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- PDB-6c13: CryoEM structure of mouse PCDH15-4EC-LHFPL5 complex -

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Basic information

Entry
Database: PDB / ID: 6c13
TitleCryoEM structure of mouse PCDH15-4EC-LHFPL5 complex
ComponentsProtocadherin-15
KeywordsMEMBRANE PROTEIN / 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 / detection of mechanical stimulus involved in sensory perception of sound / righting reflex / inner ear auditory receptor cell differentiation / stereocilium bundle / 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 / detection of mechanical stimulus involved in sensory perception of sound / righting reflex / inner ear auditory receptor cell differentiation / stereocilium bundle / stereocilium / non-motile cilium assembly / auditory receptor cell stereocilium organization / adult walking behavior / startle response / homophilic cell adhesion via plasma membrane adhesion molecules / 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 / multicellular organism growth / response to calcium ion / calcium ion binding / extracellular region / membrane / plasma membrane / cytoplasm
Similarity search - Function
PCDH15-like domain / Protocadherin-15 / Extracellular cadherin domain / Extracellular Cadherin domain / : / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherin-like ...PCDH15-like domain / 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
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 11.33 Å
AuthorsGouaux, E. / Ge, J. / Elferich, 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 1.1Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / em_imaging_optics / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _em_imaging_optics.phase_plate / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
A: Protocadherin-15
B: Protocadherin-15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,4438
Polymers145,9782
Non-polymers5,4656
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Protocadherin-15


Mass: 72989.023 Da / Num. of mol.: 2
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: Polysaccharide
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex of membrane proteins / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris1
2150 mMsodium chlorideNaCl1
30.075 %digitonine1
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 285 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingAverage exposure time: 10 sec. / Electron dose: 27 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsPhase plate: VOLTA PHASE PLATE
Image scansMovie frames/image: 50

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM software
IDNameVersionCategory
1Gautomatchparticle selection
2SerialEMimage acquisition
4RELIONCTF correction
7MDFFmodel fitting
8RosettaEMmodel fitting
11RELIONfinal Euler assignment
13RELION2.1b23D reconstruction
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 11.33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16733 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039080
ELECTRON MICROSCOPYf_angle_d0.71912414
ELECTRON MICROSCOPYf_dihedral_angle_d3.9035528
ELECTRON MICROSCOPYf_chiral_restr0.051508
ELECTRON MICROSCOPYf_plane_restr0.0071566

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