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

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Basic information

Entry
Database: PDB / ID: 4aqe
TitleCRYSTAL STRUCTURE OF DEAFNESS ASSOCIATED MUTANT MOUSE CADHERIN-23 EC1- 2S70P AND PROTOCADHERIN-15 EC1-2 FORM I
Components
  • CADHERIN-23
  • PROTOCADHERIN-15
KeywordsCELL ADHESION / HEARING / DEAFNESS / CDH23 / PCDH15 / HETEROPHILIC
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: 2.27 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 16, 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.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 1.4Oct 16, 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)51,88411
Polymers51,3692
Non-polymers5159
Water7,260403
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-35.2 kcal/mol
Surface area23840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.023, 40.866, 84.775
Angle α, β, γ (deg.)90.00, 102.95, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2146-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein CADHERIN-23 / OTOCADHERIN


Mass: 23866.471 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 , 4 types, 412 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-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, SER 70 TO PRO
Has protein modificationY
Sequence detailsRESIDUE SERINE 70 (DATABASE NUMBERING) IS MUTATED TO PROLINE. NOTE SEQUENCE CONFLICT OF GENBANK NP_ ...RESIDUE SERINE 70 (DATABASE NUMBERING) IS MUTATED TO PROLINE. NOTE SEQUENCE CONFLICT OF GENBANK NP_001136218.1 AND EMBL-BANK CDS AAG53891.1 WITH Q99PJ1 (YED TO FEN)

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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: 2.93 Å3/Da / Density % sol: 57.99 % / Description: NONE
Crystal growpH: 6.5 / Details: 0.1 M MES, 12% PEG 4000, 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: 2.27→22.69 Å / Num. obs: 27207 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 9.6
Reflection shellResolution: 2.27→2.33 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.3 / % possible all: 96.8

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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: 2.27→22.69 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.908 / SU B: 11.058 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.252 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.N-TERMINAL METHIONINES ARE A CLONING ARTIFACT. ADDITIONAL C-TERMINAL HIS-TAGS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23873 1395 5.1 %RANDOM
Rwork0.17261 ---
obs0.17601 25732 98.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.144 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20 Å2-0.36 Å2
2--1.68 Å20 Å2
3----1.35 Å2
Refinement stepCycle: LAST / Resolution: 2.27→22.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3503 0 20 403 3926
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.023614
X-RAY DIFFRACTIONr_bond_other_d0.0010.022368
X-RAY DIFFRACTIONr_angle_refined_deg1.4041.9584945
X-RAY DIFFRACTIONr_angle_other_deg0.8833.0015798
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2575448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.3124.973183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.28115573
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9081523
X-RAY DIFFRACTIONr_chiral_restr0.0850.2570
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214054
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02701
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: 2.265→2.323 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 94 -
Rwork0.202 1582 -
obs--89.39 %
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)
10.8626-0.0480.65160.04280.06393.10790.0144-0.0625-0.07480.00380.06970.00350.0408-0.1555-0.08420.0303-0.002-0.01490.11640.01040.013628.255-5.43643.38
21.78260.38771.40290.12630.1052.3671-0.07110.19660.02050.00130.05430-0.01970.11110.01680.0507-0.0011-0.01180.08770.01190.011210.757-1.728-1.836
30.2545-0.1385-0.10120.3107-0.29952.9927-0.0317-0.0541-0.0525-0.04080.04480.0421-0.1311-0.0386-0.01310.04180.01610.00460.08230.01250.011712.85414.20626.166
40.6-0.1694-0.00330.4635-1.04083.61330.03910.00610.0206-0.0320.0324-0.00870.0304-0.0071-0.07150.01420.00520.00610.07220.00620.009515.670.82474.361
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 101
2X-RAY DIFFRACTION1A1207
3X-RAY DIFFRACTION1A1208
4X-RAY DIFFRACTION1A1209
5X-RAY DIFFRACTION2A102 - 208
6X-RAY DIFFRACTION2A1210
7X-RAY DIFFRACTION3B0 - 120
8X-RAY DIFFRACTION3B1238
9X-RAY DIFFRACTION3B1239
10X-RAY DIFFRACTION4B121 - 236
11X-RAY DIFFRACTION4B1240
12X-RAY DIFFRACTION4B1241

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