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- PDB-5w4t: Crystal Structure of Fish Cadherin-23 EC1-3 -

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Basic information

Entry
Database: PDB / ID: 5w4t
TitleCrystal Structure of Fish Cadherin-23 EC1-3
ComponentsCadherin 23
KeywordsCELL ADHESION / HEARING / MECHANOTRANSDUCTION / ADHESION / CALCIUM-BINDING PROTEIN.
Function / homology
Function and homology information


neuromast hair cell morphogenesis / equilibrioception / detection of mechanical stimulus involved in sensory perception / inner ear receptor cell stereocilium organization / auditory receptor cell development / detection of mechanical stimulus involved in sensory perception of sound / hair cell differentiation / cell-cell adhesion via plasma-membrane adhesion molecules / stereocilium / cell projection organization ...neuromast hair cell morphogenesis / equilibrioception / detection of mechanical stimulus involved in sensory perception / inner ear receptor cell stereocilium organization / auditory receptor cell development / detection of mechanical stimulus involved in sensory perception of sound / hair cell differentiation / cell-cell adhesion via plasma-membrane adhesion molecules / stereocilium / cell projection organization / protein localization to cilium / catenin complex / homophilic cell adhesion via plasma membrane adhesion molecules / transmembrane transporter activity / locomotory behavior / sensory perception of sound / cilium / endocytosis / membrane => GO:0016020 / cadherin binding / calcium ion binding
Similarity search - Function
Cadherin-related family member 2 -like / Cadherin-23 / Cadherins / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily ...Cadherin-related family member 2 -like / Cadherin-23 / Cadherins / 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
Cadherin-related 23 / Cadherin 23
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsDe-la-Torre, P. / 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
DepositionJun 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 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 / 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 11, 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
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_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_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)146,15534
Polymers144,7964
Non-polymers1,35930
Water11,638646
1
C: Cadherin 23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5989
Polymers36,1991
Non-polymers3998
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Cadherin 23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5989
Polymers36,1991
Non-polymers3998
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Cadherin 23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4808
Polymers36,1991
Non-polymers2817
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cadherin 23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4808
Polymers36,1991
Non-polymers2817
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)178.055, 115.548, 67.895
Angle α, β, γ (deg.)90.00, 89.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Cadherin 23 /


Mass: 36199.109 Da / Num. of mol.: 4 / Fragment: residues 32-349
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: cdh23 / Plasmid: pET21a+ / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21-RIPL / References: UniProt: Q6QQE1, UniProt: F1R7G8*PLUS
#2: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 646 / 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: 4.83 Å3/Da / Density % sol: 74.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.6 / Details: 0.1 M Tris HCl pH 8.6 6% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.65→178.05 Å / Num. obs: 80843 / % possible obs: 99.4 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.163 / Net I/σ(I): 7.1
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.685 / Mean I/σ(I) obs: 2 / Num. unique obs: 4096 / % possible all: 99.2

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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: 2WHV

2whv


Resolution: 2.65→178.05 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.902 / SU B: 15.231 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R: 0.288 / ESU R Free: 0.227 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22652 3972 4.9 %RANDOM
Rwork0.1919 ---
obs0.19361 76387 98.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.468 Å2
Baniso -1Baniso -2Baniso -3
1-3.62 Å20 Å2-0.21 Å2
2---3.04 Å2-0 Å2
3----0.58 Å2
Refinement stepCycle: 1 / Resolution: 2.65→178.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9776 0 44 646 10466
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0210129
X-RAY DIFFRACTIONr_bond_other_d0.0020.029152
X-RAY DIFFRACTIONr_angle_refined_deg1.4641.95913852
X-RAY DIFFRACTIONr_angle_other_deg0.905321307
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9551291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.07624.979478
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.806151600
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4541559
X-RAY DIFFRACTIONr_chiral_restr0.0880.21608
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02111368
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021991
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_it0.3761.2835080
X-RAY DIFFRACTIONr_mcbond_other0.3751.2825079
X-RAY DIFFRACTIONr_mcangle_it0.6911.9226351
X-RAY DIFFRACTIONr_mcangle_other0.6911.9236352
X-RAY DIFFRACTIONr_scbond_it0.3581.3595049
X-RAY DIFFRACTIONr_scbond_other0.3581.3595050
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.6392.0137486
X-RAY DIFFRACTIONr_long_range_B_refined2.45615.04210735
X-RAY DIFFRACTIONr_long_range_B_other2.45615.04710736
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.628→2.696 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 260 -
Rwork0.318 4585 -
obs--80.6 %
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)
12.19692.04970.00564.27030.34951.29560.05140.0087-0.06420.3031-0.0570.20890.0284-0.02890.00550.0360.00640.03060.1236-0.00570.034677.865629.98062.9882
26.47274.47910.18673.38110.21070.042-0.12570.2551-0.2455-0.18650.1434-0.2734-0.02150.03-0.01770.0839-0.02210.02480.2220.00210.316245.8696-5.004-0.8441
32.34272.4725-0.42036.3944-0.72621.5315-0.1297-0.0221-0.4565-0.00860.1168-0.60180.28220.130.01290.06240.02350.01150.1853-0.00020.216914.6943-44.0154.9109
41.27440.47150.32974.4407-0.74091.5727-0.09150.0851-0.0516-0.62750.16190.0527-0.10650.1241-0.07040.1835-0.01210.03160.14410.00050.021283.138938.6942-16.6409
50.7323-0.79420.07586.91751.1890.8472-0.0137-0.05960.00010.0598-0.01050.12760.0482-0.01980.02420.0533-0.01160.02070.13240.00420.011684.9708-9.0354-17.7838
61.1965-0.0503-0.17415.90221.28472.82590.04980.08820.0024-0.0583-0.07010.45120.0136-0.29340.02020.11850.02290.00280.15620.02560.041182.5428-56.5511-33.4326
72.19682.60770.00555.5046-0.21451.03170.0574-0.02810.05360.3166-0.0963-0.1769-0.03260.03160.03880.0338-0.0051-0.0270.12580.00690.027511.1749-11.97593.0018
86.39014.3403-0.08633.4602-0.05370.0068-0.07440.23980.2568-0.20260.0680.32010.0026-0.03260.00640.0708-0.0178-0.02410.2275-0.00620.310343.145523.0126-0.8536
92.41852.28220.32836.22980.48291.5617-0.1321-0.03090.4381-0.0550.12270.5123-0.2465-0.15610.00940.0610.0237-0.0030.1790.010.215874.327261.99434.9197
100.89690.2897-0.08685.80660.65421.354-0.0350.03670.0314-0.55230.07750.04470.0946-0.1212-0.04250.1533-0.0056-0.03250.1550.00320.00915.8159-20.6723-16.6322
110.8869-0.98560.07676.3446-0.95770.8009-0.0078-0.0634-0.02310.075-0.0277-0.111-0.06050.01180.03540.0445-0.0144-0.00330.1236-0.00840.0064.008227.0225-17.7732
121.1782-0.36630.47135.6365-1.45143.10070.05240.09960.0171-0.061-0.0856-0.5436-0.05260.28460.03320.11250.0150.01260.1579-0.02610.06166.42774.5287-33.4288
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C0 - 100
2X-RAY DIFFRACTION1C401 - 403
3X-RAY DIFFRACTION2C101 - 204
4X-RAY DIFFRACTION2C404 - 405
5X-RAY DIFFRACTION3C205 - 316
6X-RAY DIFFRACTION3C407
7X-RAY DIFFRACTION4D0 - 100
8X-RAY DIFFRACTION4D405 - 406
9X-RAY DIFFRACTION4D407
10X-RAY DIFFRACTION5D101 - 204
11X-RAY DIFFRACTION5D403 - 404
12X-RAY DIFFRACTION5D401
13X-RAY DIFFRACTION6D205 - 316
14X-RAY DIFFRACTION6D402
15X-RAY DIFFRACTION7A0 - 100
16X-RAY DIFFRACTION7A401 - 403
17X-RAY DIFFRACTION8A101 - 204
18X-RAY DIFFRACTION8A404 - 406
19X-RAY DIFFRACTION9A205 - 316
20X-RAY DIFFRACTION9A407
21X-RAY DIFFRACTION10B0 - 100
22X-RAY DIFFRACTION10B405 - 406
23X-RAY DIFFRACTION10B407
24X-RAY DIFFRACTION11B101 - 204
25X-RAY DIFFRACTION11B401
26X-RAY DIFFRACTION11B403 - 404
27X-RAY DIFFRACTION12B205 - 316
28X-RAY DIFFRACTION12B402

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