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- PDB-4apx: CRYSTAL STRUCTURE OF MOUSE CADHERIN-23 EC1-2 AND PROTOCADHERIN-15... -

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Basic information

Entry
Database: PDB / ID: 4apx
TitleCRYSTAL STRUCTURE OF MOUSE CADHERIN-23 EC1-2 AND PROTOCADHERIN-15 EC1- 2 FORM I
Components
  • CADHERIN-23
  • PROTOCADHERIN-15
KeywordsCELL ADHESION / HEARING / DEAFNESS / CDH23 / PCDH15
Function / homology
Function and homology information


detection of mechanical stimulus involved in equilibrioception / equilibrioception / sensory perception of light stimulus / cochlear hair cell ribbon synapse / stereocilium tip / inner ear receptor cell stereocilium organization / photoreceptor ribbon synapse / kinocilium / righting reflex / inner ear auditory receptor cell differentiation ...detection of mechanical stimulus involved in equilibrioception / equilibrioception / sensory perception of light stimulus / cochlear hair cell ribbon synapse / stereocilium tip / inner ear receptor cell stereocilium organization / photoreceptor ribbon synapse / kinocilium / righting reflex / inner ear auditory receptor cell differentiation / stereocilium bundle / calcium-dependent cell-cell adhesion / detection of mechanical stimulus involved in sensory perception of sound / stereocilium / photoreceptor cell maintenance / non-motile cilium assembly / auditory receptor cell stereocilium organization / adult walking behavior / inner ear morphogenesis / startle response / homophilic cell-cell adhesion / inner ear development / actin filament bundle assembly / cochlea development / photoreceptor outer segment / regulation of cytosolic calcium ion concentration / photoreceptor inner segment / visual perception / actin filament organization / morphogenesis of an epithelium / locomotory behavior / sensory perception of sound / response to calcium ion / multicellular organism growth / calcium ion transport / cell adhesion / calcium ion binding / synapse / centrosome / extracellular region / membrane / plasma membrane / cytoplasm
Similarity search - Function
Immunoglobulin-like - #3430 / : / PCDH15-like domain / Protocadherin-15 / Extracellular cadherin domain / Extracellular Cadherin domain / : / Cadherins / Cadherin conserved site / Cadherin domain signature. ...Immunoglobulin-like - #3430 / : / PCDH15-like domain / Protocadherin-15 / Extracellular cadherin domain / Extracellular Cadherin domain / : / Cadherins / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherin-like / Cadherins domain profile. / 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: 1.65 Å
AuthorsSotomayor, M. / Weihofen, W. / Gaudet, R. / Corey, D.P.
CitationJournal: Nature / Year: 2012
Title: Structure of a Force-Conveying Cadherin Bond Essential for Inner-Ear Mechanotransduction
Authors: Sotomayor, M. / Weihofen, W. / Gaudet, R. / Corey, D.P.
History
DepositionApr 7, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references
Revision 1.2Dec 12, 2012Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CADHERIN-23
B: PROTOCADHERIN-15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,00113
Polymers51,3592
Non-polymers64211
Water14,826823
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-37.9 kcal/mol
Surface area23670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.606, 40.469, 84.623
Angle α, β, γ (deg.)90.00, 103.12, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1214-

CL

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein CADHERIN-23 / OTOCADHERIN


Mass: 23856.436 Da / Num. of mol.: 1 / Fragment: EC1-2, RESIDUES 24-228
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99PF4
#2: Protein PROTOCADHERIN-15


Mass: 27502.619 Da / Num. of mol.: 1 / Fragment: EC1-2, RESIDUES 27-259
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99PJ1

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Non-polymers , 6 types, 834 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 823 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence details34-FEN-36 TO 34-YED-36 A KNOWN MUTATION IN AF281899.1

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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: 2.91 Å3/Da / Density % sol: 57.69 % / Description: NONE
Crystal growpH: 6.5 / Details: 0.1M MES, 8% PEG8000, PH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97949
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.65→32.03 Å / Num. obs: 66852 / % possible obs: 96.9 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 25.6
Reflection shellResolution: 1.65→1.7 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.8 / % possible all: 92.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WHV AND HOMOLOGY MODEL

2whv


Resolution: 1.65→32.03 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.567 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. N-TERMINAL METHIONINES ARE A CLONING ARTIFACT. PROTEINS WERE CLONED WITH AN ADDITIONAL C-TERMINAL HIS-TAG.
RfactorNum. reflection% reflectionSelection details
Rfree0.19307 3359 5 %RANDOM
Rwork0.16138 ---
obs0.163 63383 96.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.489 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.65→32.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3519 0 27 823 4369
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223824
X-RAY DIFFRACTIONr_bond_other_d0.0010.022512
X-RAY DIFFRACTIONr_angle_refined_deg1.4151.9595269
X-RAY DIFFRACTIONr_angle_other_deg1.23736181
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5075500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.35225200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.16915621
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.9491526
X-RAY DIFFRACTIONr_chiral_restr0.0860.2605
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214373
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02754
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_it0.6961.52334
X-RAY DIFFRACTIONr_mcbond_other0.1651.5924
X-RAY DIFFRACTIONr_mcangle_it1.28723871
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.91931490
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.24.51375
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.654→1.697 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 222 -
Rwork0.287 4444 -
obs--92.12 %
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)
10.4345-0.25590.50460.1778-0.18651.91790.0224-0.0981-0.0563-0.00090.09730.0360.0226-0.0959-0.11970.05840.0097-0.01640.06760.0290.063427.928-5.63443.338
21.30810.3570.66950.10090.18891.0038-0.04010.22150.00220.00260.0625-0.0023-0.00690.1107-0.02240.0554-0.001-0.01950.04710.00640.071210.783-2.066-1.824
30.3133-0.09130.23780.0682-0.24181.3627-0.0104-0.0834-0.0307-0.00670.04460.0199-0.1511-0.1013-0.03420.09960.013-0.00070.04520.02510.049812.63413.75626.094
40.4011-0.1866-0.10890.2825-0.55962.04810.0330.02710.0134-0.01130.0064-0.02010.0008-0.0621-0.03930.04270.01110.00080.030.00240.061415.460.32374.198
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 101
2X-RAY DIFFRACTION1A1210
3X-RAY DIFFRACTION1A1211
4X-RAY DIFFRACTION1A1209
5X-RAY DIFFRACTION2A102 - 208
6X-RAY DIFFRACTION2A1212
7X-RAY DIFFRACTION3B0 - 120
8X-RAY DIFFRACTION3B1239
9X-RAY DIFFRACTION3B1240
10X-RAY DIFFRACTION4B121 - 236
11X-RAY DIFFRACTION4B1238
12X-RAY DIFFRACTION4B1241

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