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- PDB-5vt8: Crystal Structure of Mouse Cadherin-23 EC24-25 -

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Basic information

Entry
Database: PDB / ID: 5vt8
TitleCrystal Structure of Mouse Cadherin-23 EC24-25
ComponentsCadherin-23
KeywordsCELL ADHESION / HEARING / MECHANOTRANSDUCTION / ADHESION / CALCIUM-BINDING PROTEIN
Function / homology
Function and homology information


equilibrioception / sensory perception of light stimulus / cochlear hair cell ribbon synapse / stereocilium tip / inner ear receptor cell stereocilium organization / photoreceptor ribbon synapse / kinocilium / inner ear auditory receptor cell differentiation / calcium-dependent cell-cell adhesion / stereocilium ...equilibrioception / sensory perception of light stimulus / cochlear hair cell ribbon synapse / stereocilium tip / inner ear receptor cell stereocilium organization / photoreceptor ribbon synapse / kinocilium / inner ear auditory receptor cell differentiation / calcium-dependent cell-cell adhesion / stereocilium / photoreceptor cell maintenance / auditory receptor cell stereocilium organization / inner ear morphogenesis / homophilic cell-cell adhesion / inner ear development / cochlea development / regulation of cytosolic calcium ion concentration / photoreceptor inner segment / locomotory behavior / sensory perception of sound / calcium ion transport / cell adhesion / calcium ion binding / synapse / centrosome / plasma membrane
Similarity search - Function
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
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.92 Å
AuthorsJaiganesh, A. / Sotomayor, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)DC012534 United States
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)DC015271 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
DepositionMay 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2018Provider: 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 / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Mar 16, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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

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Assembly

Deposited unit
B: Cadherin-23
A: Cadherin-23
C: Cadherin-23
D: Cadherin-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,63913
Polymers99,2784
Non-polymers3619
Water00
1
B: Cadherin-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9003
Polymers24,8201
Non-polymers802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Cadherin-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9003
Polymers24,8201
Non-polymers802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cadherin-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9003
Polymers24,8201
Non-polymers802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cadherin-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9404
Polymers24,8201
Non-polymers1203
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
D: Cadherin-23
hetero molecules

B: Cadherin-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8407
Polymers49,6392
Non-polymers2005
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area3210 Å2
ΔGint-53 kcal/mol
Surface area20700 Å2
MethodPISA
6
A: Cadherin-23
hetero molecules

C: Cadherin-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7996
Polymers49,6392
Non-polymers1604
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area2800 Å2
ΔGint-39 kcal/mol
Surface area21710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.613, 99.387, 157.425
Angle α, β, γ (deg.)90.00, 90.07, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12B
22C
13B
23D
14A
24C
15A
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEBA2481 - 26922 - 213
21ILEILEAB2481 - 26922 - 213
12ILEILEBA2481 - 26922 - 213
22ILEILECC2481 - 26922 - 213
13ALAALABA2481 - 26882 - 209
23ALAALADD2481 - 26882 - 209
14ILEILEAB2481 - 26922 - 213
24ILEILECC2481 - 26922 - 213
15ALAALAAB2481 - 26882 - 209
25ALAALADD2481 - 26882 - 209
16ALAALACC2481 - 26882 - 209
26ALAALADD2481 - 26882 - 209

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Cadherin-23 / Otocadherin


Mass: 24819.582 Da / Num. of mol.: 4 / Fragment: residues 2504-2715
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdh23 / Plasmid: pET-21a+ / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21-RIPL / References: UniProt: Q99PF4
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca

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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: 2.18 Å3/Da / Density % sol: 43.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.9 / Details: 0.1 M TRIS pH 7.9 10% PEG 8000 / PH range: 7.9-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.499
11-h,-k,l20.501
ReflectionResolution: 2.92→50 Å / Num. obs: 18772 / % possible obs: 94.3 % / Redundancy: 1.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.097 / Rrim(I) all: 0.145 / Χ2: 1.019 / Net I/σ(I): 6.37
Reflection shellResolution: 2.92→2.97 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 1.76 / Num. unique obs: 854 / CC1/2: 0.769 / Rpim(I) all: 0.377 / Rrim(I) all: 0.568 / Χ2: 0.99 / % possible all: 93.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UZ8, 2EE0

5uz8

2ee0


Resolution: 2.92→47.39 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.9 / SU B: 23.62 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R Free: 0.088 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22142 867 4.9 %RANDOM
Rwork0.20849 ---
obs0.20915 16819 93.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 47.839 Å2
Baniso -1Baniso -2Baniso -3
1-35.38 Å20 Å20.23 Å2
2---20.08 Å20 Å2
3----15.3 Å2
Refinement stepCycle: 1 / Resolution: 2.92→47.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6432 0 9 0 6441
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.026567
X-RAY DIFFRACTIONr_bond_other_d0.0010.025903
X-RAY DIFFRACTIONr_angle_refined_deg1.4381.9718961
X-RAY DIFFRACTIONr_angle_other_deg1.26313758
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3615812
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.86225.144313
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.681151052
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5151538
X-RAY DIFFRACTIONr_chiral_restr0.0860.21028
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217294
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021244
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_it0.5250.4823275
X-RAY DIFFRACTIONr_mcbond_other0.5240.4823274
X-RAY DIFFRACTIONr_mcangle_it0.7790.7224078
X-RAY DIFFRACTIONr_mcangle_other0.7790.7224079
X-RAY DIFFRACTIONr_scbond_it0.4860.4883292
X-RAY DIFFRACTIONr_scbond_other0.4850.4893293
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.7040.7284884
X-RAY DIFFRACTIONr_long_range_B_refined1.1279.27126203
X-RAY DIFFRACTIONr_long_range_B_other1.1279.2726200
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11B123380.13
12A123380.13
21B113960.18
22C113960.18
31B108440.17
32D108440.17
41A113720.18
42C113720.18
51A107860.16
52D107860.16
61C107580.16
62D107580.16
LS refinement shellResolution: 2.905→2.981 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 49 -
Rwork0.245 1159 -
obs--85.73 %
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)
11.84020.2184-0.75265.6309-4.13453.24010.2427-0.1068-0.18531.5790.12970.6198-1.2698-0.0969-0.37250.7760.03950.11360.2917-0.07080.3159-1.7496.39740.758
20.25090.17470.29826.6006-2.8062.4416-0.22110.0970.08590.28360.0305-0.5064-0.2291-0.00610.19050.3785-0.0636-0.0780.30740.02220.36489.30642.5959.048
32.8008-0.75162.32923.3679-3.99555.57120.25250.04160.0752-1.12810.20890.5031.2194-0.2765-0.46140.7670.0536-0.14540.266-0.03440.3611-1.92141.10537.713
41.0238-1.15020.64286.1132-2.90222.8251-0.158-0.0411-0.1024-0.3175-0.2144-0.5820.22190.32190.37240.29380.01440.00640.2760.02730.32359.4454.81369.681
51.8445-0.0192-0.29783.3913-1.01471.14110.1477-0.250.04650.58240.02310.1587-0.23220.0923-0.17070.4461-0.05360.00720.3387-0.06060.342624.73828.96570.374
60.7616-1.6903-0.27626.1318-0.84421.81990.05120.21390.2301-0.06480.29650.8394-0.315-0.6213-0.34770.1472-0.0449-0.09030.50370.35411.27038.74962.55736.953
71.6029-0.43430.57574.2313-1.24411.01150.11060.14050.0289-0.04170.07170.292-0.0682-0.0315-0.18230.3476-0.00520.01230.2304-0.00090.286124.89417.9539.145
80.8803-0.15650.15822.8084-2.28632.0507-0.0572-0.4765-1.22910.11550.27080.3594-0.31-0.3471-0.21360.31780.0412-0.00230.56590.51421.8359.536-13.38240.758
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B2481 - 2582
2X-RAY DIFFRACTION1B2801
3X-RAY DIFFRACTION2B2583 - 2692
4X-RAY DIFFRACTION2B2802
5X-RAY DIFFRACTION3A2481 - 2582
6X-RAY DIFFRACTION3A2801
7X-RAY DIFFRACTION4A2583 - 2692
8X-RAY DIFFRACTION4A2802
9X-RAY DIFFRACTION5C2481 - 2582
10X-RAY DIFFRACTION5C2801
11X-RAY DIFFRACTION6C2583 - 2692
12X-RAY DIFFRACTION6C2802
13X-RAY DIFFRACTION7D2481 - 2582
14X-RAY DIFFRACTION7D2801
15X-RAY DIFFRACTION7D2803
16X-RAY DIFFRACTION8D2583 - 2688
17X-RAY DIFFRACTION8D2802

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