regulation of synapse organization / homophilic cell adhesion via plasma membrane adhesion molecules / synaptic cleft / axon terminus / response to cold / synaptic transmission, glutamatergic / synaptic membrane / adherens junction / cell morphogenesis / beta-catenin binding / cell migration / chemical synaptic transmission / cadherin binding / glutamatergic synapse / calcium ion binding / identical protein binding / plasma membrane
Similarity search - Function
Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Catenin binding domain superfamily / Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.5 Å
AuthorsPatel, S.D. / Ciatto, C. / Chen, C.P. / Bahna, F. / Arkus, N. / Schieren, I. / Jessell, T.M. / Honig, B. / Price, S.R. / Shapiro, L.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2006
Title: Type II cadherin ectodomain structures: implications for classical cadherin specificity.
Authors: Patel, S.D. / Ciatto, C. / Chen, C.P. / Bahna, F. / Rajebhosale, M. / Arkus, N. / Schieren, I. / Jessell, T.M. / Honig, B. / Price, S.R. / Shapiro, L.
History
DepositionJul 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 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_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_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_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_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_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_conn.ptnr2_label_seq_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: Cadherin-8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5417
Polymers35,3001
Non-polymers2406
Water00
1
A: Cadherin-8
hetero molecules

A: Cadherin-8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,08214
Polymers70,6012
Non-polymers48112
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_337-y-2,-x-2,-z+9/41
Unit cell
Length a, b, c (Å)75.818, 75.818, 233.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein Cadherin-8


Mass: 35300.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdh8 / Production host: Escherichia coli (E. coli) / References: UniProt: P97291
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / 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: 4.76 Å3/Da / Density % sol: 74.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG 8000, ches, ethylene glycol, calcium chloride, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 4.5→20 Å / Num. obs: 4479 / % possible obs: 100 %
Reflection shellResolution: 4.5→4.66 Å / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT1.7data extraction
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.5→20 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.866 / SU B: 180.892 / SU ML: 1.005 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 1.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: POORLY DEFINED ELECTRON DENSITY WAS OBSERVED FOR SEVERAL SIDE CHAINS. NEVERTHELESS THEIR INCLUSION LEAD TO BETTER BEHAVIOUR DURING REFINEMENT, ACCORDING TO THE RFREE VALUE, AND THE RFREE/RWORK DIFFERENTIAL
RfactorNum. reflection% reflectionSelection details
Rfree0.346 321 7.6 %RANDOM
Rwork0.271 ---
all0.276 ---
obs-4215 95.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 1.4 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 166.369 Å2
Baniso -1Baniso -2Baniso -3
1-12.96 Å20 Å20 Å2
2--12.96 Å20 Å2
3----25.93 Å2
Refinement stepCycle: LAST / Resolution: 4.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2468 0 6 0 2474
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222535
X-RAY DIFFRACTIONr_angle_refined_deg1.7861.9673453
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.6215321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.84625.739115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg25.13315418
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.518159
X-RAY DIFFRACTIONr_chiral_restr0.1420.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021936
X-RAY DIFFRACTIONr_nbd_refined0.2970.21472
X-RAY DIFFRACTIONr_nbtor_refined0.3260.21675
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2330.2100
X-RAY DIFFRACTIONr_metal_ion_refined0.3220.220
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.8060.2125
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5380.28
X-RAY DIFFRACTIONr_mcbond_it0.2451.51638
X-RAY DIFFRACTIONr_mcangle_it0.44522613
X-RAY DIFFRACTIONr_scbond_it0.5073987
X-RAY DIFFRACTIONr_scangle_it0.8924.5840
LS refinement shellResolution: 4.5→4.736 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.39 38 -
Rwork0.325 505 -
all-543 -
obs--90.35 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.8630.4537-4.17168.34450.720912.0052-0.61640.1034-0.03510.9899-0.55320.5726-0.0061-2.50021.1696-0.49450.0610.02610.46460.1766-0.2245-78.9166-86.643261.8446
212.04051.8652-12.59682.1168-5.968929.5966-0.04-0.2095-0.3454-0.2632-0.00980.68-0.0484-0.17770.0498-0.71590.0310.011-0.9103-0.0009-0.571-47.0701-83.7868229.4645
39.2523-2.9753-4.8649.370412.844755.2841-0.64480.19070.6518-0.31760.54730.85880.35390.07650.0976-0.5720.0228-0.1093-0.7320.2613-0.418-33.4782-83.7254183.828
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
111 - 981 - 98
2299 - 20799 - 207
33208 - 322208 - 322

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