[English] 日本語
Yorodumi
- PDB-6y9o: Crystal structure of Whirlin PDZ3_C-ter in complex with CASK inte... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6y9o
TitleCrystal structure of Whirlin PDZ3_C-ter in complex with CASK internal PDZ binding motif peptide
Components
  • Peripheral plasma membrane protein CASK
  • Whirlin
KeywordsSTRUCTURAL PROTEIN / Whirlin / PDZ / Myosin 15a / complex
Function / homology
Function and homology information


podocyte foot / axon collateral / Dopamine Neurotransmitter Release Cycle / paranodal junction maintenance / periciliary membrane compartment / USH2 complex / stereocilia ankle link / Neurexins and neuroligins / inner ear receptor cell differentiation / negative regulation of cellular response to growth factor stimulus ...podocyte foot / axon collateral / Dopamine Neurotransmitter Release Cycle / paranodal junction maintenance / periciliary membrane compartment / USH2 complex / stereocilia ankle link / Neurexins and neuroligins / inner ear receptor cell differentiation / negative regulation of cellular response to growth factor stimulus / stereocilia ankle link complex / sensory perception of light stimulus / cerebellar Purkinje cell layer formation / photoreceptor connecting cilium / stereocilium tip / inner ear receptor cell stereocilium organization / neurexin family protein binding / detection of mechanical stimulus involved in sensory perception of sound / stereocilium bundle / regulation of neurotransmitter secretion / negative regulation of wound healing / nuclear lamina / positive regulation of dendritic spine morphogenesis / stereocilium / apical dendrite / calcium ion import / retina homeostasis / auditory receptor cell stereocilium organization / ciliary membrane / regulation of synaptic vesicle exocytosis / negative regulation of cell-matrix adhesion / positive regulation of calcium ion import / basement membrane / negative regulation of keratinocyte proliferation / photoreceptor inner segment / ciliary basal body / dendritic shaft / synaptic membrane / establishment of localization in cell / protein localization to plasma membrane / PDZ domain binding / actin filament / protein kinase C binding / sensory perception of sound / Schaffer collateral - CA1 synapse / establishment of protein localization / positive regulation of insulin secretion / cilium / nuclear matrix / cell-cell junction / presynapse / presynaptic membrane / growth cone / postsynapse / basolateral plasma membrane / vesicle / non-specific serine/threonine protein kinase / calmodulin binding / neuron projection / protein domain specific binding / phosphorylation / protein serine kinase activity / signaling receptor binding / protein serine/threonine kinase activity / neuronal cell body / synapse / dendrite / protein-containing complex binding / positive regulation of gene expression / nucleolus / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / protein-containing complex / ATP binding / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Whirlin / : / CASK, SH3 domain / L27 domain, C-terminal / L27 domain / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / Guanylate kinase, conserved site ...Whirlin / : / CASK, SH3 domain / L27 domain, C-terminal / L27 domain / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Variant SH3 domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Protein kinase domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Peripheral plasma membrane protein CASK / Whirlin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.632 Å
AuthorsZhu, Y. / Delhommel, F. / Haouz, A. / Caillet-Saguy, C. / Vaney, M. / Mechaly, A.E. / Wolff, N.
Funding support France, 1items
OrganizationGrant numberCountry
Marie Sklodowska-Curie Actions, FragNET ITN675341 France
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Deciphering the Unexpected Binding Capacity of the Third PDZ Domain of Whirlin to Various Cochlear Hair Cell Partners.
Authors: Zhu, Y. / Delhommel, F. / Cordier, F. / Luchow, S. / Mechaly, A. / Colcombet-Cazenave, B. / Girault, V. / Pepermans, E. / Bahloul, A. / Gautier, C. / Brule, S. / Raynal, B. / Hoos, S. / ...Authors: Zhu, Y. / Delhommel, F. / Cordier, F. / Luchow, S. / Mechaly, A. / Colcombet-Cazenave, B. / Girault, V. / Pepermans, E. / Bahloul, A. / Gautier, C. / Brule, S. / Raynal, B. / Hoos, S. / Haouz, A. / Caillet-Saguy, C. / Ivarsson, Y. / Wolff, N.
History
DepositionMar 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Whirlin
C: Peripheral plasma membrane protein CASK


Theoretical massNumber of molelcules
Total (without water)12,7922
Polymers12,7922
Non-polymers00
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-9 kcal/mol
Surface area5800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.470, 50.470, 88.410
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-1008-

HOH

21A-1055-

HOH

31A-1101-

HOH

-
Components

#1: Protein Whirlin


Mass: 11359.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Whrn, Dfnb31, Kiaa1526
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q80VW5
#2: Protein/peptide Peripheral plasma membrane protein CASK / Calcium/calmodulin-dependent serine protein kinase


Mass: 1432.619 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
References: UniProt: O70589, non-specific serine/threonine protein kinase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M LiCl, 25 %w/v PEG 8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Nov 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.632→39.18 Å / Num. obs: 16757 / % possible obs: 99.73 % / Redundancy: 19.2 % / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 26.04
Reflection shellResolution: 1.632→1.691 Å / Num. unique obs: 1614 / CC1/2: 0.945 / CC star: 0.986

-
Processing

Software
NameClassification
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UFX

1ufx


Resolution: 1.632→39.18 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2286 --
Rwork0.2073 --
obs-16757 99.73 %
Displacement parametersBiso mean: 21.11 Å2
Refinement stepCycle: LAST / Resolution: 1.632→39.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms809 0 0 113 922
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057830
X-RAY DIFFRACTIONf_angle_d0.83021123
X-RAY DIFFRACTIONf_chiral_restr0.0589131
X-RAY DIFFRACTIONf_plane_restr0.0045145
X-RAY DIFFRACTIONf_dihedral_angle_d18.0672314

+
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://pdbjlvh1.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