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- PDB-5tfl: Crystal Structure of Mouse Cadherin-23 EC7+8 -

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Basic information

Entry
Database: PDB / ID: 5tfl
TitleCrystal Structure of Mouse Cadherin-23 EC7+8
ComponentsCadherin-23
KeywordsCELL ADHESION / hearing / mechanotransduction / adhesion / calcium-binding protein
Function / homology
Function and homology information


cochlear hair cell ribbon synapse / kinocilium / equilibrioception / sensory perception of light stimulus / stereocilium tip / inner ear receptor cell stereocilium organization / photoreceptor ribbon synapse / inner ear auditory receptor cell differentiation / cell-cell adhesion via plasma-membrane adhesion molecules / stereocilium ...cochlear hair cell ribbon synapse / kinocilium / equilibrioception / sensory perception of light stimulus / stereocilium tip / inner ear receptor cell stereocilium organization / photoreceptor ribbon synapse / inner ear auditory receptor cell differentiation / cell-cell adhesion via plasma-membrane adhesion molecules / stereocilium / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / photoreceptor cell maintenance / catenin complex / auditory receptor cell stereocilium organization / inner ear morphogenesis / cochlea development / homophilic cell adhesion via plasma membrane adhesion molecules / inner ear development / regulation of cytosolic calcium ion concentration / photoreceptor inner segment / locomotory behavior / sensory perception of sound / calcium ion transport / apical part of cell / cell adhesion / cadherin binding / centrosome / synapse / calcium ion binding / plasma membrane
Similarity search - Function
Cadherins / Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily / Immunoglobulin-like ...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
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.56 Å
AuthorsJaiganesh, A. / Sotomayor, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)DC012534 United States
CitationJournal: Structure / Year: 2018
Title: Zooming in on Cadherin-23: Structural Diversity and Potential Mechanisms of Inherited Deafness.
Authors: Jaiganesh, A. / De-la-Torre, P. / Patel, A.A. / Termine, D.J. / Velez-Cortes, F. / Chen, C. / Sotomayor, M.
History
DepositionSep 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 19, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / entity_src_gen
Item: _citation.journal_volume / _citation.page_first / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_label_atom_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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: Cadherin-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2638
Polymers51,0572
Non-polymers2066
Water543
1
A: Cadherin-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6324
Polymers25,5291
Non-polymers1033
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cadherin-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6324
Polymers25,5291
Non-polymers1033
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)185.809, 185.809, 185.809
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / Auth seq-ID: 645 - 860 / Label seq-ID: 4 - 219

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Cadherin-23 / / Otocadherin


Mass: 25528.568 Da / Num. of mol.: 2 / Fragment: Cadherin domains 7-8, residues 666-886
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdh23 / Plasmid: pET-21 a / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 RIPL / References: UniProt: Q99PF4
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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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: 5.24 Å3/Da / Density % sol: 76.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.7
Details: 0.1 M Sodium Acetate pH 4.7, 1.9 M Sodium Chloride, 30% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Oxford Cryo-Jet crystal cryocoolers
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97921 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 3.56→131.39 Å / Num. obs: 13716 / % possible obs: 100 % / Redundancy: 35.5 % / Biso Wilson estimate: 87.2 Å2 / Rmerge(I) obs: 0.363 / Net I/σ(I): 20
Reflection shellResolution: 3.56→3.61 Å / Redundancy: 23.7 % / Rmerge(I) obs: 1.587 / Mean I/σ(I) obs: 2.5 / CC1/2: 0.748 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Cadherin-23 (5I8D)

5i8d


Resolution: 3.56→131.39 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.921 / SU B: 41.635 / SU ML: 0.266 / Cross valid method: THROUGHOUT / ESU R: 1.781 / ESU R Free: 0.395 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22143 666 4.9 %RANDOM
Rwork0.19238 ---
obs0.19385 12849 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 90.48 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 3.56→131.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3084 0 6 3 3093
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.023143
X-RAY DIFFRACTIONr_bond_other_d0.0010.023010
X-RAY DIFFRACTIONr_angle_refined_deg1.3651.9694291
X-RAY DIFFRACTIONr_angle_other_deg0.78436942
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.0225394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.924.762126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.85315513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7031516
X-RAY DIFFRACTIONr_chiral_restr0.0840.2531
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213454
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02642
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_it2.7396.7561594
X-RAY DIFFRACTIONr_mcbond_other2.736.7561593
X-RAY DIFFRACTIONr_mcangle_it4.47910.1361982
X-RAY DIFFRACTIONr_mcangle_other4.47810.1371983
X-RAY DIFFRACTIONr_scbond_it2.977.0441549
X-RAY DIFFRACTIONr_scbond_other2.9697.0451550
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.90410.4382310
X-RAY DIFFRACTIONr_long_range_B_refined7.0054128
X-RAY DIFFRACTIONr_long_range_B_other7.0044129
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 11374 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.562→3.655 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 42 -
Rwork0.312 928 -
obs--100 %
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)
11.54010.2568-1.64293.5928-0.06977.82530.00350.13170.022-0.3547-0.0049-0.1289-0.20220.00060.00140.05-0.0038-0.02080.119-0.00940.1297-15.56764.9862-37.5772
22.04170.2527-1.45742.7646-0.678.49650.0365-0.22470.16550.35190.09380.0992-0.30150.0243-0.13030.0560.00420.03760.054-0.06660.1376-28.06761.60448.792
37.72930.4348-2.72472.09220.03564.54-0.09180.2766-0.0926-0.0167-0.00070.52240.2493-0.54810.09250.18630.05860.02310.1839-0.08070.2569-61.70339.9078.5776
46.36230.8055-4.93941.0371-2.12966.26210.09490.08950.29990.1742-0.0299-0.0619-0.375-0.0337-0.0650.35660.01920.03470.0584-0.06590.1408-22.953522.0383-14.6046
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A645 - 749
2X-RAY DIFFRACTION1A901 - 902
3X-RAY DIFFRACTION2A750 - 861
4X-RAY DIFFRACTION2A903
5X-RAY DIFFRACTION3B645 - 749
6X-RAY DIFFRACTION3B901 - 902
7X-RAY DIFFRACTION4B750 - 860
8X-RAY DIFFRACTION4B903

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