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- PDB-4aq8: CRYSTAL STRUCTURE OF MOUSE CADHERIN-23 EC1-2 AND PROTOCADHERIN-15... -

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Basic information

Entry
Database: PDB / ID: 4aq8
TitleCRYSTAL STRUCTURE OF MOUSE CADHERIN-23 EC1-2 AND PROTOCADHERIN-15 EC1- 2 FORM II
Components
  • CADHERIN-23
  • PROTOCADHERIN-15
KeywordsCELL ADHESION / DEAFNESS
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: 2.63 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 13, 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: CADHERIN-23
C: PROTOCADHERIN-15
D: PROTOCADHERIN-15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,27918
Polymers102,7184
Non-polymers56114
Water8,647480
1
A: CADHERIN-23
C: PROTOCADHERIN-15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6409
Polymers51,3592
Non-polymers2817
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-36.9 kcal/mol
Surface area23410 Å2
MethodPISA
2
B: CADHERIN-23
D: PROTOCADHERIN-15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6409
Polymers51,3592
Non-polymers2817
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-39 kcal/mol
Surface area23470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.749, 57.030, 156.164
Angle α, β, γ (deg.)90.00, 98.92, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CADHERIN-23 / OTOCADHERIN


Mass: 23856.436 Da / Num. of mol.: 2 / 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.: 2 / 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
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 480 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsNOTE SEQUENCE CONFLICT OF GENBANK NP_001136218.1 AND EMBL- BANK CDS AAG53891.1 WITH Q99PJ1 RESIDUES ...NOTE SEQUENCE CONFLICT OF GENBANK NP_001136218.1 AND EMBL- BANK CDS AAG53891.1 WITH Q99PJ1 RESIDUES 34-36(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: 3.5 Å3/Da / Density % sol: 65 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1 MES, 10% PEG 8000, PH 7.5

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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: Feb 23, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.63→38.57 Å / Num. obs: 41589 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.9
Reflection shellResolution: 2.62→2.69 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.6 / % possible all: 99.8

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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 4APX

4apx


Resolution: 2.63→38.57 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.916 / SU B: 20.982 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.455 / ESU R Free: 0.284 / 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
Rfree0.24273 2113 5.1 %RANDOM
Rwork0.18854 ---
obs0.19126 39350 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.622 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å2-0.32 Å2
2--0.15 Å20 Å2
3---0.55 Å2
Refinement stepCycle: LAST / Resolution: 2.63→38.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7013 0 14 480 7507
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0227177
X-RAY DIFFRACTIONr_bond_other_d0.0010.024670
X-RAY DIFFRACTIONr_angle_refined_deg1.2011.9549814
X-RAY DIFFRACTIONr_angle_other_deg0.832311436
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1655887
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.45325362
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.056151137
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1911544
X-RAY DIFFRACTIONr_chiral_restr0.0710.21134
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218069
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021389
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_it0.4581.54451
X-RAY DIFFRACTIONr_mcbond_other0.0651.51772
X-RAY DIFFRACTIONr_mcangle_it0.87927311
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.19632726
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.0644.52503
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: 2.626→2.694 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 152 -
Rwork0.346 2724 -
obs--93.8 %
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)
14.3791-2.53012.67384.0243-2.87013.549-0.5503-0.49930.3240.34370.3418-0.0064-0.2917-0.24040.20840.15690.1074-0.01080.0888-0.04620.2424-20.82635.665-67.483
24.7328-1.49770.9983.5423-1.93323.3451-0.1227-0.4536-0.21190.2277-0.0398-0.266-0.02680.20580.16260.14480.10110.00730.14350.03760.167311.2856.037-45.611
34.882-3.09762.30683.7204-1.54163.66870.0396-0.0315-0.10440.23660.0028-0.16110.0980.1177-0.04240.1247-0.0208-0.07010.01350.00950.104332.23627.011-8.29
44.0133-1.29361.06833.4374-2.25343.9945-0.03360.29360.35290.24150.33020.2736-0.5066-0.7281-0.29660.14730.20470.06040.34830.11390.1169-0.80555.242-30.381
57.4344-4.01371.223.8798-0.49091.09060.15490.0347-0.4547-0.00310.0240.21330.1978-0.0187-0.17890.16370.0832-0.01310.06120.01810.1494-16.6237.087-62.044
69.3473-4.82840.69244.6984-0.83012.2967-0.18710.02960.52410.05150.0893-0.3318-0.15590.06550.09780.05580.0144-0.03070.0231-0.00160.0958-53.71540.353-65.069
77.8685-3.79172.20244.0187-1.44563.35870.47490.7573-0.4735-0.4412-0.37450.33530.28510.0255-0.10050.16030.1196-0.09230.1592-0.10450.077818.46329.052-33.69
819.0675-2.84412.45992.11540.0141.85730.2254-0.8641-0.5967-0.0215-0.19770.15120.19690.0751-0.02770.09910.09280.05290.24550.10720.10462.20815.958-15.001
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 101
2X-RAY DIFFRACTION1A1209
3X-RAY DIFFRACTION1A1210
4X-RAY DIFFRACTION1A1211
5X-RAY DIFFRACTION2A102 - 208
6X-RAY DIFFRACTION2A1212
7X-RAY DIFFRACTION3B1 - 101
8X-RAY DIFFRACTION3B1209
9X-RAY DIFFRACTION3B1210
10X-RAY DIFFRACTION3B1212
11X-RAY DIFFRACTION4B102 - 208
12X-RAY DIFFRACTION4B1211
13X-RAY DIFFRACTION5C0 - 120
14X-RAY DIFFRACTION5C1239
15X-RAY DIFFRACTION5C1240
16X-RAY DIFFRACTION6C121 - 236
17X-RAY DIFFRACTION6C1238
18X-RAY DIFFRACTION7D0 - 120
19X-RAY DIFFRACTION7D1238
20X-RAY DIFFRACTION7D1239
21X-RAY DIFFRACTION8D121 - 236
22X-RAY DIFFRACTION8D1240

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