[English] 日本語
- PDB-6c13: CryoEM structure of mouse PCDH15-4EC-LHFPL5 complex -

Open data

ID or keywords:


no data

Basic information

Database: PDB / ID: 6c13
TitleCryoEM structure of mouse PCDH15-4EC-LHFPL5 complex
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

Structure visualization

  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-7327
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-7327
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:

Downloads & links


Deposited unit
A: Protocadherin-15
B: Protocadherin-15
hetero molecules

Theoretical massNumber of molelcules
Total (without water)151,87532

TypeNameSymmetry operationNumber
identity operation1_555x,y,z1


#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

Mass: 221.208 Da / Num. of mol.: 12 / Formula: C8H15NO6 / N-Acetylglucosamine
#3: Chemical

Mass: 180.156 Da / Num. of mol.: 6 / Formula: C6H12O6
#4: Chemical

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

Experimental details


EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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

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


SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM software
1Gautomatchparticle selection
2SerialEMimage acquisition
4RELIONCTF correction
7MDFFmodel fitting
8RosettaEMmodel fitting
11RELIONfinal Euler assignment
13RELION2.1b23D reconstruction
14PHENIXmodel refinement
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

About Yorodumi


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. (see PDBe EMDB page)
  • 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 at EBI / 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. See below links for details.
  • 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

Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more


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.

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