[English] 日本語
Yorodumi
- EMDB-7327: CryoEM structure of mouse PCDH15-4EC-LHFPL5 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-7327
TitleCryoEM structure of mouse PCDH15-4EC-LHFPL5 complex
Map dataprimary map
Sample
  • Complex: Complex of membrane proteins
    • Protein or peptide: Protocadherin-15
Function / homology
Function and homology information


detection of mechanical stimulus involved in equilibrioception / equilibrioception / sensory perception of light stimulus / 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 / photoreceptor cell maintenance ...detection of mechanical stimulus involved in equilibrioception / equilibrioception / sensory perception of light stimulus / 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 / photoreceptor cell maintenance / adult walking behavior / auditory receptor cell stereocilium organization / startle response / homophilic cell adhesion via plasma membrane adhesion molecules / inner ear development / photoreceptor outer segment / visual perception / locomotory behavior / actin filament organization / morphogenesis of an epithelium / sensory perception of sound / multicellular organism growth / response to calcium ion / cell adhesion / synapse / calcium ion binding / extracellular space / membrane / plasma membrane / cytoplasm
Similarity search - Function
Extracellular cadherin domain / Protocadherin-15 / Extracellular Cadherin domain / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / 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 / 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-
UpdateAug 12, 2020-
Current statusAug 12, 2020Processing site: RCSB / Status: Released

-
Structure visualization

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

Downloads & links

-
Map

FileDownload / File: emd_7327.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationprimary map
Voxel sizeX=Y=Z: 1.72 Å
Density
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.027673589 - 0.15490283
Average (Standard dev.)0.00009451305 (±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

-
Supplemental data

-
Sample components

-
Entire : Complex of membrane proteins

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

-
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)
Recombinant expressionOrganism: Homo sapiens (human)

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.5 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
20.0 mMTris
150.0 mMsodium chlorideNaClSodium chloride
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

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

CTF correctionSoftware - Name: RELION
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION
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
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more