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- PDB-5uz8: Crystal Structure of Mouse Cadherin-23 EC22-24 -

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Basic information

Entry
Database: PDB / ID: 5uz8
TitleCrystal Structure of Mouse Cadherin-23 EC22-24
ComponentsCadherin-23
KeywordsCELL ADHESION / Hearing / Mechanotransduction / Adhesion / Calcium-binding proteins
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
Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily
Similarity search - Domain/homology
GLUTATHIONE / Cadherin-23
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsPatel, A. / Jaiganesh, A. / Sotomayor, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)R00 DC012534 United States
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)R01 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
DepositionFeb 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 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 / Category: citation / Item: _citation.journal_volume / _citation.page_first
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_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.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)37,22812
Polymers36,5331
Non-polymers69411
Water9,746541
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-67 kcal/mol
Surface area17270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.537, 57.208, 114.667
Angle α, β, γ (deg.)90.00, 112.55, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cadherin-23 / / Otocadherin


Mass: 36533.301 Da / Num. of mol.: 1 / Fragment: residues 2288-2607
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdh23 / Plasmid: pET-21a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q99PF4
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 541 / 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: 3.71 Å3/Da / Density % sol: 66.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5 3.5 M Ammonium Chloride

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Data collection

DiffractionMean temperature: 100 K
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: 1.85→50 Å / Num. obs: 45949 / % possible obs: 99.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 12.8
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.657 / Mean I/σ(I) obs: 1.75 / Num. unique obs: 2224 / Χ2: 1.01 / % possible all: 97.9

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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: 1.85→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.704 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.095 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18788 2251 4.9 %RANDOM
Rwork0.17051 ---
obs0.17136 43480 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.397 Å2
Baniso -1Baniso -2Baniso -3
1-1.44 Å20 Å20.04 Å2
2---0.05 Å2-0 Å2
3----1.06 Å2
Refinement stepCycle: 1 / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2431 0 30 541 3002
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022613
X-RAY DIFFRACTIONr_bond_other_d0.0010.022349
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.9723596
X-RAY DIFFRACTIONr_angle_other_deg0.87335503
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7355352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.87225.6125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.95415417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3511514
X-RAY DIFFRACTIONr_chiral_restr0.0930.2421
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212987
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02493
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_it0.761.4291308
X-RAY DIFFRACTIONr_mcbond_other0.7591.4281307
X-RAY DIFFRACTIONr_mcangle_it1.3042.1361642
X-RAY DIFFRACTIONr_mcangle_other1.3032.1381643
X-RAY DIFFRACTIONr_scbond_it0.8721.5211305
X-RAY DIFFRACTIONr_scbond_other0.8731.5181302
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4222.2441935
X-RAY DIFFRACTIONr_long_range_B_refined6.31319.5823050
X-RAY DIFFRACTIONr_long_range_B_other6.31319.5823050
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.849→1.897 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 156 -
Rwork0.266 3120 -
obs--95.79 %
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)
11.4861-0.2952-0.60462.11131.192.9005-0.014-0.25230.15310.29520.0636-0.1125-0.06950.1568-0.04960.068-0.0001-0.01240.0443-0.0220.0525-91.0577135.1131293.5208
20.27850.38770.4061.8542.50823.47830.02010.06050.0413-0.07130.0226-0.0225-0.1105-0.0197-0.04270.00980.00390.01290.0270.00220.0219-104.1591108.3672253.5477
30.3636-0.4481-0.28122.37733.37735.28420.05690.0569-0.0748-0.11770.0346-0.0135-0.07130.1192-0.09160.0959-0.01680.02510.0411-0.01460.0488-107.466478.0205214.6904
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2265 - 2373
2X-RAY DIFFRACTION1A2609 - 2610
3X-RAY DIFFRACTION1A2607
4X-RAY DIFFRACTION2A2374 - 2480
5X-RAY DIFFRACTION2A2608
6X-RAY DIFFRACTION2A2605
7X-RAY DIFFRACTION3A2481 - 2581
8X-RAY DIFFRACTION3A2604

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