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- PDB-4aqa: CRYSTAL STRUCTURE OF DEAFNESS ASSOCIATED MUTANT MOUSE CADHERIN-23... -

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Basic information

Entry
Database: PDB / ID: 4aqa
TitleCRYSTAL STRUCTURE OF DEAFNESS ASSOCIATED MUTANT MOUSE CADHERIN-23 EC1- 2D124G AND PROTOCADHERIN-15 EC1-2 FORM I
Components
  • CADHERIN-23
  • PROTOCADHERIN-15
KeywordsCELL ADHESION / HEARING / CDH23 / PCDH15 / HETEROPHILIC
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 / auditory receptor cell stereocilium organization / adult walking behavior / 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 / actin filament organization / morphogenesis of an epithelium / 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: 1.96 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 15, 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

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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)51,85112
Polymers51,3012
Non-polymers55010
Water10,917606
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-58.7 kcal/mol
Surface area23100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.293, 40.506, 84.629
Angle α, β, γ (deg.)90.00, 102.86, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2126-

HOH

21A-2211-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein CADHERIN-23 / / OTOCADHERIN


Mass: 23798.400 Da / Num. of mol.: 1 / Fragment: EC1-2, RESIDUES 24-228 / Mutation: YES
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 , 5 types, 616 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 / MES (buffer)


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


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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 606 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsSEQUENCE. NOTE SEQUENCE CONFLICT OF GENBANK NP_001136218.1 AND EMBL- BANK CDS AAG53891.1 WITH ...SEQUENCE. NOTE SEQUENCE CONFLICT OF GENBANK NP_001136218.1 AND EMBL- BANK CDS AAG53891.1 WITH Q99PJ1 (YED TO FEN). N-TERMINAL METHIONINES ARE A CLONING ARTIFACT. PROTEINS WERE CLONED WITH AN ADDITIONAL C-TERMINAL HIS-TAG.

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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: 2.9 Å3/Da / Density % sol: 57.53 % / Description: NONE
Crystal growpH: 6.5 / Details: 0.1 MES, 8% PEG 20000, PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97919
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 1.96→34.19 Å / Num. obs: 41729 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.5
Reflection shellResolution: 1.96→2 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.4 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4APX

4apx


Resolution: 1.96→34.19 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.923 / SU B: 6.402 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.22775 2101 5.1 %RANDOM
Rwork0.17782 ---
obs0.18035 39390 98.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-0.46 Å2
2--1.27 Å20 Å2
3----1.45 Å2
Refinement stepCycle: LAST / Resolution: 1.96→34.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3488 0 21 606 4115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.023621
X-RAY DIFFRACTIONr_bond_other_d0.0010.022385
X-RAY DIFFRACTIONr_angle_refined_deg1.3271.9584956
X-RAY DIFFRACTIONr_angle_other_deg0.8573.0015836
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8275453
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.79124.837184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32115579
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8491525
X-RAY DIFFRACTIONr_chiral_restr0.0820.2571
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214071
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02710
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.955→2.006 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 133 -
Rwork0.221 2573 -
obs--92.77 %
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)
10.9643-0.41091.44160.3755-0.35363.8970.0355-0.1487-0.2820.00970.27610.142-0.1505-0.1411-0.31160.03880.048-0.01810.26040.0560.088928.103-5.15543.411
21.61640.29980.91360.07560.05031.78230.00790.2684-0.05810.02540.0732-0.0139-0.04490.0932-0.08110.05440.0195-0.02140.1368-0.00280.039810.664-1.808-1.914
30.4125-0.15920.17090.2448-0.48522.8498-0.038-0.058-0.067-0.01790.09610.0451-0.2298-0.1199-0.05810.11880.03780.00990.09130.02590.014312.7113.92626.125
40.4829-0.40710.02250.6409-0.94593.37510.05520.00050.0324-0.03740.0075-0.0448-0.0095-0.0379-0.06270.04480.00530.00850.09670.0070.034315.6460.65274.29
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 101
2X-RAY DIFFRACTION1A1207
3X-RAY DIFFRACTION1A1209
4X-RAY DIFFRACTION1A1210
5X-RAY DIFFRACTION1A1212
6X-RAY DIFFRACTION2A102 - 208
7X-RAY DIFFRACTION2A1208
8X-RAY DIFFRACTION3B0 - 120
9X-RAY DIFFRACTION3B1238
10X-RAY DIFFRACTION3B1237
11X-RAY DIFFRACTION4B121 - 236
12X-RAY DIFFRACTION4B1239
13X-RAY DIFFRACTION4B1240

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