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- PDB-6c10: Crystal structure of mouse PCDH15 EC11-EL -

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Basic information

Entry
Database: PDB / ID: 6c10
TitleCrystal structure of mouse PCDH15 EC11-EL
ComponentsProtocadherin-15
Keywordsmembrane protein / metal transport / PCDH15 / LHFPL5 / protocadherin / tip link / hair cell / TMHS / hearing
Function / homology
Function and homology information


detection of mechanical stimulus involved in equilibrioception / 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 / auditory receptor cell stereocilium organization / adult walking behavior / homophilic cell adhesion via plasma membrane adhesion molecules ...detection of mechanical stimulus involved in equilibrioception / 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 / auditory receptor cell stereocilium organization / adult walking behavior / homophilic cell adhesion via plasma membrane adhesion molecules / startle response / inner ear development / photoreceptor outer segment / visual perception / actin filament organization / morphogenesis of an epithelium / locomotory behavior / sensory perception of sound / multicellular organism growth / response to calcium ion / cell adhesion / calcium ion binding / extracellular region / membrane / plasma membrane / cytoplasm
Similarity search - Function
Protocadherin-15 / Extracellular cadherin domain / Extracellular Cadherin domain / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily
Similarity search - Domain/homology
alpha-D-mannopyranose / Protocadherin-15
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.399 Å
AuthorsGouaux, E. / Elferich, J. / Ge, J.
CitationJournal: Elife / Year: 2018
Title: Structure of mouse protocadherin 15 of the stereocilia tip link in complex with LHFPL5.
Authors: Jingpeng Ge / Johannes Elferich / April Goehring / Huaying Zhao / Peter Schuck / Eric Gouaux /
Abstract: Hearing and balance involve the transduction of mechanical stimuli into electrical signals by deflection of bundles of stereocilia linked together by protocadherin 15 (PCDH15) and cadherin 23 'tip ...Hearing and balance involve the transduction of mechanical stimuli into electrical signals by deflection of bundles of stereocilia linked together by protocadherin 15 (PCDH15) and cadherin 23 'tip links'. PCDH15 transduces tip link tension into opening of a mechano-electrical transduction (MET) ion channel. PCDH15 also interacts with LHFPL5, a candidate subunit of the MET channel. Here we illuminate the PCDH15-LHFPL5 structure, showing how the complex is composed of PCDH15 and LHFPL5 subunit pairs related by a 2-fold axis. The extracellular cadherin domains define a mobile tether coupled to a rigid, 2-fold symmetric 'collar' proximal to the membrane bilayer. LHFPL5 forms extensive interactions with the PCDH15 transmembrane helices and stabilizes the overall PCDH15-LHFPL5 assembly. Our studies illuminate the architecture of the PCDH15-LHFPL5 complex, localize mutations associated with deafness, and shed new light on how forces in the PCDH15 tether may be transduced into the stereocilia membrane.
History
DepositionJan 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protocadherin-15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0922
Polymers27,9121
Non-polymers1801
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.680, 57.680, 159.180
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: 27911.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pcdh15 / Production host: Homo sapiens (human) / References: UniProt: Q99PJ1
#2: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.37 Å3/Da / Density % sol: 48.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M Lithium sulfate, 30% (w/v) PEG4000, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.4→54.23 Å / Num. obs: 53914 / % possible obs: 99.73 % / Redundancy: 9.7 % / Net I/σ(I): 25.05
Reflection shellResolution: 1.4→1.45 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.399→54.23 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 21.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1951 5014 4.98 %
Rwork0.1693 --
obs0.1706 100675 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.399→54.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1935 0 11 187 2133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061987
X-RAY DIFFRACTIONf_angle_d0.7332685
X-RAY DIFFRACTIONf_dihedral_angle_d5.9071239
X-RAY DIFFRACTIONf_chiral_restr0.079301
X-RAY DIFFRACTIONf_plane_restr0.005346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.399-1.41490.35431500.33412906X-RAY DIFFRACTION91
1.4149-1.43160.33461670.34443235X-RAY DIFFRACTION99
1.4316-1.4490.35281670.31963147X-RAY DIFFRACTION99
1.449-1.46740.35081660.30433173X-RAY DIFFRACTION99
1.4674-1.48670.28681650.29153203X-RAY DIFFRACTION99
1.4867-1.50710.29441590.26593181X-RAY DIFFRACTION99
1.5071-1.52860.30031650.25333168X-RAY DIFFRACTION99
1.5286-1.55140.28161610.24163200X-RAY DIFFRACTION99
1.5514-1.57570.32351680.23823165X-RAY DIFFRACTION99
1.5757-1.60150.2541730.21793227X-RAY DIFFRACTION99
1.6015-1.62910.2881660.20293167X-RAY DIFFRACTION100
1.6291-1.65870.21981670.19363211X-RAY DIFFRACTION100
1.6587-1.69060.20681630.17143216X-RAY DIFFRACTION100
1.6906-1.72520.2091630.16423185X-RAY DIFFRACTION100
1.7252-1.76270.22521670.16463212X-RAY DIFFRACTION100
1.7627-1.80370.19241690.16053231X-RAY DIFFRACTION100
1.8037-1.84880.24611710.17323182X-RAY DIFFRACTION100
1.8488-1.89880.17431710.16733215X-RAY DIFFRACTION100
1.8988-1.95460.19531690.16933174X-RAY DIFFRACTION100
1.9546-2.01770.191700.16593211X-RAY DIFFRACTION100
2.0177-2.08990.19311710.1553221X-RAY DIFFRACTION100
2.0899-2.17350.20241660.16763174X-RAY DIFFRACTION100
2.1735-2.27250.20771690.15783212X-RAY DIFFRACTION100
2.2725-2.39230.21351700.15713233X-RAY DIFFRACTION100
2.3923-2.54210.16911720.16123183X-RAY DIFFRACTION100
2.5421-2.73840.20921720.17523225X-RAY DIFFRACTION100
2.7384-3.0140.22081730.17123205X-RAY DIFFRACTION100
3.014-3.450.15421700.16623189X-RAY DIFFRACTION100
3.45-4.34640.18581630.14223213X-RAY DIFFRACTION100
4.3464-54.27030.16221710.16253197X-RAY DIFFRACTION100

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