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- EMDB-7328: cryoEM structure of membrane protein complex -

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Basic information

Entry
Database: EMDB / ID: EMD-7328
TitlecryoEM structure of membrane protein complex
Map dataprimary map
Sample
  • Complex: membrane protein complex
    • Protein or peptide: Protocadherin-15
    • Protein or peptide: LHFPL tetraspan subfamily member 5 protein
KeywordsPCDH15 / LHFPL5 / protocadherin / tip link / hair cell / TMHS / hearing / membrane protein / metal transport
Function / homology
Function and homology information


detection of mechanical stimulus involved in equilibrioception / stereocilium tip / inner ear receptor cell stereocilium organization / righting reflex / inner ear auditory receptor cell differentiation / stereocilium bundle / detection of mechanical stimulus involved in sensory perception of sound / stereocilium / non-motile cilium assembly / auditory receptor cell stereocilium organization ...detection of mechanical stimulus involved in equilibrioception / stereocilium tip / inner ear receptor cell stereocilium organization / righting reflex / inner ear auditory receptor cell differentiation / stereocilium bundle / detection of mechanical stimulus involved in sensory perception of sound / stereocilium / non-motile cilium assembly / auditory receptor cell stereocilium organization / adult walking behavior / startle response / homophilic cell-cell adhesion / inner ear development / actin filament bundle assembly / photoreceptor outer segment / monoatomic ion transport / visual perception / actin filament organization / morphogenesis of an epithelium / locomotory behavior / sensory perception of sound / response to calcium ion / multicellular organism growth / apical plasma membrane / calcium ion binding / extracellular region / membrane / plasma membrane / cytoplasm
Similarity search - Function
Lipoma HMGIC fusion partner-like protein / Lipoma HMGIC fusion partner-like protein / : / PCDH15-like domain / Protocadherin-15 / Extracellular cadherin domain / Extracellular Cadherin domain / : / Cadherin conserved site / Cadherin domain signature. ...Lipoma HMGIC fusion partner-like protein / Lipoma HMGIC fusion partner-like protein / : / 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
LHFPL tetraspan subfamily member 5 protein / Protocadherin-15
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsGouaux E / 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, 2018-
Header (metadata) releaseFeb 28, 2018-
Map releaseAug 15, 2018-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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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

emd_7328.png

Downloads & links

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Map

FileDownload / File: emd_7328.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationprimary map
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 7.0 / Movie #1: 7
Minimum - Maximum-12.049251 - 22.620622999999998
Average (Standard dev.)-0.000000000000668 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 312.0 Å
α=β=γ: 90.0 °

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
Components
  • Complex: membrane protein complex
    • Protein or peptide: Protocadherin-15
    • Protein or peptide: LHFPL tetraspan subfamily member 5 protein

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Supramolecule #1: membrane protein complex

SupramoleculeName: membrane protein complex / 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: 37.458129 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GQYDDHPPVF QKKFYIGGVS EDARMFASVL RVKATDRDTG NYSAMAYRLI IPPIKEGKEG FVVETYTGLI KTAMLFHNMR RSYFKFQVI ATDDYGKGLS GKADVLVSVV NQLDMQVIVS NVPPTLVEKK IEDLTEILDR YVQEQIPGAK VVVESIGARR H GDAYSLED ...String:
GQYDDHPPVF QKKFYIGGVS EDARMFASVL RVKATDRDTG NYSAMAYRLI IPPIKEGKEG FVVETYTGLI KTAMLFHNMR RSYFKFQVI ATDDYGKGLS GKADVLVSVV NQLDMQVIVS NVPPTLVEKK IEDLTEILDR YVQEQIPGAK VVVESIGARR H GDAYSLED YSKCDLTVYA IDPQTNRAID RNELFKFLDG KLLDINKDFQ PYYGEGGRIL EIRTPEAVTS IKKRGESLGY TE GALLALA FIIILCCIPA ILVVLVSYRQ FKVRQAECTK TARIQSAMPA AKPAAPVPAA PAPPPPPPPP PPGAHLYEEL GES AMHKYE TALFESRLVP R

UniProtKB: Protocadherin-15

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Macromolecule #2: LHFPL tetraspan subfamily member 5 protein

MacromoleculeName: LHFPL tetraspan subfamily member 5 protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 25.06732 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GSGGRATMVK LLPAQEAAKI YHTNYVRNSR AVGVMWGTLT ICFSVLVMAL FIQPYWIGDS VSTPQAGYFG LFSYCVGNVL SSELICKGG PLDFSSIPSR AFKTAMFFVA LAMFLIIGSI ICFSLFFVCN TATVYKICAW MQLAAATGLM IGCLVYPDGW D SSEVRRMC ...String:
GSGGRATMVK LLPAQEAAKI YHTNYVRNSR AVGVMWGTLT ICFSVLVMAL FIQPYWIGDS VSTPQAGYFG LFSYCVGNVL SSELICKGG PLDFSSIPSR AFKTAMFFVA LAMFLIIGSI ICFSLFFVCN TATVYKICAW MQLAAATGLM IGCLVYPDGW D SSEVRRMC GEQTGKYTLG HCTIRWAFML AILSIGDALI LSFLAFVLGY RQDKLLPDDY KADGNEEVFE

UniProtKB: LHFPL tetraspan subfamily member 5 protein

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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

BufferpH: 8
Component:
ConcentrationNameFormula
20.0 mMTris
150.0 mMSodium ChlorideNaCl
0.075 %Digitonin
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 285 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 74.0 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

CTF correctionSoftware - Name: Gctf (ver. 1.06) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1b2) / Number images used: 78792
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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