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- EMDB-7327: Structure of a membrane protein complex -

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Basic information

Entry
Database: EMDB / ID: EMD-7327
TitleStructure of a membrane protein complex
Map dataprimary map
Sample
  • Complex: Complex of membrane proteins
    • Protein or peptide: Protocadherin-15
KeywordsPCDH15 / LHFPL5 / protocadherin / tip link / hair cell / TMHS / hearing / MEMBRANE PROTEIN
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
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 11.33 Å
AuthorsGouaux E / 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, 2018-
Header (metadata) releaseFeb 28, 2018-
Map releaseAug 15, 2018-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6c13
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6c13
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7327.png

Downloads & links

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Map

FileDownload / File: emd_7327.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationprimary map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.72 Å/pix.
x 280 pix.
= 481.6 Å		1.72 Å/pix.
x 280 pix.
= 481.6 Å		1.72 Å/pix.
x 280 pix.
= 481.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.72 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.027673589 - 0.15490283
Average (Standard dev.)0.000094513045 (±0.0041813934)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 481.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.721.721.72
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z481.600481.600481.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-163-114-126
NX/NY/NZ210124170
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.0280.1550.000

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Supplemental data

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Sample components

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Entire : Complex of membrane proteins

EntireName: Complex of membrane proteins
Components
  • Complex: Complex of membrane proteins
    • Protein or peptide: Protocadherin-15

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Supramolecule #1: Complex of membrane proteins

SupramoleculeName: Complex of membrane proteins / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Protocadherin-15

MacromoleculeName: Protocadherin-15 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 72.989023 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QYDDSPVFTN STYTVVVEEN LPAGTSFLQI EAKDVDLGAN VSYRIRSPEV KHLFALHPFT GELSLLRSLD YEAFPDQEAS ITFLAEAFD IYGTMPPGIA TVTVIVKDMN DYPPVFSKRI YKGMVAPDAV KGTPITTVYA EDADPPGMPA SRVRYRVDDV Q FPYPASIF ...String:
QYDDSPVFTN STYTVVVEEN LPAGTSFLQI EAKDVDLGAN VSYRIRSPEV KHLFALHPFT GELSLLRSLD YEAFPDQEAS ITFLAEAFD IYGTMPPGIA TVTVIVKDMN DYPPVFSKRI YKGMVAPDAV KGTPITTVYA EDADPPGMPA SRVRYRVDDV Q FPYPASIF DVEEDSGRVV TRVNLNEEPT TIFKLVVVAF DDGEPVMSSS ATVRILVLHP GEIPRFTQEE YRPPPVSELA AR GTVVGVI SAAAINQSIV YSIVAGNEED KFGINNVTGV IYVNSPLDYE TRTSYVLRVQ ADSLEVVLAN LRVPSKSNTA KVY IEIQDE NDHPPVFQKK FYIGGVSEDA RMFASVLRVK ATDRDTGNYS AMAYRLIIPP IKEGKEGFVV ETYTGLIKTA MLFH NMRRS YFKFQVIATD DYGKGLSGKA DVLVSVVNQL DMQVIVSNVP PTLVEKKIED LTEILDRYVQ EQIPGAKVVV ESIGA RRHG DAYSLEDYSK CDLTVYAIDP QTNRAIDRNE LFKFLDGKLL DINKDFQPYY GEGGRILEIR TPEAVTSIKK RGESLG YTE GALLALAFII ILCCIPAILV VLVSYRQFKV RQAECTKTAR IQSAMPAAKP AAPVPAAPAP PPPPPPPPPG AHLYEEL GE SAMHKYETAL FESRLVPR

UniProtKB: Protocadherin-15

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.5 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
20.0 mMTris
150.0 mMsodium chlorideNaCl
0.075 %digitonine
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 285 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 10.0 sec. / Average electron dose: 27.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 11.33 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1b2) / Number images used: 16733
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

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

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