[English] 日本語
Yorodumi
- PDB-2mh3: NMR structure of the basic helix-loop-helix region of the transcr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2mh3
TitleNMR structure of the basic helix-loop-helix region of the transcriptional repressor HES-1
ComponentsTranscription factor HES-1
KeywordsDNA BINDING PROTEIN / bHLH
Function / homology
Function and homology information


trochlear nerve development / stomach neuroendocrine cell differentiation / negative regulation of stomach neuroendocrine cell differentiation / N-box binding / comma-shaped body morphogenesis / S-shaped body morphogenesis / renal interstitial fibroblast development / negative regulation of cell fate determination / negative regulation of pancreatic A cell differentiation / positive regulation of mitotic cell cycle, embryonic ...trochlear nerve development / stomach neuroendocrine cell differentiation / negative regulation of stomach neuroendocrine cell differentiation / N-box binding / comma-shaped body morphogenesis / S-shaped body morphogenesis / renal interstitial fibroblast development / negative regulation of cell fate determination / negative regulation of pancreatic A cell differentiation / positive regulation of mitotic cell cycle, embryonic / regulation of timing of neuron differentiation / midbrain-hindbrain boundary morphogenesis / metanephric nephron tubule morphogenesis / common bile duct development / pancreatic A cell differentiation / negative regulation of amacrine cell differentiation / ureteric bud morphogenesis / hindbrain morphogenesis / lateral inhibition / oculomotor nerve development / ascending aorta morphogenesis / amacrine cell differentiation / cardiac neural crest cell development involved in outflow tract morphogenesis / glomerulus vasculature development / vascular associated smooth muscle cell development / cell morphogenesis involved in neuron differentiation / adenohypophysis development / HLH domain binding / negative regulation of pro-B cell differentiation / negative regulation of inner ear auditory receptor cell differentiation / Cajal-Retzius cell differentiation / pharyngeal arch artery morphogenesis / regulation of secondary heart field cardioblast proliferation / negative regulation of calcium ion import / NOTCH2 intracellular domain regulates transcription / inner ear receptor cell stereocilium organization / establishment of epithelial cell polarity / telencephalon development / inner ear auditory receptor cell differentiation / neuronal stem cell population maintenance / negative regulation of oligodendrocyte differentiation / positive regulation of astrocyte differentiation / response to thyroid hormone / forebrain radial glial cell differentiation / cell fate determination / negative regulation of stem cell differentiation / JUN kinase binding / positive regulation of BMP signaling pathway / regulation of epithelial cell proliferation / embryonic heart tube morphogenesis / response to alkaloid / regulation of receptor signaling pathway via JAK-STAT / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / regulation of fat cell differentiation / NOTCH4 Intracellular Domain Regulates Transcription / labyrinthine layer blood vessel development / anterior/posterior pattern specification / ventricular septum development / artery morphogenesis / cellular response to fatty acid / NOTCH3 Intracellular Domain Regulates Transcription / negative regulation of glial cell proliferation / midbrain development / smoothened signaling pathway / ventricular septum morphogenesis / cochlea development / positive regulation of DNA binding / positive regulation of Notch signaling pathway / outflow tract morphogenesis / E-box binding / RUNX2 regulates osteoblast differentiation / somatic stem cell population maintenance / regulation of neurogenesis / negative regulation of neuron differentiation / regulation of protein-containing complex assembly / cellular response to interleukin-1 / BMP signaling pathway / T cell proliferation / positive regulation of T cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / cell maturation / Notch signaling pathway / transcription corepressor binding / cellular response to nerve growth factor stimulus / thymus development / liver development / positive regulation of receptor signaling pathway via JAK-STAT / lung development / negative regulation of forebrain neuron differentiation / negative regulation of DNA-binding transcription factor activity / response to organic cyclic compound / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / DNA-binding transcription repressor activity, RNA polymerase II-specific / histone deacetylase binding / nuclear matrix / sequence-specific double-stranded DNA binding / negative regulation of neuron projection development
Similarity search - Function
Orange domain / Hairy Orange / Orange domain profile. / Orange domain / Helix-loop-helix DNA-binding domain / MYOD Basic-Helix-Loop-Helix Domain, subunit B / Helix-loop-helix DNA-binding domain / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain ...Orange domain / Hairy Orange / Orange domain profile. / Orange domain / Helix-loop-helix DNA-binding domain / MYOD Basic-Helix-Loop-Helix Domain, subunit B / Helix-loop-helix DNA-binding domain / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Transcription factor HES-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / restrained molecular dynamics
AuthorsWienk, H. / Popovic, M. / Coglievina, M. / Boelens, R. / Pongor, S. / Pintar, A.
CitationJournal: Proteins / Year: 2014
Title: The basic helix-loop-helix region of the transcriptional repressor hairy and enhancer of split 1 is preorganized to bind DNA.
Authors: Popovic, M. / Wienk, H. / Coglievina, M. / Boelens, R. / Pongor, S. / Pintar, A.
History
DepositionNov 15, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2014Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transcription factor HES-1
B: Transcription factor HES-1


Theoretical massNumber of molelcules
Total (without water)16,4552
Polymers16,4552
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Transcription factor HES-1 / Class B basic helix-loop-helix protein 39 / bHLHb39 / Hairy and enhancer of split 1 / Hairy homolog ...Class B basic helix-loop-helix protein 39 / bHLHb39 / Hairy and enhancer of split 1 / Hairy homolog / Hairy-like protein / hHL


Mass: 8227.726 Da / Num. of mol.: 2 / Fragment: UNP residues 27-95
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HES1, BHLHB39, HL, HRY / Production host: Escherichia coli (E. coli) / References: UniProt: Q14469

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111triple resonance assignment
121relaxation
131DNA titration
141NOESY

-
Sample preparation

DetailsContents: 2 mM [U-99% 13C; U-99% 15N] protein, 50 mM potassium phosphate, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMentity-1[U-99% 13C; U-99% 15N]1
50 mMpotassium phosphate-21
Sample conditionsIonic strength: 50 / pH: 6.5 / Pressure: ambient / Temperature: 288 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE9002

-
Processing

NMR software
NameDeveloperClassification
CCPN_ANALYSISCCPNchemical shift assignment
CS-ROSETTAShen, Vernon, Baker and Baxdata analysis
TALOS+Cornilescu, Delaglio and Baxdata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CINGVuister et al.data analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: restrained molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 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://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