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- PDB-7uqu: Crystal Structure of Mouse Cadherin-23 EC9 -

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Basic information

Entry
Database: PDB / ID: 7uqu
TitleCrystal Structure of Mouse Cadherin-23 EC9
ComponentsCadherin-23
KeywordsCELL ADHESION / HEARING / MECHANOTRANSDUCTION / 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 / inner ear auditory receptor cell differentiation / cell-cell adhesion via plasma-membrane adhesion molecules / photoreceptor ribbon synapse / stereocilium ...cochlear hair cell ribbon synapse / kinocilium / equilibrioception / sensory perception of light stimulus / stereocilium tip / inner ear receptor cell stereocilium organization / inner ear auditory receptor cell differentiation / cell-cell adhesion via plasma-membrane adhesion molecules / photoreceptor ribbon synapse / 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
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.976 Å
AuthorsSandhu, J.S. / De La Torre, P. / Sotomayor, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)R01 DC015271 United States
CitationJournal: To be published
Title: Crystal Structure of Mouse Cadherin-23 EC9
Authors: Sandhu, J.S. / De La Torre, P. / Sotomayor, M.
History
DepositionApr 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 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

Downloads & links

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Assembly

Deposited unit
AAA: Cadherin-23
BBB: Cadherin-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9094
Polymers25,8292
Non-polymers802
Water1,31573
1
AAA: Cadherin-23
hetero molecules


  • defined by author
  • Evidence: gel filtration
  • 13 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)12,9542
Polymers12,9141
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Cadherin-23
hetero molecules


  • defined by author
  • 13 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)12,9542
Polymers12,9141
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.308, 41.661, 56.908
Angle α, β, γ (deg.)90.000, 114.196, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cadherin-23 / Otocadherin


Mass: 12914.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: While in crystallization tray, the protein degraded and crystallized as just EC9 instead of EC8-9
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdh23 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta / References: UniProt: Q99PF4
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.06 Å3/Da / Density % sol: 40.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Magnesium Chloride 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.976→51.909 Å / Num. obs: 14817 / % possible obs: 97 % / Redundancy: 4.2 % / CC1/2: 0.991 / Net I/σ(I): 13.4
Reflection shellResolution: 2→2.03 Å / Mean I/σ(I) obs: 4.8 / Num. unique obs: 701 / CC1/2: 0.907

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5tfl,5i8d

5tfl

5i8d


Resolution: 1.976→51.909 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.561 / SU ML: 0.101 / Cross valid method: FREE R-VALUE / ESU R: 0.182 / ESU R Free: 0.16
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2241 681 4.742 %
Rwork0.1802 13681 -
all0.182 --
obs-14362 95.836 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 24.745 Å2
Baniso -1Baniso -2Baniso -3
1--1.676 Å20 Å2-0.583 Å2
2--0.461 Å2-0 Å2
3---1.239 Å2
Refinement stepCycle: LAST / Resolution: 1.976→51.909 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1617 0 2 73 1692
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0131637
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171535
X-RAY DIFFRACTIONr_angle_refined_deg1.4861.652234
X-RAY DIFFRACTIONr_angle_other_deg1.3011.5723546
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1775211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.21822.09386
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.79515267
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0851514
X-RAY DIFFRACTIONr_chiral_restr0.0580.2229
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021845
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02325
X-RAY DIFFRACTIONr_nbd_refined0.1980.2258
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1810.21439
X-RAY DIFFRACTIONr_nbtor_refined0.150.2771
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.2874
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.286
X-RAY DIFFRACTIONr_metal_ion_refined0.170.210
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1930.28
X-RAY DIFFRACTIONr_nbd_other0.1330.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1150.26
X-RAY DIFFRACTIONr_mcbond_it2.2652.531850
X-RAY DIFFRACTIONr_mcbond_other2.2562.529849
X-RAY DIFFRACTIONr_mcangle_it3.7213.781059
X-RAY DIFFRACTIONr_mcangle_other3.723.7821060
X-RAY DIFFRACTIONr_scbond_it2.542.796787
X-RAY DIFFRACTIONr_scbond_other2.5432.794785
X-RAY DIFFRACTIONr_scangle_it4.0124.0771175
X-RAY DIFFRACTIONr_scangle_other4.0124.0771175
X-RAY DIFFRACTIONr_lrange_it6.35830.4271668
X-RAY DIFFRACTIONr_lrange_other6.35430.4311656
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.976-2.0270.276370.2078120.2110800.9180.91878.61110.207
2.027-2.0830.235550.2119940.21310890.9320.92196.32690.211
2.083-2.1430.23620.199560.19310510.9270.93596.86010.19
2.143-2.2090.256390.1929160.1949970.8950.93595.78740.192
2.209-2.2810.344310.1829010.1879730.8810.9495.78620.182
2.281-2.3610.192470.1788630.1799460.9420.94796.19450.178
2.361-2.450.229430.178710.1739240.9380.95298.91770.17
2.45-2.550.249510.1778050.1828740.9320.94597.94050.177
2.55-2.6630.236360.1767960.1798480.9290.94798.11320.176
2.663-2.7920.235260.1797630.1818170.9350.94996.57280.179
2.792-2.9430.176230.1787350.1787820.9540.94996.93090.178
2.943-3.1210.209410.1776690.1797190.9450.95198.74830.177
3.121-3.3350.281280.1916590.1956930.9220.94499.13420.191
3.335-3.6010.197220.1896090.1896490.950.94697.22650.189
3.601-3.9430.211320.1695430.1715900.950.95997.45760.169
3.943-4.4050.172290.1535090.1545480.9710.97198.17520.153
4.405-5.0810.212170.1454490.1484790.9720.97697.2860.145
5.081-6.2080.224330.2063500.2084020.9590.96195.27360.206
6.208-8.7170.212220.1923040.1933290.9370.94999.08810.192
8.717-51.9090.27170.2231770.2251950.9580.95194.3590.223

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