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- PDB-2wbx: Crystal structure of mouse cadherin-23 EC1 -

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Basic information

Entry
Database: PDB / ID: 2wbx
TitleCrystal structure of mouse cadherin-23 EC1
ComponentsCADHERIN-23
KeywordsCELL ADHESION / HEARING / DEAFNESS
Function / homology
Function and homology information


cochlear hair cell ribbon synapse / kinocilium / equilibrioception / sensory perception of light stimulus / stereocilium tip / inner ear receptor cell stereocilium organization / inner ear auditory receptor cell differentiation / cell-cell adhesion via plasma-membrane adhesion molecules / photoreceptor ribbon synapse / stereocilium ...cochlear hair cell ribbon synapse / kinocilium / equilibrioception / sensory perception of light stimulus / stereocilium tip / inner ear receptor cell stereocilium organization / inner ear auditory receptor cell differentiation / cell-cell adhesion via plasma-membrane adhesion molecules / photoreceptor ribbon synapse / stereocilium / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / photoreceptor cell maintenance / catenin complex / 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 / apical part of cell / cell adhesion / cadherin binding / centrosome / synapse / calcium ion binding / plasma membrane
Similarity search - Function
Cadherins / Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily / Immunoglobulin-like ...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
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSotomayor, M. / Weihofen, W. / Gaudet, R. / Corey, D.P.
CitationJournal: Neuron / Year: 2010
Title: Structural Determinants of Cadherin-23 Function in Hearing and Deafness.
Authors: Sotomayor, M. / Weihofen, W. / Gaudet, R. / Corey, D.P.
History
DepositionMar 5, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jun 6, 2012Group: Other
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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 / _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_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-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5892
Polymers11,5491
Non-polymers401
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.891, 49.540, 45.883
Angle α, β, γ (deg.)90.00, 98.97, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2044-

HOH

21A-2103-

HOH

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Components

#1: Protein CADHERIN-23 / OTOCADHERIN


Mass: 11548.818 Da / Num. of mol.: 1 / Fragment: EC1, RESIDUES 24-124
Source method: isolated from a genetically manipulated source
Details: CDH23 ECTODOMAIN 1 (EC1) CONSTRUCT DOES NOT CONTAIN PREDICTED SIGNAL SEQUENCE. THE N-TEMRINAL METHIONINE IS A CLONING ARTIFACT. ASPARTATE 102 WAS SELECTED AS THE C-TERMINAL RESIDUE OF ...Details: CDH23 ECTODOMAIN 1 (EC1) CONSTRUCT DOES NOT CONTAIN PREDICTED SIGNAL SEQUENCE. THE N-TEMRINAL METHIONINE IS A CLONING ARTIFACT. ASPARTATE 102 WAS SELECTED AS THE C-TERMINAL RESIDUE OF ECTODOMAIN 1 (EC1) AND IS FOLLOWED BY A 6-HIS-TAG.
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99PF4
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL METHIONINE IS A CLONING ARTIFACT. PROTEIN WAS CLONED WITH AN ADDITIONAL C-TERMINAL HIS- ...N-TERMINAL METHIONINE IS A CLONING ARTIFACT. PROTEIN WAS CLONED WITH AN ADDITIONAL C-TERMINAL HIS-TAG WHICH IS NOT SEEN IN ELECTRON DENSITY AND WAS OMITTED IN THE SEQUENCE.

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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: 2.3 Å3/Da / Density % sol: 47.5 % / Description: NONE
Crystal growpH: 6 / Details: 0.1 M SODIUM CACODYLATE PH 6.0 40% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 8, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 16290 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.7
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.5 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0070refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FF5

1ff5


Resolution: 1.5→25.54 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.559 / SU ML: 0.047 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1987 811 5 %RANDOM
Rwork0.17218 ---
obs0.17343 15473 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.759 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å2-0.67 Å2
2--0.52 Å20 Å2
3----0.8 Å2
Refinement stepCycle: LAST / Resolution: 1.5→25.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms815 0 1 105 921
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022863
X-RAY DIFFRACTIONr_bond_other_d0.0110.02579
X-RAY DIFFRACTIONr_angle_refined_deg1.3681.9451183
X-RAY DIFFRACTIONr_angle_other_deg0.86931412
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0365113
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.5572445
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.2315141
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.238157
X-RAY DIFFRACTIONr_chiral_restr0.0840.2135
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021986
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02188
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8391.5527
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5692870
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4923336
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0144.5307
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 67 -
Rwork0.219 1114 -
obs--98.5 %
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)
10.7096-0.48280.11231.5159-1.35393.25560.06930.0043-0.1567-0.2142-0.1839-0.08410.18280.17340.11460.04760.010.01420.04460.02190.0772-5.568523.4789-0.3129
21.1385-0.6861-0.32691.59380.77871.06860.09820.2680.0673-0.3601-0.0761-0.00420.09580.0361-0.02210.20510.02760.0170.2226-0.01730.1793-6.076232.3202-21.2344
31.2767-1.27981.23454.7767-4.63125.05470.17970.0615-0.1372-0.449-0.12740.20610.44350.0742-0.05230.06550.0069-0.02520.0104-0.01980.0547-13.247429.1407-9.2696
41.2731.5811-1.05236.445-5.88745.55480.07360.024-0.00650.0426-0.04130.0251-0.00650.0596-0.03230.02020.00970.01560.0175-0.01140.0464-9.028834.8474-2.883
52.8407-0.05840.26323.7386-2.18084.21770.01910.08640.1732-0.03010.07960.1624-0.03620.1674-0.09870.0050.0036-0.00770.0352-0.00910.0353-10.551341.1941-10.0347
62.053-1.1252.43521.0806-0.30955.53770.1130.40320.0675-0.2516-0.12140.0297-0.09890.74910.00840.1581-0.0122-0.08820.13840.0210.1274-10.472941.4899-18.5415
73.77511.3268-2.06842.4672-4.04049.91160.16810.34240.2355-0.0388-0.05190.0161-0.1160.1244-0.11630.02320.02220.02030.04610.02640.0223-3.641136.3578-9.4403
82.12410.706-1.02551.3165-2.655210.0128-0.02480.2356-0.0696-0.2352-0.2436-0.18080.3850.27740.26840.05070.07210.03630.14140.0450.0293-1.898533.0128-13.4214
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 13
2X-RAY DIFFRACTION2A14 - 24
3X-RAY DIFFRACTION3A25 - 39
4X-RAY DIFFRACTION4A40 - 51
5X-RAY DIFFRACTION5A52 - 61
6X-RAY DIFFRACTION6A62 - 74
7X-RAY DIFFRACTION7A75 - 89
8X-RAY DIFFRACTION8A90 - 102

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