[English] 日本語
Yorodumi
- PDB-1ihq: GLYTM1BZIP: A CHIMERIC PEPTIDE MODEL OF THE N-TERMINUS OF A RAT S... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ihq
TitleGLYTM1BZIP: A CHIMERIC PEPTIDE MODEL OF THE N-TERMINUS OF A RAT SHORT ALPHA TROPOMYOSIN WITH THE N-TERMINUS ENCODED BY EXON 1B
ComponentsCHIMERIC PEPTIDE GlyTM1bZip: TROPOMYOSIN ALPHA CHAIN, BRAIN-3 and GENERAL CONTROL PROTEIN GCN4
KeywordsDE NOVO PROTEIN / TROPOMYOSIN / EXON 1B / ACTIN-BINDING / THIN-FILAMENT-REGULATION / NON-MUSCLE / ALPHA-HELIX / COILED-COIL / DIMER / GCN4 / CHIMERIC-PEPTIDE-MODEL / TW0-CHAINED / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


Striated Muscle Contraction / Smooth Muscle Contraction / positive regulation of heart rate by epinephrine / bleb / FCERI mediated MAPK activation / protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation ...Striated Muscle Contraction / Smooth Muscle Contraction / positive regulation of heart rate by epinephrine / bleb / FCERI mediated MAPK activation / protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / mediator complex binding / actin filament capping / ruffle organization / Oxidative Stress Induced Senescence / muscle filament sliding / sarcomere organization / ventricular cardiac muscle tissue morphogenesis / negative regulation of vascular associated smooth muscle cell migration / myofibril / TFIID-class transcription factor complex binding / amino acid biosynthetic process / negative regulation of vascular associated smooth muscle cell proliferation / positive regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of transcription initiation by RNA polymerase II / cellular response to nutrient levels / cytoskeletal protein binding / cardiac muscle contraction / stress fiber / positive regulation of stress fiber assembly / positive regulation of cell adhesion / muscle contraction / cellular response to amino acid starvation / actin filament organization / negative regulation of cell migration / cellular response to reactive oxygen species / actin filament / wound healing / RNA polymerase II transcription regulator complex / ruffle membrane / disordered domain specific binding / actin filament binding / regulation of cell shape / actin cytoskeleton / actin binding / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / in utero embryonic development / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein heterodimerization activity / chromatin binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Tropomyosins signature. / Tropomyosin / Tropomyosin / : / Basic region leucine zipper / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily
Similarity search - Domain/homology
General control transcription factor GCN4 / Tropomyosin alpha-1 chain
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Saccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / 1156 CONFORMATIONALLY-RESTRICTING NOE CONSTRAINTS (OUT OF A TOTAL OF 1746 NOE DERIVED DISTANCES) 112 LOOSE DIHEDRAL ANGLE CONSTRAINTS, FORTY-EIGHT BACKBONE INTRA-HELICAL HYDROGEN BOND CONSTRAINTS WERE UTILILIZED.
AuthorsGreenfield, N.J. / Yuang, Y.J. / Palm, T. / Swapna, G.V. / Monleon, D. / Montelione, G.T. / Hitchcock-Degregori, S.E. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Solution NMR structure and folding dynamics of the N terminus of a rat non-muscle alpha-tropomyosin in an engineered chimeric protein.
Authors: Greenfield, N.J. / Huang, Y.J. / Palm, T. / Swapna, G.V. / Monleon, D. / Montelione, G.T. / Hitchcock-DeGregori, S.E.
History
DepositionApr 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CHIMERIC PEPTIDE GlyTM1bZip: TROPOMYOSIN ALPHA CHAIN, BRAIN-3 and GENERAL CONTROL PROTEIN GCN4
B: CHIMERIC PEPTIDE GlyTM1bZip: TROPOMYOSIN ALPHA CHAIN, BRAIN-3 and GENERAL CONTROL PROTEIN GCN4


Theoretical massNumber of molelcules
Total (without water)8,6642
Polymers8,6642
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)10 / 200structures with acceptable covalent geometry, structures with the least restraint violations,target function
RepresentativeModel #1fewest violations

-
Components

#1: Protein/peptide CHIMERIC PEPTIDE GlyTM1bZip: TROPOMYOSIN ALPHA CHAIN, BRAIN-3 and GENERAL CONTROL PROTEIN GCN4


Mass: 4331.915 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The chimera consists of an initial GLY, residues 2-20 of TROPOMYOSIN ALPHA CHAIN, BRAIN-3 and residues 21-38 of GENERAL CONTROL PROTEIN GCN4.
Source: (gene. exp.) Rattus norvegicus, Saccharomyces cerevisiae
Genus: Rattus, Saccharomyces / Species: , / Strain: , / Plasmid: pPROEX HTa / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 / References: UniProt: P18344, UniProt: P03069

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: TRIPLE RESONANCE
NMR detailsText: The structure was determine using triple-resonance NMR spectroscopy. Inter-chain interactions were determined using X-filtered NOESY experiments

-
Sample preparation

DetailsContents: 1-2 mM
Solvent system: 100 mM NaCl, 10 mM phosphate, 10% Deuterium Oxide, pH 6.4
Sample conditionsIonic strength: 0.12 N / pH: 6.4 / Pressure: atmospheric atm / Temperature: 281 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Varian INOVA 500 / Manufacturer: Varian / Model: INOVA 500 / Field strength: 500 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5GUNTERT,WUTHRICHrefinement
VNMR5.3bVARIANdata analysis
DYANA1.5GUNTERT,WUTHRICHstructure solution
AutoAssign1.5ZIMMERMAN, MONTELIONEdata analysis
AutoStructure1HUANG, MONTELIONEstructure solution
Sparky3.74GODDARD, KNELLERdata analysis
RefinementMethod: 1156 CONFORMATIONALLY-RESTRICTING NOE CONSTRAINTS (OUT OF A TOTAL OF 1746 NOE DERIVED DISTANCES) 112 LOOSE DIHEDRAL ANGLE CONSTRAINTS, FORTY-EIGHT BACKBONE INTRA-HELICAL HYDROGEN BOND CONSTRAINTS WERE UTILILIZED.
Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JOURNAL CITATION ABOVE.
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry, structures with the least restraint violations,target function
Conformers calculated total number: 200 / Conformers submitted total number: 10

+
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