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- PDB-5tfm: Crystal Structure of Human Cadherin-23 EC6-8 -

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Basic information

Entry
Database: PDB / ID: 5tfm
TitleCrystal Structure of Human Cadherin-23 EC6-8
ComponentsCadherin-23
KeywordsCELL ADHESION / hearing / mechanotransduction / adhesion / calcium-binding protein
Function / homology
Function and homology information


equilibrioception / sensory perception of light stimulus / cochlear hair cell ribbon synapse / stereocilium tip / photoreceptor ribbon synapse / kinocilium / : / calcium-dependent cell-cell adhesion / catenin complex / stereocilium ...equilibrioception / sensory perception of light stimulus / cochlear hair cell ribbon synapse / stereocilium tip / photoreceptor ribbon synapse / kinocilium / : / calcium-dependent cell-cell adhesion / 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 / homophilic cell-cell adhesion / cochlea development / 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 / calcium ion binding / centrosome / 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: 2.92 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_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.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_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

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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)37,7097
Polymers37,4861
Non-polymers2236
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.407, 93.407, 122.386
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11A-1014-

HOH

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Components

#1: Protein Cadherin-23 / Otocadherin


Mass: 37485.625 Da / Num. of mol.: 1 / Fragment: Cadherin domains 6-8, residues 557-886
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDH23, KIAA1774, KIAA1812, UNQ1894/PRO4340 / Plasmid: pET-21a / Production host: Escherichia coli BL21 / Strain (production host): BL21 RIPL / References: UniProt: Q9H251
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 4.12 Å3/Da / Density % sol: 70.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.8 / Details: 0.1 M MES pH 6.8, 1.2 M NaCl

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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: 2.92→80.89 Å / Num. obs: 13518 / % possible obs: 99.9 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 17.08
Reflection shellResolution: 2.92→2.97 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.592 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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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: 5TFL

5tfl


Resolution: 2.92→80.89 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.912 / SU B: 34.236 / SU ML: 0.278 / Cross valid method: THROUGHOUT / ESU R: 0.557 / ESU R Free: 0.324 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24635 648 4.8 %RANDOM
Rwork0.19773 ---
obs0.20006 12825 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 88.416 Å2
Baniso -1Baniso -2Baniso -3
1-2.57 Å21.28 Å20 Å2
2--2.57 Å2-0 Å2
3----8.32 Å2
Refinement stepCycle: 1 / Resolution: 2.92→80.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2476 0 6 24 2506
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022529
X-RAY DIFFRACTIONr_bond_other_d0.0020.022365
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.9633454
X-RAY DIFFRACTIONr_angle_other_deg0.89535453
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1025320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.89124.867113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.30515404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5381514
X-RAY DIFFRACTIONr_chiral_restr0.070.2410
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212863
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02543
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_it1.5425.5671280
X-RAY DIFFRACTIONr_mcbond_other1.5415.5681279
X-RAY DIFFRACTIONr_mcangle_it2.5768.3491597
X-RAY DIFFRACTIONr_mcangle_other2.5768.3481598
X-RAY DIFFRACTIONr_scbond_it1.5365.7621249
X-RAY DIFFRACTIONr_scbond_other1.5355.7621250
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6338.5721856
X-RAY DIFFRACTIONr_long_range_B_refined4.11864.1122606
X-RAY DIFFRACTIONr_long_range_B_other4.09664.112605
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.921→2.996 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 46 -
Rwork0.333 939 -
obs--99.9 %
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)
12.25472.0895-2.07816.9277-5.487210.1776-0.1273-0.3641-0.27260.52980.0092-0.0027-0.5245-0.60580.11810.11280.0852-0.01870.16720.06270.29686.250317.714158.8874
20.96661.3645-3.27742.9413-4.117211.9931-0.20150.56190.0602-0.33920.55460.03430.3945-1.719-0.3530.1117-0.18560.0070.5247-0.03170.148611.259735.983815.6401
32.90230.7295-0.59593.8187-2.6278.45320.26770.25110.148-0.6146-0.4144-0.18140.3065-0.17550.14670.3799-0.0850.09810.3404-0.07960.252923.14451.2558-31.6852
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A534 - 642
2X-RAY DIFFRACTION1A902 - 903
3X-RAY DIFFRACTION2A643 - 749
4X-RAY DIFFRACTION2A901
5X-RAY DIFFRACTION2A904 - 905
6X-RAY DIFFRACTION3A750 - 858
7X-RAY DIFFRACTION3A906

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