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- PDB-5tfk: Crystal Structure of Mouse Cadherin-23 EC19-21 WT -

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Basic information

Entry
Database: PDB / ID: 5tfk
TitleCrystal Structure of Mouse Cadherin-23 EC19-21 WT
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 / photoreceptor ribbon synapse / inner ear auditory receptor cell differentiation / cell-cell adhesion via plasma-membrane adhesion molecules / stereocilium ...cochlear hair cell ribbon synapse / kinocilium / equilibrioception / sensory perception of light stimulus / stereocilium tip / inner ear receptor cell stereocilium organization / photoreceptor ribbon synapse / inner ear auditory receptor cell differentiation / cell-cell adhesion via plasma-membrane adhesion molecules / 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: 2.8 Å
AuthorsJaiganesh, A. / Sotomayor, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)DC012534 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
DepositionSep 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: 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 19, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / entity_src_gen
Item: _citation.journal_volume / _citation.page_first / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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 / 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_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_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)38,5289
Polymers38,2071
Non-polymers3218
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-37 kcal/mol
Surface area18130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.408, 66.932, 112.815
Angle α, β, γ (deg.)90.00, 98.72, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2410-

HOH

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Components

#1: Protein Cadherin-23 / / Otocadherin


Mass: 38207.375 Da / Num. of mol.: 1 / Fragment: Cadherin domains 19-21, residues 1949-2289
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdh23 / 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.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.78 Å3/Da / Density % sol: 67.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.1 M Sodium Cacodylate pH 6.2, 0.075 M Calcium Acetate, 28% MPD

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Oxford Cryo-jet crystal cryocoolers
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.8→111.51 Å / Num. obs: 14163 / % possible obs: 97.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 17.3
Reflection shellResolution: 2.8→2.86 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.504 / Mean I/σ(I) obs: 2 / % possible all: 85.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I8D

5i8d


Resolution: 2.8→111.51 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.937 / SU B: 36.304 / SU ML: 0.285 / Cross valid method: THROUGHOUT / ESU R: 0.558 / ESU R Free: 0.312 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24386 706 5.1 %RANDOM
Rwork0.20096 ---
obs0.20318 13110 97.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 81.977 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å22.4 Å2
2--10.87 Å2-0 Å2
3----11.08 Å2
Refinement stepCycle: 1 / Resolution: 2.8→111.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2561 0 8 10 2579
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192614
X-RAY DIFFRACTIONr_bond_other_d0.0010.022470
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.973590
X-RAY DIFFRACTIONr_angle_other_deg0.86535693
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3665336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.68525.966119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.9515406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.0421511
X-RAY DIFFRACTIONr_chiral_restr0.0870.2446
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212981
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02532
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_it1.834.8411341
X-RAY DIFFRACTIONr_mcbond_other1.8274.8421340
X-RAY DIFFRACTIONr_mcangle_it2.8927.2641675
X-RAY DIFFRACTIONr_mcangle_other2.8927.2641676
X-RAY DIFFRACTIONr_scbond_it1.6814.9841273
X-RAY DIFFRACTIONr_scbond_other1.684.9841274
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7677.421915
X-RAY DIFFRACTIONr_long_range_B_refined4.38275.3973263
X-RAY DIFFRACTIONr_long_range_B_other4.43975.4143262
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.801→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 37 -
Rwork0.367 822 -
obs--81.5 %
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)
11.2034-0.95960.06593.9413-1.481211.2759-0.10640.0105-0.09140.0242-0.2669-0.051-0.00610.03540.37320.02530.0429-0.05060.34490.02080.4035165.814-46.169129.543
21.31930.7323-3.66760.7459-1.940110.6094-0.02430.17450.0264-0.17370.0968-0.00720.3211-0.4193-0.07250.3313-0.0421-0.04530.34710.01730.426155.606-63.055174.633
34.33320.17470.09182.0956-2.068910.0782-0.22630.0111-0.43260.15930.0351-0.05260.111-1.04540.19120.0386-0.0311-0.01010.1296-0.04730.4344149.401-74.877222.19
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1929 - 2040
2X-RAY DIFFRACTION1A2301 - 2303
3X-RAY DIFFRACTION2A2041 - 2145
4X-RAY DIFFRACTION2A2305 - 2307
5X-RAY DIFFRACTION3A2146 - 2263
6X-RAY DIFFRACTION3A2308

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