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- PDB-4xxw: Crystal structure of mouse Cadherin-23 EC1-2 and Protocadherin-15... -

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Basic information

Entry
Database: PDB / ID: 4xxw
TitleCrystal structure of mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1-2 splice variant
Components
  • Cadherin-23
  • Protocadherin-15
KeywordsCELL ADHESION / Mechanotransduction / calcium binding protein / hearing
Function / homology
Function and homology information


detection of mechanical stimulus involved in equilibrioception / cochlear hair cell ribbon synapse / kinocilium / equilibrioception / sensory perception of light stimulus / stereocilium tip / inner ear receptor cell stereocilium organization / righting reflex / detection of mechanical stimulus involved in sensory perception of sound / inner ear auditory receptor cell differentiation ...detection of mechanical stimulus involved in equilibrioception / cochlear hair cell ribbon synapse / kinocilium / equilibrioception / sensory perception of light stimulus / stereocilium tip / inner ear receptor cell stereocilium organization / righting reflex / detection of mechanical stimulus involved in sensory perception of sound / 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 / non-motile cilium assembly / photoreceptor cell maintenance / catenin complex / adult walking behavior / auditory receptor cell stereocilium organization / inner ear morphogenesis / cochlea development / startle response / homophilic cell adhesion via plasma membrane adhesion molecules / inner ear development / photoreceptor outer segment / regulation of cytosolic calcium ion concentration / visual perception / photoreceptor inner segment / locomotory behavior / morphogenesis of an epithelium / actin filament organization / sensory perception of sound / multicellular organism growth / response to calcium ion / calcium ion transport / apical part of cell / cell adhesion / cadherin binding / centrosome / synapse / calcium ion binding / extracellular region / membrane / plasma membrane / cytoplasm
Similarity search - Function
Immunoglobulin-like - #3430 / Extracellular cadherin domain / Protocadherin-15 / Extracellular Cadherin domain / Cadherins / Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain ...Immunoglobulin-like - #3430 / Extracellular cadherin domain / Protocadherin-15 / Extracellular Cadherin domain / Cadherins / Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cadherin-23 / Protocadherin-15
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.261 Å
AuthorsNarui, Y. / Sotomayor, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)R00 DC012534 United States
CitationJournal: Biochemistry / Year: 2018
Title: Tuning Inner-Ear Tip-Link Affinity Through Alternatively Spliced Variants of Protocadherin-15.
Authors: Narui, Y. / Sotomayor, M.
History
DepositionJan 31, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Aug 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Protocadherin-15
A: Protocadherin-15
C: Cadherin-23
D: Cadherin-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,90720
Polymers101,2754
Non-polymers63216
Water8,341463
1
B: Protocadherin-15
C: Cadherin-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,95310
Polymers50,6372
Non-polymers3168
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-47 kcal/mol
Surface area22050 Å2
MethodPISA
2
A: Protocadherin-15
D: Cadherin-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,95310
Polymers50,6372
Non-polymers3168
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-49 kcal/mol
Surface area22150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.746, 57.789, 155.264
Angle α, β, γ (deg.)90.00, 99.17, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protocadherin-15


Mass: 26780.904 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pcdh15 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q99PJ1
#2: Protein Cadherin-23 / Otocadherin


Mass: 23856.436 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-CodonPlus(DE3)-RIPL / References: UniProt: Q99PF4
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 463 / 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: 3.56 Å3/Da / Density % sol: 65.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Ammonium Acetate 0.1 M HEPES, pH 7.5 25% (v/v) isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.261→50 Å / Num. obs: 62947 / % possible obs: 96.8 % / Redundancy: 3.2 % / Biso Wilson estimate: 38.6 Å2 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.05 / Rrim(I) all: 0.094 / Χ2: 1.02 / Net I/av σ(I): 13.381 / Net I/σ(I): 6.7 / Num. measured all: 200718
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.261-2.32.50.4022.327360.8440.2830.4940.99684.9
2.3-2.342.70.35528680.890.2410.4310.96489.4
2.34-2.392.90.35930300.8830.2350.4310.97393.5
2.39-2.432.90.35630480.8740.2320.4270.98895.2
2.43-2.4930.331500.9050.1980.3610.97197.3
2.49-2.553.10.28332050.9250.1840.3390.97298.3
2.55-2.613.10.26631400.9260.1730.3191.01797.4
2.61-2.683.10.23431300.9520.1510.280.98898
2.68-2.763.10.20431810.9610.1340.2450.99597.7
2.76-2.8530.17431060.9670.1170.2111.02596.1
2.85-2.953.40.14631950.9780.0920.1731.06299
2.95-3.073.40.12532450.9840.0790.1491.0499.2
3.07-3.213.40.09432140.9910.0590.1111.06499.2
3.21-3.383.40.0832130.9920.050.0951.07399
3.38-3.593.30.06931870.9940.0440.0821.0897.9
3.59-3.863.30.06131980.9930.0380.0721.01797.9
3.86-4.253.60.05332490.9950.0320.0621.03799.4
4.25-4.873.50.04732750.9960.0290.0561.04299.4
4.87-6.133.40.04532180.9960.0280.0530.99997.4
6.13-503.60.04333590.9940.0260.0511.01998.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4APX

4apx


Resolution: 2.261→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.933 / SU B: 12.037 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23288 3126 5 %RANDOM
Rwork0.18717 ---
obs0.18945 59821 96.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20.31 Å2
2---0.07 Å2-0 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.261→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6790 0 16 463 7269
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0196978
X-RAY DIFFRACTIONr_bond_other_d0.0020.026515
X-RAY DIFFRACTIONr_angle_refined_deg1.8061.9539544
X-RAY DIFFRACTIONr_angle_other_deg1.027314989
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3055872
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.54824.957347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.682151107
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2611544
X-RAY DIFFRACTIONr_chiral_restr0.1010.21113
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218009
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021571
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_it1.9322.6243470
X-RAY DIFFRACTIONr_mcbond_other1.9312.6223469
X-RAY DIFFRACTIONr_mcangle_it3.2723.9154333
X-RAY DIFFRACTIONr_mcangle_other3.2733.9174334
X-RAY DIFFRACTIONr_scbond_it1.8792.9023508
X-RAY DIFFRACTIONr_scbond_other1.8792.9043509
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.234.265207
X-RAY DIFFRACTIONr_long_range_B_refined7.01221.5447721
X-RAY DIFFRACTIONr_long_range_B_other6.99621.4957700
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.261→2.319 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 196 -
Rwork0.284 3788 -
obs--82.98 %
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)
13.11441.95511.21991.31030.62541.06660.07490.2025-0.4468-0.05130.2388-0.25150.0243-0.033-0.31370.2347-0.138-0.07390.1766-0.04050.23-60.62-22.13661.49
26.22363.25550.732.46890.3750.5601-0.2890.03220.4541-0.03620.05230.2858-0.0475-0.03320.23670.187-0.0443-0.0620.1452-0.02790.1449-26.23910.95964.949
34.21583.5290.8944.0621.59050.84151.1925-0.4506-0.42140.8531-0.8407-0.66340.191-0.4987-0.35190.5452-0.2643-0.19310.4480.29390.1978-19.76328.47333.874
419.60383.70291.93040.82420.56011.94490.75710.9497-0.11760.2457-0.1045-0.08690.3219-0.1272-0.65260.1174-0.174-0.08940.68710.05970.2295-61.25615.11714.879
52.91632.59161.76182.6182.10142.0665-0.45740.33080.4143-0.14020.31360.29430.1070.30510.14370.3579-0.0855-0.18590.08810.07140.1744-58.6985.83366.758
62.61591.3271.10761.85721.8122.0201-0.08740.1774-0.17390.0002-0.08290.0473-0.1123-0.09340.17030.2367-0.1355-0.06220.2171-0.04160.0822-90.169-23.60345.576
73.49392.38981.86591.88711.30061.63810.1084-0.113-0.0222-0.122-0.06750.08860.01710.0333-0.04090.2968-0.0241-0.14040.1821-0.00650.0718-31.63826.8168.292
81.30661.05480.7073.40763.16713.08410.001-0.4401-0.1527-0.5360.5133-0.5046-0.44860.6022-0.51430.2716-0.29540.03940.6328-0.12960.14140.80754.73930.015
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B9 - 119
2X-RAY DIFFRACTION1B1001 - 1002
3X-RAY DIFFRACTION1B1004
4X-RAY DIFFRACTION2B120 - 234
5X-RAY DIFFRACTION2B1003
6X-RAY DIFFRACTION3A9 - 119
7X-RAY DIFFRACTION3A1001 - 1002
8X-RAY DIFFRACTION3A1004
9X-RAY DIFFRACTION4A120 - 234
10X-RAY DIFFRACTION4A1003
11X-RAY DIFFRACTION5C2 - 101
12X-RAY DIFFRACTION5C1001 - 1003
13X-RAY DIFFRACTION6C102 - 203
14X-RAY DIFFRACTION6C1004
15X-RAY DIFFRACTION7D2 - 101
16X-RAY DIFFRACTION7D1001 - 1003
17X-RAY DIFFRACTION8D102 - 203
18X-RAY DIFFRACTION8D1004

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