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- PDB-6n22: Crystal structure of mouse Protocadherin-15 EC1-2 BAP -

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Basic information

Entry
Database: PDB / ID: 6n22
TitleCrystal structure of mouse Protocadherin-15 EC1-2 BAP
ComponentsProtocadherin-15
KeywordsCELL ADHESION / Mechanotransduction / calcium binding protein / hearing / stereocilia / tip link
Function / homology
Function and homology information


detection of mechanical stimulus involved in equilibrioception / equilibrioception / sensory perception of light stimulus / inner ear receptor cell stereocilium organization / righting reflex / detection of mechanical stimulus involved in sensory perception of sound / inner ear auditory receptor cell differentiation / stereocilium / non-motile cilium assembly / photoreceptor cell maintenance ...detection of mechanical stimulus involved in equilibrioception / equilibrioception / sensory perception of light stimulus / inner ear receptor cell stereocilium organization / righting reflex / detection of mechanical stimulus involved in sensory perception of sound / inner ear auditory receptor cell differentiation / stereocilium / non-motile cilium assembly / photoreceptor cell maintenance / adult walking behavior / auditory receptor cell stereocilium organization / startle response / homophilic cell adhesion via plasma membrane adhesion molecules / inner ear development / photoreceptor outer segment / visual perception / locomotory behavior / actin filament organization / morphogenesis of an epithelium / sensory perception of sound / multicellular organism growth / response to calcium ion / cell adhesion / synapse / calcium ion binding / extracellular space / membrane / plasma membrane / cytoplasm
Similarity search - Function
Immunoglobulin-like - #3430 / Extracellular cadherin domain / Protocadherin-15 / Extracellular Cadherin domain / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like ...Immunoglobulin-like - #3430 / Extracellular cadherin domain / Protocadherin-15 / Extracellular Cadherin domain / 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: 2.4 Å
AuthorsNarui, Y. / Sotomayor, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)R01 DC015271 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Structural determinants of protocadherin-15 mechanics and function in hearing and balance perception.
Authors: Choudhary, D. / Narui, Y. / Neel, B.L. / Wimalasena, L.N. / Klanseck, C.F. / De-la-Torre, P. / Chen, C. / Araya-Secchi, R. / Tamilselvan, E. / Sotomayor, M.
History
DepositionNov 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 7, 2020Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.3Oct 21, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protocadherin-15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9194
Polymers29,7991
Non-polymers1203
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The monomeric state was also verified by analytical ultracentrifugation.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-14 kcal/mol
Surface area13000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.616, 99.616, 58.560
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein Protocadherin-15 /


Mass: 29798.994 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Protein includes biotin acceptor peptide (BAP) and expression tag GLNDIFEAQKIEWHELEHHHHHH
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pcdh15 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / References: UniProt: Q99PJ1
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.88 Å3/Da / Density % sol: 57.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.02 M calcium chloride, 0.1 M sodium acetate, 30% (v/v) MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 13043 / % possible obs: 100 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.047 / Net I/σ(I): 17.833
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.802 / Num. unique obs: 646 / Rpim(I) all: 0.311 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4APX

4apx


Resolution: 2.4→49.86 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.916 / SU B: 14.1 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.262 / ESU R Free: 0.223 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23289 640 4.9 %RANDOM
Rwork0.17048 ---
obs0.17326 12383 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.48 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20.59 Å20 Å2
2--1.18 Å2-0 Å2
3----3.83 Å2
Refinement stepCycle: 1 / Resolution: 2.4→49.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1826 0 3 49 1878
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131879
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171722
X-RAY DIFFRACTIONr_angle_refined_deg1.7061.6582567
X-RAY DIFFRACTIONr_angle_other_deg1.251.5794000
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6175234
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.24822.661109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.23615316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7491515
X-RAY DIFFRACTIONr_chiral_restr0.0770.2257
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022116
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02377
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_it2.3943.722927
X-RAY DIFFRACTIONr_mcbond_other2.393.719926
X-RAY DIFFRACTIONr_mcangle_it3.8635.5681158
X-RAY DIFFRACTIONr_mcangle_other3.8625.5711159
X-RAY DIFFRACTIONr_scbond_it3.4284.295952
X-RAY DIFFRACTIONr_scbond_other3.4174.287950
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6966.2541407
X-RAY DIFFRACTIONr_long_range_B_refined7.47143.2661931
X-RAY DIFFRACTIONr_long_range_B_other7.47443.271930
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.404→2.467 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 67 -
Rwork0.23 887 -
obs--99.38 %
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)
10.4609-0.63640.17521.7608-1.51942.05980.0036-0.0011-0.0262-0.0343-0.1143-0.0003-0.02890.11110.11080.04740.0099-0.04430.0382-0.01150.0492-1.1583-46.064919.3213
20.7414-0.82871.04391.5044-1.20331.963-0.0541-0.0833-0.0224-0.02970.1918-0.0415-0.072-0.0522-0.13770.04270.00010.00590.0471-0.01850.0461-18.8646-11.3674-10.1726
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 119
2X-RAY DIFFRACTION1A1001 - 1002
3X-RAY DIFFRACTION2A120 - 236
4X-RAY DIFFRACTION2A1003

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