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- PDB-5wj8: Crystal Structure of Human Cadherin-23 EC13-14 -

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Basic information

Entry
Database: PDB / ID: 5wj8
TitleCrystal Structure of Human Cadherin-23 EC13-14
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 / stereocilium tip / cell-cell adhesion via plasma-membrane adhesion molecules / photoreceptor ribbon synapse / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / catenin complex / stereocilium ...kinocilium / equilibrioception / sensory perception of light stimulus / cochlear hair cell ribbon synapse / stereocilium tip / cell-cell adhesion via plasma-membrane adhesion molecules / photoreceptor ribbon synapse / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / catenin complex / stereocilium / photoreceptor cell maintenance / auditory receptor cell stereocilium organization / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / cochlea development / homophilic cell adhesion via plasma membrane adhesion molecules / regulation of cytosolic calcium ion concentration / photoreceptor inner segment / visual perception / locomotory behavior / sensory perception of sound / beta-catenin binding / neuron projection development / calcium ion transport / cell migration / cadherin binding / centrosome / calcium ion binding / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsVelez-Cortes, F. / Conghui, C. / De-la-Torre, P. / Sotomayor, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)R01 DC015271 United States
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)R00 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
DepositionJul 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 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 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 11, 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 / struct_conn_type
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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)24,9777
Polymers24,7421
Non-polymers2356
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.712, 74.712, 213.507
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-1605-

CL

21A-1606-

K

31A-1819-

HOH

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Components

#1: Protein Cadherin-23 / Otocadherin


Mass: 24742.354 Da / Num. of mol.: 1 / Fragment: residues 1308-1523
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDH23, KIAA1774, KIAA1812, UNQ1894/PRO4340 / Plasmid: pET21a / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21-RIPL / References: UniProt: Q9H251
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.48 Å3/Da / Density % sol: 64.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M NaOAc pH 4.5 0.2 M CaCl2 30 (v/v) isopropanol 20% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.86→71.17 Å / Num. obs: 30738 / % possible obs: 94.4 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 26.8
Reflection shellResolution: 1.86→1.89 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 2 / Num. unique obs: 1246 / % possible all: 83.3

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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: 5VH2

5vh2


Resolution: 1.86→71.17 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.943 / SU B: 7.581 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.121 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24828 1422 4.9 %RANDOM
Rwork0.2169 ---
obs0.21843 27574 94.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 45.936 Å2
Baniso -1Baniso -2Baniso -3
1-1.66 Å20.83 Å20 Å2
2--1.66 Å20 Å2
3----5.37 Å2
Refinement stepCycle: 1 / Resolution: 1.86→71.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1610 0 6 133 1749
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021664
X-RAY DIFFRACTIONr_bond_other_d0.0020.021526
X-RAY DIFFRACTIONr_angle_refined_deg1.51.9472275
X-RAY DIFFRACTIONr_angle_other_deg0.98233538
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9355215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.2625.1979
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.42115263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.959159
X-RAY DIFFRACTIONr_chiral_restr0.0880.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021884
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02329
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_it0.8682.149845
X-RAY DIFFRACTIONr_mcbond_other0.8682.148844
X-RAY DIFFRACTIONr_mcangle_it1.4543.2151056
X-RAY DIFFRACTIONr_mcangle_other1.4533.2161057
X-RAY DIFFRACTIONr_scbond_it0.952.331818
X-RAY DIFFRACTIONr_scbond_other0.9472.328816
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6093.4391216
X-RAY DIFFRACTIONr_long_range_B_refined6.00826.3141790
X-RAY DIFFRACTIONr_long_range_B_other5.88725.6741766
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.86→1.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 98 -
Rwork0.307 1766 -
obs--84 %
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)
10.53-0.0627-0.51361.8822-0.99974.3640.0589-0.14430.0480.1742-0.02690.0708-0.396-0.1207-0.0320.04350.02760.0140.36290.03970.227-10.4609142.3836214.0662
21.93830.3140.89670.9666-1.63096.53060.1589-0.17620.1293-0.1383-0.1060.0165-0.3872-0.1487-0.05290.39110.16720.05950.1228-0.00780.2363-11.098151.6922167.0537
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1287 - 1386
2X-RAY DIFFRACTION1A1601 - 1603
3X-RAY DIFFRACTION2A1387 - 1496
4X-RAY DIFFRACTION2A1604

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