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- EMDB-7328: CryoEM structure of mouse PCDH15-1EC-LHFPL5 complex -

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Basic information

Entry
Database: EMDB / ID: 7328
TitleCryoEM structure of mouse PCDH15-1EC-LHFPL5 complex
Map dataprimary map
Samplemembrane protein complexBiological membrane
  • Protocadherin-15
  • LHFPL tetraspan subfamily member 5 protein
Function / homologyCadherin-like / Lipoma HMGIC fusion partner-like protein / Cadherins domain profile. / Cadherin domain signature. / Lipoma HMGIC fusion partner-like protein / Cadherin domain / Protocadherin-15 / Cadherin conserved site / Cadherin-like superfamily / detection of mechanical stimulus involved in equilibrioception ...Cadherin-like / Lipoma HMGIC fusion partner-like protein / Cadherins domain profile. / Cadherin domain signature. / Lipoma HMGIC fusion partner-like protein / 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 / stereocilium tip / 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 / ion transport / locomotory behavior / sensory perception of sound / multicellular organism growth / morphogenesis of an epithelium / response to calcium ion / apical plasma membrane / 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 / LHFPL tetraspan subfamily member 5 protein / Protocadherin-15
Function and homology information
SourceMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / 4.5 Å resolution
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
Validation ReportPDB-ID: 6c14

SummaryFull reportAbout validation report
DateDeposition: Jan 3, 2018 / Header (metadata) release: Feb 28, 2018 / Map release: Aug 15, 2018 / Last update: Aug 15, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 7
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 7
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6c14
  • Surface level: 7
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7328.map.gz (map file in CCP4 format, 108001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
300 pix
1.04 Å/pix.
= 312. Å
300 pix
1.04 Å/pix.
= 312. Å
300 pix
1.04 Å/pix.
= 312. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density
Contour Level:7.0 (by author), 7 (movie #1):
Minimum - Maximum-12.049251 - 22.620622999999998
Average (Standard dev.)-0.000000000000668 (1.)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderZYX
Dimensions300300300
Origin0.0.0.
Limit299.299.299.
Spacing300300300
CellA=B=C: 312.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z312.000312.000312.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-12.04922.621-0.000

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Supplemental data

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Sample components

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Entire membrane protein complex

EntireName: membrane protein complex / Number of components: 3

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Component #1: protein, membrane protein complex

ProteinName: membrane protein complexBiological membrane / Recombinant expression: No
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Homo sapiens (human)

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Component #2: protein, Protocadherin-15

ProteinName: Protocadherin-15 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 37.458129 kDa
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, LHFPL tetraspan subfamily member 5 protein

ProteinName: LHFPL tetraspan subfamily member 5 protein / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 25.06732 kDa
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Homo sapiens (human)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 8
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: OTHER / Temperature: 285 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 74 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C2 (2 fold cyclic) / Number of projections: 78792
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Output model

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