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- PDB-6bxu: Crystal Structure of Mouse Protocadherin-15 EC5-7 I582T -

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Basic information

Entry
Database: PDB / ID: 6bxu
TitleCrystal Structure of Mouse Protocadherin-15 EC5-7 I582T
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
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.79 Å
AuthorsNeel, 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
DepositionDec 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 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 / 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 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
B: Protocadherin-15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,81912
Polymers70,4182
Non-polymers40110
Water00
1
A: Protocadherin-15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4096
Polymers35,2091
Non-polymers2005
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protocadherin-15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4096
Polymers35,2091
Non-polymers2005
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)180.905, 180.905, 127.161
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222

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Components

#1: Protein Protocadherin-15


Mass: 35208.910 Da / Num. of mol.: 2 / Fragment: CADHERIN DOMAINS 5-7, RESIDUES 507-818
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 / Variant (production host): Rosetta / References: UniProt: Q99PJ1
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / 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: 7.66 Å3/Da / Density % sol: 83.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Na formate, 40% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 3.79→180.9 Å / Num. obs: 21629 / % possible obs: 97.6 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.231 / Net I/σ(I): 7.43
Reflection shellResolution: 3.79→3.87 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 0.545 / Num. unique obs: 946 / CC1/2: 0.269 / % possible all: 87.8

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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: 5W1D

5w1d


Resolution: 3.79→180.9 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.918 / SU B: 76.706 / SU ML: 0.465 / Cross valid method: THROUGHOUT / ESU R: 2.039 / ESU R Free: 0.537 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28349 1020 4.8 %RANDOM
Rwork0.23962 ---
obs0.24169 20056 97.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 150.424 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å2-0 Å2-0 Å2
2--0.84 Å2-0 Å2
3----1.68 Å2
Refinement stepCycle: 1 / Resolution: 3.79→180.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4756 0 10 0 4766
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194846
X-RAY DIFFRACTIONr_bond_other_d0.0020.024382
X-RAY DIFFRACTIONr_angle_refined_deg1.4861.9656634
X-RAY DIFFRACTIONr_angle_other_deg0.998310176
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.245621
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.41924.956226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.49215741
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6511530
X-RAY DIFFRACTIONr_chiral_restr0.0910.2785
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215499
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02915
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_it1.7919.4672490
X-RAY DIFFRACTIONr_mcbond_other1.7899.4662489
X-RAY DIFFRACTIONr_mcangle_it3.07814.1963109
X-RAY DIFFRACTIONr_mcangle_other3.07814.1983110
X-RAY DIFFRACTIONr_scbond_it1.3579.5872354
X-RAY DIFFRACTIONr_scbond_other1.3579.5892355
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.46214.3443526
X-RAY DIFFRACTIONr_long_range_B_refined5.4339437
X-RAY DIFFRACTIONr_long_range_B_other5.4339438
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.785→3.883 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.428 78 -
Rwork0.379 1297 -
obs--87.08 %
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)
13.1006-0.12132.56480.7378-0.01143.7106-0.4127-0.00270.47360.16230.20270.1134-0.7269-0.48710.210.21250.1268-0.1170.26750.28510.748854.48475.488-23.78
22.6594-0.58842.04830.5057-0.14712.48510.3502-0.3805-0.13510.1435-0.00670.09720.525-0.89-0.34350.2254-0.2059-0.20050.51120.38180.941846.47357.951-18.502
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A481 - 790
2X-RAY DIFFRACTION2B481 - 790

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