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- PDB-5tpk: Crystal Structure of Mouse Protocadherin-15 EC7-8 V875A -

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Basic information

Entry
Database: PDB / ID: 5tpk
TitleCrystal Structure of Mouse Protocadherin-15 EC7-8 V875A
ComponentsProtocadherin-15
KeywordsCELL ADHESION / hearing / mechanotransduction / adhesion / calcium-binding protein
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
Extracellular cadherin domain / Protocadherin-15 / Extracellular Cadherin domain / Cadherins / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like ...Extracellular cadherin domain / Protocadherin-15 / Extracellular Cadherin domain / 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
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChen, C. / Sotomayor, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)R00 DC012534 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
DepositionOct 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2017Provider: 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 ...citation / citation_author / pdbx_struct_conn_angle / 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 / _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_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_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.3Oct 4, 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)24,3995
Polymers24,2391
Non-polymers1604
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-27 kcal/mol
Surface area11330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.796, 22.990, 70.741
Angle α, β, γ (deg.)90.00, 97.27, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protocadherin-15 /


Mass: 24239.008 Da / Num. of mol.: 1 / Fragment: Extracellular domain residues 715-924 / Mutation: V875A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pcdh15 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q99PJ1
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.26 Å3/Da / Density % sol: 45.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.2M AMMONIUM CHLORIDE, 10% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Oxford Cryo-Jet crystal cryocoolers
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→70.17 Å / Num. obs: 15280 / % possible obs: 96.5 % / Redundancy: 3.1 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 23.12
Reflection shellResolution: 2→2.03 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.141 / Mean I/σ(I) obs: 5.4 / % possible all: 82.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XHZ

4xhz


Resolution: 2→70.17 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 7.663 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.165 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22897 711 4.8 %RANDOM
Rwork0.18995 ---
obs0.19177 14026 96.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.26 Å2
Baniso -1Baniso -2Baniso -3
1--1.95 Å2-0 Å2-1.37 Å2
2--0.09 Å2-0 Å2
3---2.13 Å2
Refinement stepCycle: 1 / Resolution: 2→70.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1572 0 4 121 1697
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191624
X-RAY DIFFRACTIONr_bond_other_d0.0020.021518
X-RAY DIFFRACTIONr_angle_refined_deg1.3151.9492223
X-RAY DIFFRACTIONr_angle_other_deg0.8833483
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3595204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.74324.30479
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.30215245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.062159
X-RAY DIFFRACTIONr_chiral_restr0.0780.2260
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211866
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02379
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_it0.9162.529810
X-RAY DIFFRACTIONr_mcbond_other0.9172.527809
X-RAY DIFFRACTIONr_mcangle_it1.6033.7771010
X-RAY DIFFRACTIONr_mcangle_other1.6023.7781011
X-RAY DIFFRACTIONr_scbond_it0.8482.669814
X-RAY DIFFRACTIONr_scbond_other0.8482.667812
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4333.9631211
X-RAY DIFFRACTIONr_long_range_B_refined5.00630.4061705
X-RAY DIFFRACTIONr_long_range_B_other4.90329.9661682
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 48 -
Rwork0.211 877 -
obs--81.93 %
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)
13.5490.1162-0.02442.45690.112.9710.02270.0865-0.026-0.35420.05020.12470.0746-0.3883-0.07290.0559-0.0227-0.01640.0943-0.00530.0212-30.6925-15.9745-10.603
26.28920.01832.27521.76050.13974.2247-0.0684-0.34130.15290.2009-0.04380.0574-0.0679-0.24560.11220.107-0.00360.03380.024-0.01320.04847.2615-9.595619.4973
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A691 - 791
2X-RAY DIFFRACTION1A1001 - 1002
3X-RAY DIFFRACTION2A792 - 897
4X-RAY DIFFRACTION2A1003

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