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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 / homologyCadherin-like / Cadherins domain profile. / Cadherin domain signature. / Cadherin domain / Protocadherin-15 / Cadherin conserved site / Cadherin-like superfamily / detection of mechanical stimulus involved in equilibrioception / righting reflex / detection of mechanical stimulus involved in sensory perception of sound ...Cadherin-like / Cadherins domain profile. / Cadherin domain signature. / Cadherin domain / Protocadherin-15 / Cadherin conserved site / Cadherin-like superfamily / detection of mechanical stimulus involved in equilibrioception / righting reflex / detection of mechanical stimulus involved in sensory perception of sound / equilibrioception / sensory perception of light stimulus / inner ear receptor cell stereocilium organization / stereocilium bundle / inner ear auditory receptor cell differentiation / non-motile cilium assembly / startle response / stereocilium / adult walking behavior / photoreceptor cell maintenance / photoreceptor outer segment / auditory receptor cell stereocilium organization / homophilic cell adhesion via plasma membrane adhesion molecules / inner ear development / actin filament bundle assembly / visual perception / actin filament organization / locomotory behavior / sensory perception of sound / multicellular organism growth / morphogenesis of an epithelium / response to calcium ion / protein N-terminus binding / protein-containing complex binding / synapse / cell adhesion / calcium ion binding / integral component of plasma membrane / extracellular space / integral component of membrane / plasma membrane / cytoplasm / Protocadherin-15
Function and homology information
Specimen sourceMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 11.33 Å resolution
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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 3, 2018 / Release: Aug 15, 2018

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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)151,87532
Polyers145,9782
Non-polymers5,89730
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein/peptide Protocadherin-15 /


Mass: 72989.023 Da / Num. of mol.: 2 / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pcdh15 / Production host: Homo sapiens (human) / References: UniProt: Q99PJ1
#2: Chemical
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 12 / Formula: C8H15NO6 / N-Acetylglucosamine
#3: Chemical
ChemComp-BMA / BETA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 6 / Formula: C6H12O6
#4: Chemical
ChemComp-MAN / ALPHA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 12 / Formula: C6H12O6

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 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 / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 285

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingAverage exposure time: 10 / Electron dose: 27 / 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
3D reconstructionResolution: 11.33 / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 16733 / Symmetry type: POINT
Atomic model buildingRef protocol: 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_restr0.0501508
ELECTRON MICROSCOPYf_plane_restr0.0071566

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