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- PDB-3mvs: Structure of the N-terminus of Cadherin 23 -

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Basic information

Entry
Database: PDB / ID: 3mvs
TitleStructure of the N-terminus of Cadherin 23
ComponentsCadherin-23
KeywordsCELL ADHESION / cadherin / adhesion / extracellular domain
Function / homology
Function and homology information


kinocilium / equilibrioception / sensory perception of light stimulus / cochlear hair cell ribbon synapse / inner ear receptor cell stereocilium organization / stereocilium tip / inner ear auditory receptor cell differentiation / photoreceptor ribbon synapse / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / stereocilium ...kinocilium / equilibrioception / sensory perception of light stimulus / cochlear hair cell ribbon synapse / inner ear receptor cell stereocilium organization / stereocilium tip / inner ear auditory receptor cell differentiation / photoreceptor ribbon synapse / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / stereocilium / photoreceptor cell maintenance / auditory receptor cell stereocilium organization / inner ear morphogenesis / cochlea development / homophilic cell adhesion via plasma membrane adhesion molecules / inner ear development / regulation of cytosolic calcium ion concentration / photoreceptor inner segment / locomotory behavior / sensory perception of sound / calcium ion transport / cell adhesion / synapse / centrosome / calcium ion binding / plasma membrane
Similarity search - Function
Cadherins / 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: 1.1 Å
AuthorsClark, P. / Joseph, J.S. / Kolatkar, A.R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structure of the N terminus of cadherin 23 reveals a new adhesion mechanism for a subset of cadherin superfamily members.
Authors: Elledge, H.M. / Kazmierczak, P. / Clark, P. / Joseph, J.S. / Kolatkar, A. / Kuhn, P. / Muller, U.
History
DepositionMay 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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_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_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-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,88129
Polymers23,2751
Non-polymers1,60628
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.375, 64.208, 47.859
Angle α, β, γ (deg.)90.00, 110.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cadherin-23 / Otocadherin


Mass: 23274.785 Da / Num. of mol.: 1 / Fragment: UNP residues 24-233
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdh23 / Plasmid: pTXB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q99PF4
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O

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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: 2.37 Å3/Da / Density % sol: 48.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 200 nl of 6.9 mg/ml protein in 1 mM CaCl2, 50 mM Tris-HCl, pH 8.5, 200 nl crystallant (22.5% ethylene glycol and 0.2 M NDSB-201), VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.95369 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 6, 2010
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 1.1→23 Å / Num. obs: 77493 / % possible obs: 92.02 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 15 Å2 / Rsym value: 0.08 / Net I/σ(I): 11.5
Reflection shellResolution: 1.1→1.14 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 1.51 / Num. unique all: 6601 / Rsym value: 0.49 / % possible all: 75.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→23 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.075 / SU ML: 0.023 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18791 4098 5 %RANDOM
Rwork0.16296 ---
obs0.16421 77493 92.02 %-
all-81640 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.952 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å20.66 Å2
2--0.88 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.1→23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1610 0 94 279 1983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221785
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.9692430
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3035236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.1225.67981
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.54415255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.409156
X-RAY DIFFRACTIONr_chiral_restr0.0950.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211356
X-RAY DIFFRACTIONr_mcbond_it1.2431.51094
X-RAY DIFFRACTIONr_mcangle_it1.94621817
X-RAY DIFFRACTIONr_scbond_it2.3373691
X-RAY DIFFRACTIONr_scangle_it3.3224.5599
X-RAY DIFFRACTIONr_rigid_bond_restr1.24531785
X-RAY DIFFRACTIONr_sphericity_free4.763286
X-RAY DIFFRACTIONr_sphericity_bonded4.38131754
LS refinement shellResolution: 1.1→1.125 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 248 -
Rwork0.286 4286 -
obs--69.47 %

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