[English] 日本語
Yorodumi
- PDB-2kbq: Solution structure of harmonin N terminal domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kbq
TitleSolution structure of harmonin N terminal domain
ComponentsHarmoninUSH1C
KeywordsSTRUCTURAL PROTEIN / PROTEIN / Alternative splicing / Coiled coil / Deafness / Hearing / Non-syndromic deafness / Polymorphism / Retinitis pigmentosa / Sensory transduction / Usher syndrome / Vision
Function / homology
Function and homology information


protein localization to microvillus / brush border assembly / regulation of microvillus length / stereocilia ankle link complex / parallel actin filament bundle assembly / equilibrioception / sensory perception of light stimulus / retinal cone cell development / stereocilium tip / inner ear receptor cell stereocilium organization ...protein localization to microvillus / brush border assembly / regulation of microvillus length / stereocilia ankle link complex / parallel actin filament bundle assembly / equilibrioception / sensory perception of light stimulus / retinal cone cell development / stereocilium tip / inner ear receptor cell stereocilium organization / inner ear auditory receptor cell differentiation / stereocilium / photoreceptor cell maintenance / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / inner ear morphogenesis / spectrin binding / brush border / microvillus / actin filament bundle assembly / photoreceptor outer segment / photoreceptor inner segment / sensory perception of sound / cilium / G2/M transition of mitotic cell cycle / apical part of cell / protein-containing complex assembly / cytoskeleton / synapse / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Paired amphipathic helix 2 (pah2 repeat) - #20 / Harmonin, N-terminal domain / Harmonin / Paired amphipathic helix 2 (pah2 repeat) / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 20
AuthorsZhang, M. / Pan, L. / Yan, J. / Wu, L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Assembling stable hair cell tip link complex via multidentate interactions between harmonin and cadherin 23
Authors: Pan, L. / Yan, J. / Wu, L. / Zhang, M.
History
DepositionDec 5, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Harmonin


Theoretical massNumber of molelcules
Total (without water)9,5671
Polymers9,5671
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Harmonin / USH1C / Usher syndrome type-1C protein / Autoimmune enteropathy-related antigen AIE-75 / Antigen NY-CO- ...Usher syndrome type-1C protein / Autoimmune enteropathy-related antigen AIE-75 / Antigen NY-CO-38/NY-CO-37 / PDZ-73 protein / Renal carcinoma antigen NY-REN-3


Mass: 9567.099 Da / Num. of mol.: 1 / Fragment: N terminal domain, residues 1-80
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HARMONIN / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y6N9

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HN(CA)CB
1413D 1H-13C NOESY
1513D 1H-15N NOESY
1612D 1H-1H COSY

-
Sample preparation

DetailsContents: 100mM potassium phosphate-1, 1mM DTT-2, 1mM EDTA-3, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
100 mMpotassium phosphate-11
1 mMDTT-21
1 mMEDTA-31
Sample conditionsIonic strength: 0.1 / pH: 6.5 / Pressure: ambient / Temperature: 303 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA7502

-
Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readdata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readchemical shift calculation
CNSrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 20

+
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