[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 / Cadherin conserved site / Cadherin-like superfamily / Cadherins domain profile. / Cadherin domain signature. / Cadherin domain / Protocadherin-15 / detection of mechanical stimulus involved in equilibrioception / righting reflex / detection of mechanical stimulus involved in sensory perception of sound ...Cadherin-like / Cadherin conserved site / Cadherin-like superfamily / Cadherins domain profile. / Cadherin domain signature. / Cadherin domain / Protocadherin-15 / 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 auditory receptor cell differentiation / stereocilium bundle / inner ear receptor cell stereocilium organization / startle response / non-motile cilium assembly / stereocilium / adult walking behavior / photoreceptor cell maintenance / photoreceptor outer segment / auditory receptor cell stereocilium organization / homophilic cell adhesion via plasma membrane adhesion molecules / actin filament bundle assembly / inner ear development / visual perception / actin filament organization / locomotory behavior / sensory perception of sound / multicellular organism growth / morphogenesis of an epithelium / response to calcium ion / cell-cell signaling / 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 mg/ml / 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 kelvins

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 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingAverage exposure time: 10 sec. / Electron dose: 27 e/Å2 / 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 Å / 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


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

Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

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