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- PDB-7suu: Crystal Structure of Mouse Cadherin-23 EC25-26 -

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Basic information

Entry
Database: PDB / ID: 7suu
TitleCrystal Structure of Mouse Cadherin-23 EC25-26
ComponentsCadherin-23
KeywordsCELL ADHESION / HEARING / MECHANOTRANSDUCTION / CALCIUM-BINDING PROTEIN
Function / homology
Function and homology information


kinocilium / equilibrioception / sensory perception of light stimulus / cochlear hair cell ribbon synapse / inner ear receptor cell stereocilium organization / stereocilium tip / inner ear auditory receptor cell differentiation / cell-cell adhesion via plasma-membrane adhesion molecules / photoreceptor ribbon synapse / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules ...kinocilium / equilibrioception / sensory perception of light stimulus / cochlear hair cell ribbon synapse / inner ear receptor cell stereocilium organization / stereocilium tip / inner ear auditory receptor cell differentiation / cell-cell adhesion via plasma-membrane adhesion molecules / photoreceptor ribbon synapse / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / stereocilium / 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 / beta-catenin binding / calcium ion transport / neuron projection development / cell migration / apical part of cell / cell adhesion / cadherin binding / centrosome / calcium ion binding / synapse / plasma membrane
Similarity search - Function
Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.248 Å
AuthorsBoyer, M.D. / Sandhu, J.S. / 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 EC25-26
Authors: Boyer, M.D. / Sandhu, J.S. / Sotomayor, M.
History
DepositionNov 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)57,24421
Polymers56,4912
Non-polymers75319
Water3,819212
1
A: Cadherin-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5609
Polymers28,2451
Non-polymers3158
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cadherin-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,68312
Polymers28,2451
Non-polymers43811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.237, 88.488, 206.783
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-3098-

HOH

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Components

#1: Protein Cadherin-23 / Otocadherin


Mass: 28245.406 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 BL21 (bacteria) / References: UniProt: Q99PF4
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 3.35 Å3/Da / Density % sol: 63.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.8 / Details: 0.1 M HEPES ph 7.8 0.35 M CaCl2 28 % PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.248→45.055 Å / Num. obs: 35493 / % possible obs: 98.7 % / Redundancy: 9.1 % / CC1/2: 0.968 / Net I/σ(I): 11.08
Reflection shellResolution: 2.248→2.3 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 4.7 / Num. unique obs: 1498 / CC1/2: 0.894 / % possible all: 84.4

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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: 5VT8

5vt8


Resolution: 2.248→45.055 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.589 / SU ML: 0.139 / Cross valid method: FREE R-VALUE / ESU R: 0.217 / ESU R Free: 0.201
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2533 1730 4.947 %
Rwork0.1976 33241 -
all0.2 --
obs-34971 98.602 %
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: 37.253 Å2
Baniso -1Baniso -2Baniso -3
1-0.953 Å20 Å2-0 Å2
2--0.199 Å20 Å2
3----1.152 Å2
Refinement stepCycle: LAST / Resolution: 2.248→45.055 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3717 0 19 212 3948
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133818
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153578
X-RAY DIFFRACTIONr_angle_refined_deg1.5931.6525221
X-RAY DIFFRACTIONr_angle_other_deg1.2621.588236
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1795469
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.4622.743226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.83615609
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8191530
X-RAY DIFFRACTIONr_chiral_restr0.0720.2499
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024384
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02864
X-RAY DIFFRACTIONr_nbd_refined0.2450.2656
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1810.23317
X-RAY DIFFRACTIONr_nbtor_refined0.1610.21821
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.21921
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2192
X-RAY DIFFRACTIONr_metal_ion_refined0.2040.269
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3110.220
X-RAY DIFFRACTIONr_nbd_other0.1960.271
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.120.25
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1490.22
X-RAY DIFFRACTIONr_mcbond_it3.1783.721882
X-RAY DIFFRACTIONr_mcbond_other3.1773.7181881
X-RAY DIFFRACTIONr_mcangle_it4.4995.5622349
X-RAY DIFFRACTIONr_mcangle_other4.55.5642350
X-RAY DIFFRACTIONr_scbond_it3.9084.1011936
X-RAY DIFFRACTIONr_scbond_other3.9024.0991934
X-RAY DIFFRACTIONr_scangle_it5.8516.0092872
X-RAY DIFFRACTIONr_scangle_other5.8516.0092872
X-RAY DIFFRACTIONr_lrange_it7.37943.3974064
X-RAY DIFFRACTIONr_lrange_other7.35343.224019
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.248-2.3060.3191000.2382174X-RAY DIFFRACTION88.2079
2.306-2.3690.3061140.2312399X-RAY DIFFRACTION99.2496
2.369-2.4380.3161260.2162303X-RAY DIFFRACTION99.7946
2.438-2.5130.311150.2092299X-RAY DIFFRACTION99.6697
2.513-2.5950.2721280.2012186X-RAY DIFFRACTION99.7844
2.595-2.6860.251120.2042097X-RAY DIFFRACTION99.7742
2.686-2.7870.2861090.2032049X-RAY DIFFRACTION99.815
2.787-2.9010.295950.2151975X-RAY DIFFRACTION99.3282
2.901-3.030.286940.2281910X-RAY DIFFRACTION99.5035
3.03-3.1780.28880.2231830X-RAY DIFFRACTION99.7919
3.178-3.350.255900.221732X-RAY DIFFRACTION99.3457
3.35-3.5530.26990.211624X-RAY DIFFRACTION99.5378
3.553-3.7980.259790.191546X-RAY DIFFRACTION99.3276
3.798-4.1010.215730.171424X-RAY DIFFRACTION98.4868
4.101-4.4920.206730.1541316X-RAY DIFFRACTION97.2008
4.492-5.0210.188640.1561215X-RAY DIFFRACTION99.2242
5.021-5.7960.253700.1691059X-RAY DIFFRACTION99.735
5.796-7.0930.224570.202915X-RAY DIFFRACTION99.8972
7.093-10.0070.243310.188749X-RAY DIFFRACTION99.3631
10.007-45.0550.234130.237439X-RAY DIFFRACTION98.9059

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