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- PDB-5vvm: Crystal structure of human CDH23 EC21-23 -

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Basic information

Entry
Database: PDB / ID: 5vvm
TitleCrystal structure of human CDH23 EC21-23
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 / photoreceptor ribbon synapse / cell-cell adhesion via plasma-membrane adhesion molecules / stereocilium / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / photoreceptor cell maintenance ...cochlear hair cell ribbon synapse / kinocilium / equilibrioception / sensory perception of light stimulus / stereocilium tip / photoreceptor ribbon synapse / 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 / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / response to stimulus / cochlea development / homophilic cell adhesion via plasma membrane adhesion molecules / regulation of cytosolic calcium ion concentration / photoreceptor inner segment / visual perception / locomotory behavior / sensory perception of sound / calcium ion transport / cadherin binding / centrosome / calcium ion binding / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.54 Å
AuthorsPatel, A. / 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)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 19, 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 / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _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_seq_id / _struct_conn.ptnr2_label_asym_id
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)76,26514
Polymers75,7842
Non-polymers48112
Water0
1
A: Cadherin-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1337
Polymers37,8921
Non-polymers2406
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cadherin-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1337
Polymers37,8921
Non-polymers2406
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.714, 166.806, 47.930
Angle α, β, γ (deg.)90.00, 102.53, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 0 / Auth seq-ID: 2153 - 2473 / Label seq-ID: 9 - 329

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

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Components

#1: Protein Cadherin-23 / / Otocadherin


Mass: 37892.051 Da / Num. of mol.: 2 / Fragment: residues 2169-2505
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDH23, KIAA1774, KIAA1812, UNQ1894/PRO4340 / Plasmid: pET21-a+ / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21-RIPL / References: UniProt: Q9H251
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / 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: 3.01 Å3/Da / Density % sol: 59.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.05 M TRIS pH 8.5 0.5 M NaCl 10% PEG-4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Aug 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.54→94.08 Å / Num. obs: 10856 / % possible obs: 99.4 % / Redundancy: 2.9 % / Biso Wilson estimate: 68 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 5.95
Reflection shellResolution: 3.54→3.61 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 2.2 / % possible all: 99.6

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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: 5I8D, 5UZ8

5i8d

5uz8


Resolution: 3.54→94.08 Å / Cor.coef. Fo:Fc: 0.804 / Cor.coef. Fo:Fc free: 0.727 / SU B: 109.744 / SU ML: 0.7 / Cross valid method: THROUGHOUT / ESU R Free: 0.851 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.346 577 5.4 %RANDOM
Rwork0.303 ---
obs0.305 10174 98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 66.92 Å2
Baniso -1Baniso -2Baniso -3
1-10.6 Å20 Å23.71 Å2
2---10.8 Å20 Å2
3----1.32 Å2
Refinement stepCycle: LAST / Resolution: 3.54→94.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4658 0 12 0 4670
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.024737
X-RAY DIFFRACTIONr_bond_other_d0.0020.024338
X-RAY DIFFRACTIONr_angle_refined_deg1.3491.9696488
X-RAY DIFFRACTIONr_angle_other_deg0.86310096
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1375603
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.4526.186215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.89415733
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5511519
X-RAY DIFFRACTIONr_chiral_restr0.0790.2790
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215280
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02819
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_it00.12439
X-RAY DIFFRACTIONr_mcbond_other00.12438
X-RAY DIFFRACTIONr_mcangle_it00.153032
X-RAY DIFFRACTIONr_mcangle_other00.153033
X-RAY DIFFRACTIONr_scbond_it00.12298
X-RAY DIFFRACTIONr_scbond_other00.12299
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other00.153456
X-RAY DIFFRACTIONr_long_range_B_refined0.0821.91518685
X-RAY DIFFRACTIONr_long_range_B_other0.0811.91518684
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 16460 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.54→3.63 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.522 37 -
Rwork0.463 662 -
obs--86.08 %
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)
10.92010.8061-0.022411.3105-0.17690.883-0.11440.00630.106-0.8407-0.0293-0.318-0.00750.20290.14370.09550.0087-0.08561.0251-0.01090.3789000
20.99530.1794-0.04367.8377-0.52691.2655-0.0196-0.0436-0.1760.5031-0.012-0.0760.04250.16220.03170.0524-0.0017-0.06840.9681-0.03270.3825-42.8812.028-2.895
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2147 - 2481
2X-RAY DIFFRACTION2B2147 - 2481

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