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- PDB-7t80: Crystal Structure of Mouse Cadherin-23 EC18-19 -

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Basic information

Entry
Database: PDB / ID: 7t80
TitleCrystal Structure of Mouse Cadherin-23 EC18-19
ComponentsCadherin-23
KeywordsCELL ADHESION / HEARING / MECHANOTRANSDUCTION / ADHESION / 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: 2.301 Å
AuthorsHarrison-Rawn, T. / Sotomayor, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)DC015271 United States
CitationJournal: to be published
Title: Crystal Structure of Mouse Cadherin-23 EC18-19
Authors: Harrison-Rawn, T. / Sotomayor, M.
History
DepositionDec 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2022Provider: 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

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Assembly

Deposited unit
A: Cadherin-23
B: Cadherin-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,04510
Polymers49,7342
Non-polymers3118
Water1,22568
1
A: Cadherin-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0235
Polymers24,8671
Non-polymers1564
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cadherin-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0235
Polymers24,8671
Non-polymers1564
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.073, 76.073, 201.319
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Cadherin-23 / Otocadherin


Mass: 24866.822 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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.: 6 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 3.38 Å3/Da / Density % sol: 63.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M (NH4)2SO4 25% w/v PEG 3350 0.1 M Tris-HCl 8.5 pH

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.3→67.106 Å / Num. obs: 30864 / % possible obs: 100 % / Redundancy: 17.6 % / CC1/2: 0.999 / Net I/σ(I): 21.28
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 13.4 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1495 / CC1/2: 0.706 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WJM, 5TFK

5wjm

5tfk


Resolution: 2.301→67.106 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.246 / SU ML: 0.144 / Cross valid method: FREE R-VALUE / ESU R: 0.215 / ESU R Free: 0.184
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2324 1549 5.03 %
Rwork0.1996 29247 -
all0.201 --
obs-30796 99.773 %
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: 58.004 Å2
Baniso -1Baniso -2Baniso -3
1-2.046 Å21.023 Å20 Å2
2--2.046 Å2-0 Å2
3----6.637 Å2
Refinement stepCycle: LAST / Resolution: 2.301→67.106 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3274 0 8 68 3350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133333
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153167
X-RAY DIFFRACTIONr_angle_refined_deg1.6411.6384564
X-RAY DIFFRACTIONr_angle_other_deg1.2161.5717276
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2625422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.45923.409176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.39315522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9821520
X-RAY DIFFRACTIONr_chiral_restr0.0650.2466
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023810
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02722
X-RAY DIFFRACTIONr_nbd_refined0.210.2498
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.22785
X-RAY DIFFRACTIONr_nbtor_refined0.1520.21554
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.21731
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2210.284
X-RAY DIFFRACTIONr_metal_ion_refined0.1110.233
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1860.218
X-RAY DIFFRACTIONr_nbd_other0.1850.272
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1350.28
X-RAY DIFFRACTIONr_mcbond_it5.0945.8821697
X-RAY DIFFRACTIONr_mcbond_other5.0855.881696
X-RAY DIFFRACTIONr_mcangle_it7.3698.7942116
X-RAY DIFFRACTIONr_mcangle_other7.3698.7972117
X-RAY DIFFRACTIONr_scbond_it5.3556.441636
X-RAY DIFFRACTIONr_scbond_other5.3446.4341634
X-RAY DIFFRACTIONr_scangle_it8.1459.4252448
X-RAY DIFFRACTIONr_scangle_other8.1449.4252448
X-RAY DIFFRACTIONr_lrange_it10.5267.6933237
X-RAY DIFFRACTIONr_lrange_other10.53467.6693224
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
2.301-2.3610.372940.32920810.33122370.7760.77297.22840.329
2.361-2.4250.3341120.30820780.30921910.8010.81799.95440.308
2.425-2.4960.3141000.28420270.28621270.8430.8671000.284
2.496-2.5720.279800.25419540.25520340.8980.9021000.254
2.572-2.6570.291140.24819210.25120350.9010.9141000.248
2.657-2.750.262900.2218400.22219300.9110.9311000.22
2.75-2.8530.209870.2117850.2118730.9330.93899.94660.21
2.853-2.970.2741040.22317110.22618150.8990.9191000.223
2.97-3.1010.275930.2516410.25117340.8960.91000.25
3.101-3.2520.322840.23715860.24116700.890.9151000.237
3.252-3.4280.252870.23515120.23615990.9190.9291000.235
3.428-3.6350.2991000.22514040.2315040.9130.9331000.225
3.635-3.8850.238760.20313630.20414390.9270.9471000.203
3.885-4.1960.182570.16812870.16813440.9550.9631000.168
4.196-4.5940.175620.13611560.13812180.9670.9771000.136
4.594-5.1330.189600.13810660.1411260.960.9761000.138
5.133-5.9220.155510.1579630.15710140.970.9731000.157
5.922-7.2390.179510.1678020.1678530.9660.9741000.167
7.239-10.1780.132310.1366610.1366920.9790.9811000.136
10.178-67.1060.161160.2024090.2014310.9840.96698.60790.202

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