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- PDB-5vh2: Crystal Structure of Mouse Cadherin-23 EC12-13 with Engineered Mu... -

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Basic information

Entry
Database: PDB / ID: 5vh2
TitleCrystal Structure of Mouse Cadherin-23 EC12-13 with Engineered Mutation S1339D
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 / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsTermine, D.J. / Jaiganesh, A. / Sotomayor, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)R01-DC015271 United States
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)R00-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
DepositionApr 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.2Aug 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 1.3Sep 19, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.4Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 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_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_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
C: Cadherin-23
D: Cadherin-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,54918
Polymers97,0564
Non-polymers49314
Water0
1
A: Cadherin-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4075
Polymers24,2641
Non-polymers1434
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cadherin-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4075
Polymers24,2641
Non-polymers1434
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cadherin-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3674
Polymers24,2641
Non-polymers1033
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cadherin-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3674
Polymers24,2641
Non-polymers1033
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.738, 47.210, 113.044
Angle α, β, γ (deg.)89.95, 90.02, 115.76
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNVALVALAA1179 - 13852 - 208
21ASNASNVALVALBB1179 - 13852 - 208
12ASPASPASPASPAA1180 - 13873 - 210
22ASPASPASPASPCC1180 - 13873 - 210
13ASPASPLEULEUAA1180 - 13863 - 209
23ASPASPLEULEUDD1180 - 13863 - 209
14ASPASPLEULEUBB1180 - 13863 - 209
24ASPASPLEULEUCC1180 - 13863 - 209
15ASPASPVALVALBB1180 - 13853 - 208
25ASPASPVALVALDD1180 - 13853 - 208
16ASPASPGLUGLUCC1180 - 13883 - 211
26ASPASPGLUGLUDD1180 - 13883 - 211

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Cadherin-23 / / Otocadherin


Mass: 24263.949 Da / Num. of mol.: 4 / Fragment: residues 1202-1412 / Mutation: S1339D
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.: 10 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na

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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: 2.19 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.05 M Tris pH 8.5 0.5 M NaCl 22% PEG 4000 / PH range: 8.1-8.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.542 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jul 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.564
11-h,-k,l20.436
ReflectionResolution: 2.84→50 Å / Num. obs: 19387 / % possible obs: 93.9 % / Redundancy: 1.6 % / Rmerge(I) obs: 0.165 / Net I/σ(I): 4.3269
Reflection shellResolution: 2.84→2.89 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 2.05 / % possible all: 89.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WHV, 5TFK

2whv

5tfk


Resolution: 2.84→33.99 Å / Cor.coef. Fo:Fc: 0.831 / Cor.coef. Fo:Fc free: 0.779 / SU B: 28.631 / SU ML: 0.26 / Cross valid method: FREE R-VALUE / ESU R Free: 0.104 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1084 6 %RANDOM
Rwork0.238 ---
obs0.24 17103 92.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å2-6.49 Å20.1 Å2
2---11.33 Å27.99 Å2
3---11.62 Å2
Refinement stepCycle: LAST / Resolution: 2.84→33.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6376 0 14 0 6390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.026466
X-RAY DIFFRACTIONr_bond_other_d0.0010.025952
X-RAY DIFFRACTIONr_angle_refined_deg1.4751.9618792
X-RAY DIFFRACTIONr_angle_other_deg0.806313774
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5795822
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.13825.497302
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.534151060
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7661528
X-RAY DIFFRACTIONr_chiral_restr0.0930.21052
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027278
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021270
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_it00.13306
X-RAY DIFFRACTIONr_mcbond_other00.13305
X-RAY DIFFRACTIONr_mcangle_it00.154122
X-RAY DIFFRACTIONr_mcangle_other00.154123
X-RAY DIFFRACTIONr_scbond_it00.13160
X-RAY DIFFRACTIONr_scbond_other00.13158
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other00.154670
X-RAY DIFFRACTIONr_long_range_B_refined01.90725817
X-RAY DIFFRACTIONr_long_range_B_other01.90725816
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)
11A125860.06
12B125860.06
21A120020.07
22C120020.07
31A123280.08
32D123280.08
41B119580.08
42C119580.08
51B122320.08
52D122320.08
61C121040.08
62D121040.08
LS refinement shellResolution: 2.82→2.89 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 86 -
Rwork0.274 1012 -
obs--75.36 %
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)
10.7479-0.5917-0.32611.20670.67320.3758-0.08140.128-0.07360.01090.1379-0.08440.0080.0842-0.05650.19280.0131-0.06020.2216-0.04360.27882.763163.696-10.73
20.7361-1.19480.5673.0901-0.52930.70310.054-0.0711-0.09040.0185-0.0976-0.00040.1167-0.02480.04350.17560.0060.01160.2783-0.00230.40363.091124.50213.066
30.88870.5116-0.05880.5283-0.10890.02860.04-0.0318-0.0099-0.1409-0.0688-0.06470.05050.00940.02880.13380.0087-0.01030.1715-0.05930.332272.79136.99845.804
40.925-1.07010.15461.2828-0.51612.9017-0.1306-0.18690.18620.20070.2032-0.1883-0.04940.1158-0.07270.2184-0.03840.01840.2649-0.06050.353992.301176.02769.52
50.5512-0.7459-0.46691.05340.5260.6802-0.0682-0.03580.10690.15550.0997-0.1814-0.07-0.0324-0.03150.11290.0404-0.00230.1177-0.07720.345598.633147.68958.141
60.25260.53210.28282.64590.92461.8309-0.06640.1624-0.1376-0.16980.1897-0.08680.29350.1087-0.12330.15930.00780.01570.2011-0.06860.295578.672108.85735.475
70.5457-0.2488-0.30331.246-1.56012.7185-0.17970.0855-0.09860.08520.23990.1160.111-0.4365-0.06010.25410.00630.01080.3027-0.07690.273876.98109.8911.959
80.7138-0.52480.30380.5568-0.0570.3042-0.04390.00050.0539-0.0423-0.03380.0749-0.04080.01740.07780.28730.04470.0210.3302-0.04440.302197.428149.346-21.038
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1179 - 1284
2X-RAY DIFFRACTION1A1401 - 1402
3X-RAY DIFFRACTION2A1285 - 1387
4X-RAY DIFFRACTION2A1403
5X-RAY DIFFRACTION3B1179 - 1284
6X-RAY DIFFRACTION3B1401 - 1403
7X-RAY DIFFRACTION4B1285 - 1386
8X-RAY DIFFRACTION4B1404
9X-RAY DIFFRACTION5C1180 - 1284
10X-RAY DIFFRACTION5C1401 - 1402
11X-RAY DIFFRACTION6C1285 - 1388
12X-RAY DIFFRACTION6C1403
13X-RAY DIFFRACTION7D1180 - 1284
14X-RAY DIFFRACTION7D1401 - 1402
15X-RAY DIFFRACTION8D1285 - 1388
16X-RAY DIFFRACTION8D1403

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