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- PDB-5un2: Crystal Structure of Mouse Cadherin-23 EC19-21 with non-syndromic... -

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Basic information

Entry
Database: PDB / ID: 5un2
TitleCrystal Structure of Mouse Cadherin-23 EC19-21 with non-syndromic deafness (DFNB12) associated mutation R2029W
ComponentsCadherin-23
KeywordsCELL ADHESION / hearing / mechanotransduction / adhesion / calcium-binding protein
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 / cell-cell adhesion via plasma-membrane adhesion molecules / photoreceptor ribbon synapse / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules ...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 / cell-cell adhesion via plasma-membrane adhesion molecules / photoreceptor ribbon synapse / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / stereocilium / 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 / beta-catenin binding / calcium ion transport / neuron projection development / cell migration / apical part of cell / cell adhesion / cadherin binding / centrosome / calcium ion binding / synapse / plasma membrane
Similarity search - Function
Cadherins / Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily / Immunoglobulin-like ...Cadherins / Cadherin / 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 / MOLECULAR REPLACEMENT / Resolution: 2.96 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 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.2Mar 21, 2018Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.3Aug 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 1.4Sep 19, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.5Mar 16, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / 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_audit_support.funding_organization / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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_symmetry
Revision 1.6Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)37,97811
Polymers37,5791
Non-polymers39910
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)189.475, 73.908, 49.375
Angle α, β, γ (deg.)90.00, 96.62, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2459-

HOH

DetailsMonomer as determined by Size exclusion chromatography

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Components

#1: Protein Cadherin-23 / Otocadherin


Mass: 37578.770 Da / Num. of mol.: 1 / Fragment: residues 1955-2289 / Mutation: R2029W
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.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 4.64 Å3/Da / Density % sol: 73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 0.1 M HEPES pH 7.3 0.1 M CaCl2 27% PEG 400 5% glycerol
PH range: 7.1-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.542 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jan 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.96→50 Å / Num. obs: 14294 / % possible obs: 91.5 % / Redundancy: 3.8 % / Biso Wilson estimate: 36.3 Å2 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.087 / Rrim(I) all: 0.187 / Χ2: 1.013 / Net I/σ(I): 7.863
Reflection shellResolution: 2.96→3.01 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 1.97 / Num. unique obs: 667 / Rpim(I) all: 0.294 / Rrim(I) all: 0.631 / Χ2: 1.025 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TFK

5tfk


Resolution: 2.96→50 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.905 / SU B: 26.728 / SU ML: 0.227 / Cross valid method: THROUGHOUT / ESU R: 0.729 / ESU R Free: 0.338 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23582 668 5.1 %RANDOM
Rwork0.19618 ---
obs0.19818 12402 91.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 48.334 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å2-0 Å22.12 Å2
2--5.61 Å2-0 Å2
3----6.65 Å2
Refinement stepCycle: 1 / Resolution: 2.96→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2563 0 10 59 2632
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192621
X-RAY DIFFRACTIONr_bond_other_d0.0020.022407
X-RAY DIFFRACTIONr_angle_refined_deg1.441.9673600
X-RAY DIFFRACTIONr_angle_other_deg0.92735596
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1525336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.7825.847118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.83915407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7011511
X-RAY DIFFRACTIONr_chiral_restr0.0760.2446
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212925
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02466
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_it0.5342.6231341
X-RAY DIFFRACTIONr_mcbond_other0.5342.6221340
X-RAY DIFFRACTIONr_mcangle_it0.9523.9321675
X-RAY DIFFRACTIONr_mcangle_other0.9523.9331676
X-RAY DIFFRACTIONr_scbond_it0.442.6741279
X-RAY DIFFRACTIONr_scbond_other0.4372.6721277
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.8023.9931924
X-RAY DIFFRACTIONr_long_range_B_refined2.44530.8482666
X-RAY DIFFRACTIONr_long_range_B_other2.37530.8292662
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.96→3.037 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 48 -
Rwork0.356 933 -
obs--94.69 %
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)
15.71961.2079-5.51862.3404-1.62788.29930.1822-0.0235-0.0072-0.0654-0.0937-0.1343-0.38130.5994-0.08850.0893-0.0727-0.0920.23520.02250.2115-66.618-31.03935.962
25.03291.9242-5.48431.4184-2.25676.2025-0.07750.1331-0.03770.22040.07360.16530.133-0.4080.00380.2-0.1515-0.040.35910.02740.2994-38.94-13.875-0.966
37.91161.975-4.35261.7386-1.64764.94860.08680.2903-0.1821-0.0354-0.05110.0109-0.0439-0.2551-0.03570.02790.0143-0.04710.0334-0.01240.0906-2.902-1.14-32.634
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1931 - 2040
2X-RAY DIFFRACTION1A2301 - 2302
3X-RAY DIFFRACTION1A2309 - 2310
4X-RAY DIFFRACTION2A2041 - 2145
5X-RAY DIFFRACTION2A2303 - 2305
6X-RAY DIFFRACTION3A2146 - 2265
7X-RAY DIFFRACTION3A2306 - 2308

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