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- PDB-5ulu: Crystal Structure of Mouse Cadherin-23 EC19-21 (S2087P) with non-... -

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Basic information

Entry
Database: PDB / ID: 5ulu
TitleCrystal Structure of Mouse Cadherin-23 EC19-21 (S2087P) with non-syndromic deafness (DFNB12) associated mutation D2148N
ComponentsCadherin-23
KeywordsCELL ADHESION / hearing / mechanotransduction / adhesion / calcium-binding protein
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: 2.85 Å
AuthorsJaiganesh, A. / Sotomayor, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)DC012534 United States
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)DC015271 United States
CitationJournal: Structure / Year: 2018
Title: Zooming in on Cadherin-23: Structural Diversity and Potential Mechanisms of Inherited Deafness.
Authors: Jaiganesh, A. / De-la-Torre, P. / Patel, A.A. / Termine, D.J. / Velez-Cortes, F. / Chen, C. / Sotomayor, M.
History
DepositionJan 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 5, 2018Group: Data collection / Database references / Source and taxonomy
Category: entity_src_gen / pdbx_related_exp_data_set / Item: _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.3Sep 19, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.4Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / refine_hist / struct_conn
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 / _refine_hist.d_res_low / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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)37,7997
Polymers37,5591
Non-polymers2406
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-29 kcal/mol
Surface area17370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.238, 65.386, 114.651
Angle α, β, γ (deg.)90.00, 98.62, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cadherin-23 / Otocadherin


Mass: 37558.805 Da / Num. of mol.: 1 / Fragment: residues 1955-2289 / Mutation: S2087P, D2148N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdh23 / Plasmid: pet-21a+ / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21-RIPL / References: UniProt: Q99PF4
#2: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 7 / 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: 4.16 Å3/Da / Density % sol: 70.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris pH 8.5 0.05M MgCl2 25% MPD / PH range: 7.5-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 14561 / % possible obs: 95.7 % / Redundancy: 3.1 % / Biso Wilson estimate: 73 Å2 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.044 / Rrim(I) all: 0.081 / Net I/σ(I): 15.74
Reflection shellResolution: 2.85→2.9 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.181 / Mean I/σ(I) obs: 3.375 / Num. unique obs: 556 / CC1/2: 0.97 / Rpim(I) all: 0.13 / Rrim(I) all: 0.224 / Χ2: 1.089 / % possible all: 77.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I8D

5i8d


Resolution: 2.85→30.337 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.934 / SU B: 37.953 / SU ML: 0.302 / Cross valid method: THROUGHOUT / ESU R: 0.484 / ESU R Free: 0.309 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24429 645 4.6 %RANDOM
Rwork0.19549 ---
obs0.19771 13292 95.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 103.515 Å2
Baniso -1Baniso -2Baniso -3
1-5.47 Å20 Å2-0.42 Å2
2--8.66 Å20 Å2
3----13.39 Å2
Refinement stepCycle: 1 / Resolution: 2.85→30.337 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2443 0 6 7 2456
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192488
X-RAY DIFFRACTIONr_bond_other_d0.0020.022311
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.9723412
X-RAY DIFFRACTIONr_angle_other_deg0.92635371
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8655318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.77825.741108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.26415389
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6541511
X-RAY DIFFRACTIONr_chiral_restr0.0810.2427
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212750
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02437
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_it2.6197.1321278
X-RAY DIFFRACTIONr_mcbond_other2.627.1311277
X-RAY DIFFRACTIONr_mcangle_it4.1310.7011594
X-RAY DIFFRACTIONr_mcangle_other4.12810.7021595
X-RAY DIFFRACTIONr_scbond_it2.397.3331210
X-RAY DIFFRACTIONr_scbond_other2.3877.331208
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.98110.9171818
X-RAY DIFFRACTIONr_long_range_B_refined6.04785.0242553
X-RAY DIFFRACTIONr_long_range_B_other6.04685.0422553
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.848→2.922 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 34 -
Rwork0.372 770 -
obs--74.31 %
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)
12.5260.71632.10872.753-1.277411.72410.15260.51910.177-0.4907-0.0408-0.1739-0.37530.1246-0.11180.28310.21610.04680.29760.04970.3073-4.90421.882-34.936
22.65980.5085-4.18671.1126-2.420812.39190.0440.3932-0.2050.0061-0.12160.05570.5461-1.12640.07760.163-0.1426-0.11320.2989-0.03830.2276-11.8786.3418.041
33.3225-0.58020.46870.9594-2.221810.198-0.3734-0.3465-0.26930.10460.139-0.01061.2833-0.9180.23440.5065-0.18740.04460.1869-0.05340.261-18.744-6.15655.542
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1934 - 2040
2X-RAY DIFFRACTION1A2301 - 2302
3X-RAY DIFFRACTION2A2041 - 2145
4X-RAY DIFFRACTION2A2303 - 2305
5X-RAY DIFFRACTION3A2146 - 2262
6X-RAY DIFFRACTION3A2306

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