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- PDB-5w1d: Crystal Structure of Mouse Protocadherin-15 EC4-7 -

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Basic information

Entry
Database: PDB / ID: 5w1d
TitleCrystal Structure of Mouse Protocadherin-15 EC4-7
ComponentsProtocadherin-15
KeywordsCELL ADHESION / Hearing / Mechanotransduction / Adhesion / Calcium-binding protein
Function / homology
Function and homology information


detection of mechanical stimulus involved in equilibrioception / inner ear receptor cell stereocilium organization / righting reflex / inner ear auditory receptor cell differentiation / stereocilium bundle / detection of mechanical stimulus involved in sensory perception of sound / stereocilium / non-motile cilium assembly / auditory receptor cell stereocilium organization / adult walking behavior ...detection of mechanical stimulus involved in equilibrioception / inner ear receptor cell stereocilium organization / righting reflex / inner ear auditory receptor cell differentiation / stereocilium bundle / detection of mechanical stimulus involved in sensory perception of sound / stereocilium / non-motile cilium assembly / auditory receptor cell stereocilium organization / adult walking behavior / startle response / homophilic cell-cell adhesion / inner ear development / actin filament bundle assembly / photoreceptor outer segment / visual perception / actin filament organization / morphogenesis of an epithelium / locomotory behavior / sensory perception of sound / response to calcium ion / multicellular organism growth / calcium ion binding / extracellular region / membrane / plasma membrane / cytoplasm
Similarity search - Function
: / PCDH15-like domain / Protocadherin-15 / Extracellular cadherin domain / Extracellular Cadherin domain / : / Cadherins / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. ...: / PCDH15-like domain / Protocadherin-15 / Extracellular cadherin domain / Extracellular Cadherin domain / : / Cadherins / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Protocadherin-15
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsKlanseck, C.F. / Neel, B.L. / Sotomayor, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)R01DC015271 United States
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)R00DC012534 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
DepositionJun 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 11, 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_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)47,4018
Polymers47,1211
Non-polymers2807
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.863, 78.863, 289.469
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Protocadherin-15


Mass: 47121.254 Da / Num. of mol.: 1 / Fragment: residues 401-818
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pcdh15 / Plasmid: pET21a / 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.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 4.79 Å3/Da / Density % sol: 74.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris pH 8.5 2.0 M MgAc 23% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.35→76.09 Å / Num. obs: 14064 / % possible obs: 98.5 % / Redundancy: 11.2 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 16.9
Reflection shellResolution: 3.35→3.41 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.601 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 596 / % possible all: 86.4

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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: 5t4m, 5tpk

5t4m

5tpk


Resolution: 3.35→76.09 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.906 / SU B: 56.847 / SU ML: 0.372 / Cross valid method: THROUGHOUT / ESU R: 1.744 / ESU R Free: 0.466 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27884 648 4.7 %RANDOM
Rwork0.22705 ---
obs0.22955 13124 98.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 120.669 Å2
Baniso -1Baniso -2Baniso -3
1-9.58 Å2-0 Å2-0 Å2
2--9.58 Å2-0 Å2
3----19.17 Å2
Refinement stepCycle: 1 / Resolution: 3.35→76.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3118 0 7 1 3126
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193178
X-RAY DIFFRACTIONr_bond_other_d0.0020.022895
X-RAY DIFFRACTIONr_angle_refined_deg1.621.9694352
X-RAY DIFFRACTIONr_angle_other_deg1.02136717
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7215403
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.83824.863146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.98115491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4171519
X-RAY DIFFRACTIONr_chiral_restr0.0940.2522
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213572
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02603
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_it2.7448.4431618
X-RAY DIFFRACTIONr_mcbond_other2.7438.4431617
X-RAY DIFFRACTIONr_mcangle_it4.47812.6642019
X-RAY DIFFRACTIONr_mcangle_other4.47812.6652020
X-RAY DIFFRACTIONr_scbond_it2.6458.681560
X-RAY DIFFRACTIONr_scbond_other2.6448.681561
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.50712.9342334
X-RAY DIFFRACTIONr_long_range_B_refined7.0476281
X-RAY DIFFRACTIONr_long_range_B_other7.0476282
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.35→3.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.44 42 -
Rwork0.392 847 -
obs--88.11 %
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)
12.9388-0.49411.44266.27421.60827.45390.1835-0.52880.13520.6863-0.1966-0.23780.0057-0.34210.01310.127-0.12410.06130.6173-0.10070.436-56.2622-27.375555.3939
22.3412-0.2661-1.9731.74020.82448.59710.1539-0.0933-0.062-0.032-0.1454-0.1748-0.04810.0865-0.00850.0144-0.00360.02540.1359-0.11030.4201-53.7144-36.679514.3679
34.2790.7253-5.07330.3499-0.86177.62330.08330.09090.2453-0.18170.08210.0788-0.5098-0.6135-0.16550.34830.06850.02730.1805-0.02190.5478-40.1265-37.2517-32.4956
46.44861.5458-2.29662.64690.19873.5615-0.28091.0522-0.3925-0.46970.2485-0.54660.50780.11430.03240.57890.03790.19680.2701-0.04140.5855-3.8339-32.2577-65.0113
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A370 - 480
2X-RAY DIFFRACTION1A1 - 1007
3X-RAY DIFFRACTION2A481 - 588
4X-RAY DIFFRACTION2A1005 - 1006
5X-RAY DIFFRACTION3A589 - 689
6X-RAY DIFFRACTION3A1002 - 1004
7X-RAY DIFFRACTION4A690 - 791
8X-RAY DIFFRACTION4A1001

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