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

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Entry
Database: PDB / ID: 4axw
TitleCRYSTAL STRUCTURE OF MOUSE CADHERIN-23 EC1-2 AND PROTOCADHERIN-15 EC1- 2, FORM I 2.2A.
Components
  • CADHERIN-23
  • PROTOCADHERIN-15
KeywordsCELL ADHESION / HEARING / DEAFNESS / CADHERIN / 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
: / Protocadherin-15 / Cadherin-23 / Protocadherin-15
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 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
DepositionJun 14, 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

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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)52,19614
Polymers51,3592
Non-polymers83712
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-35.3 kcal/mol
Surface area24020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.649, 40.468, 85.187
Angle α, β, γ (deg.)90.00, 102.92, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1215-

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) / Plasmid: PET21A / 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: H3BKS0, UniProt: Q99PJ1*PLUS

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Non-polymers , 7 types, 360 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-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-CL / CHLORIDE ION


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


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


Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.94 Å3/Da / Density % sol: 58.24 % / Description: NONE
Crystal growpH: 6.5
Details: 0.1 M MES PH 6.5, 15% W/V PEG550MME, 25% GLYCEROL, 0.2M POTASSIUM CHLORIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.138
DetectorType: E. WESTBROOK NOIR-1 MBC SYSTEM / Detector: CCD / Date: Dec 21, 2010
RadiationMonochromator: ROSENBAUM-ROCK SI(111) SAGITALLY FOCUSED / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.138 Å / Relative weight: 1
ReflectionResolution: 2.23→50 Å / Num. obs: 27442 / % possible obs: 96.2 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.65
Reflection shellResolution: 2.23→2.27 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.69 / % possible all: 87.5

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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

2whv


Resolution: 2.23→41.08 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.921 / SU B: 11.598 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.249 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.23634 1394 5.1 %RANDOM
Rwork0.17459 ---
obs0.17777 25940 95.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.536 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å20.23 Å2
2---0.18 Å20 Å2
3---0.57 Å2
Refinement stepCycle: LAST / Resolution: 2.23→41.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3501 0 40 348 3889
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223645
X-RAY DIFFRACTIONr_bond_other_d0.0010.022399
X-RAY DIFFRACTIONr_angle_refined_deg1.541.9624982
X-RAY DIFFRACTIONr_angle_other_deg0.87335874
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7875452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.56224.946184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.96915577
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8651524
X-RAY DIFFRACTIONr_chiral_restr0.1070.2572
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214088
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02705
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_it1.0751.52241
X-RAY DIFFRACTIONr_mcbond_other0.2881.5891
X-RAY DIFFRACTIONr_mcangle_it1.98323686
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.19731404
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.1814.51293
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: 2.233→2.291 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 87 -
Rwork0.25 1696 -
obs--86.3 %
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)
10.5191-0.12440.56810.1444-0.0232.765-0.0011-0.0223-0.06250.03320.11810.01760.0305-0.1176-0.1170.16570.0124-0.02470.11970.02410.035228.066-5.6843.652
21.8640.44440.7215-0.03670.21471.727-0.07340.2884-0.01220.0460.0764-0.011-0.00470.0708-0.00310.163-0.0025-0.0390.15420.01060.019210.492-2.058-1.973
30.279-0.07950.14440.2194-0.31192.6111-0.0558-0.0848-0.0901-0.0640.05140.0299-0.2172-0.07150.00440.18590.02470.00130.10460.01490.030212.4613.63426.763
40.4358-0.3338-0.06080.5289-0.70792.95110.02960.01210.0179-0.01330.0203-0.03360.0353-0.0659-0.050.13580.00760.00130.1340.00870.019715.4720.25274.731
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 DIFFRACTION3B1238
9X-RAY DIFFRACTION3B1239
10X-RAY DIFFRACTION4B121 - 236
11X-RAY DIFFRACTION4B1237

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