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- PDB-8e51: Crystal Structure of Iridescent Shark Catfish Cadherin-23 EC1-2 a... -

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Basic information

Entry
Database: PDB / ID: 8.0E+51
TitleCrystal Structure of Iridescent Shark Catfish Cadherin-23 EC1-2 and Protocadherin-15 EC1-2
Components
  • Cadherin-23
  • Protocadherin-15
KeywordsCELL ADHESION / HEARING / DEAFNESS / CDH23 / PCDH15 / EVOLUTION / TIP LINK
Function / homology
Function and homology information


stereocilium / homophilic cell adhesion via plasma membrane adhesion molecules / inner ear development / sensory perception of sound / calcium ion binding / plasma membrane
Similarity search - Function
Extracellular cadherin domain / Protocadherin-15 / Extracellular Cadherin domain / Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily
Similarity search - Domain/homology
: / Cadherin domain-containing protein
Similarity search - Component
Biological speciesPangasianodon hypophthalmus (striped catfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.594 Å
AuthorsScheib, E. / Nisler, C.R. / Sotomayor, M.
Funding support France, 1items
OrganizationGrant numberCountry
Human Frontier Science Program (HFSP)RGP0056/2018 France
CitationJournal: Mol.Biol.Evol. / Year: 2023
Title: Interpreting the Evolutionary Echoes of a Protein Complex Essential for Inner-Ear Mechanosensation.
Authors: Nisler, C.R. / Narui, Y. / Scheib, E. / Choudhary, D. / Bowman, J.D. / Mandayam Bharathi, H. / Lynch, V.J. / Sotomayor, M.
History
DepositionAug 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Apr 3, 2024Group: 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
C: Protocadherin-15
B: Cadherin-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,64417
Polymers53,0452
Non-polymers59915
Water55831
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.816, 75.816, 242.680
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 Protocadherin-15


Mass: 28839.947 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Initiating methionine and C-terminal histidine tag added.
Source: (gene. exp.) Pangasianodon hypophthalmus (striped catfish)
Gene: PHYPO_G00032920 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 RIPL / References: UniProt: A0A5N5MKD0
#2: Protein Cadherin-23


Mass: 24204.658 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Initiating methionine and C-terminal histidine tag added
Source: (gene. exp.) Pangasianodon hypophthalmus (striped catfish)
Gene: CDH23 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 RIPL
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 3.8 Å3/Da / Density % sol: 67.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M CaCl2, 0.1 M HEPES pH 7.5, 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.594→44.599 Å / Num. obs: 26033 / % possible obs: 100 % / Redundancy: 28.1 % / CC1/2: 0.975 / Net I/σ(I): 12.907
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 20.7 % / Mean I/σ(I) obs: 6.53 / Num. unique obs: 1264 / CC1/2: 0.95 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0349refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold2 Model

Resolution: 2.594→44.599 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.929 / SU B: 8.582 / SU ML: 0.181 / Cross valid method: FREE R-VALUE / ESU R: 0.307 / ESU R Free: 0.242
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2424 1255 4.835 %
Rwork0.2019 24699 -
all0.204 --
obs-25954 99.792 %
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: 62.724 Å2
Baniso -1Baniso -2Baniso -3
1-3.185 Å21.593 Å20 Å2
2--3.185 Å2-0 Å2
3----10.332 Å2
Refinement stepCycle: LAST / Resolution: 2.594→44.599 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3479 0 15 31 3525
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123624
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163133
X-RAY DIFFRACTIONr_angle_refined_deg1.5261.6474862
X-RAY DIFFRACTIONr_angle_other_deg0.4941.5477327
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6415441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.5641024
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.65410552
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.53410178
X-RAY DIFFRACTIONr_chiral_restr0.0660.2562
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024099
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02665
X-RAY DIFFRACTIONr_nbd_refined0.1990.2499
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.22779
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21687
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21982
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.270
X-RAY DIFFRACTIONr_metal_ion_refined0.270.210
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.4170.210
X-RAY DIFFRACTIONr_nbd_other0.2720.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1570.24
X-RAY DIFFRACTIONr_mcbond_it5.4816.3091786
X-RAY DIFFRACTIONr_mcbond_other5.4816.3091786
X-RAY DIFFRACTIONr_mcangle_it7.5359.4632211
X-RAY DIFFRACTIONr_mcangle_other7.5369.4662212
X-RAY DIFFRACTIONr_scbond_it6.5446.791838
X-RAY DIFFRACTIONr_scbond_other6.4236.7871835
X-RAY DIFFRACTIONr_scangle_it8.70910.0312651
X-RAY DIFFRACTIONr_scangle_other8.70810.0332652
X-RAY DIFFRACTIONr_lrange_it10.79977.4233517
X-RAY DIFFRACTIONr_lrange_other10.79877.4153507
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
2.594-2.6610.3091030.27117260.27318700.930.95397.80750.271
2.661-2.7340.3321070.25817610.26218680.9470.9641000.258
2.734-2.8130.41690.25516960.26117650.930.9621000.255
2.813-2.8990.386610.26616730.2717350.9080.95799.94240.266
2.899-2.9940.331030.25915940.26316970.9350.961000.259
2.994-3.0980.283590.24215380.24415970.9430.9641000.242
3.098-3.2150.284600.23715330.23915940.9470.96499.93730.237
3.215-3.3450.32550.24214550.24515110.9310.96299.93380.242
3.345-3.4930.231760.22213990.22314750.9570.971000.222
3.493-3.6620.261610.20813390.20914000.9560.9741000.208
3.662-3.8590.246670.19812660.20113330.960.9771000.198
3.859-4.0910.168710.18112040.1812750.980.9811000.181
4.091-4.3710.228520.15511520.15812040.9730.9861000.155
4.371-4.7180.202680.14410520.14711200.9790.9881000.144
4.718-5.1620.207490.1519910.15410400.9790.9871000.151
5.162-5.7620.233480.1719030.1749510.9680.9841000.171
5.762-6.6350.22520.1858000.1878520.970.981000.185
6.635-8.0810.202450.1766900.1787350.9770.9791000.176
8.081-11.2450.169260.1825680.1815950.9850.97999.83190.182
11.245-44.5990.219230.2583590.2563830.9650.95399.73890.258

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