[English] 日本語
Yorodumi
- PDB-2g9j: Complex of TM1a(1-14)Zip with TM9a(251-284): a model for the poly... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2g9j
TitleComplex of TM1a(1-14)Zip with TM9a(251-284): a model for the polymerization domain ("overlap region") of tropomyosin, Northeast Structural Genomics Target OR9
Components
  • Tropomyosin 1 alpha chain
  • Tropomyosin 1 alpha chain/General control protein GCN4
KeywordsSTRUCTURAL PROTEIN / TROPOMYOSIN / PEPTIDE COMPLEX / OVERLAP COMPLEX / INTERMOLECULAR JUNCTION / N-TERMINAL:C-TERMINAL INTERFACE / PARALLEL COILED COIL / POLYMERIZATION DOMAIN / Structural Genomics / PSI-2 / 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 / regulation of ATP-dependent activity / : / bleb / negative regulation of vascular associated smooth muscle cell migration / muscle filament sliding / protein localization to nuclear periphery / FCERI mediated MAPK activation ...Striated Muscle Contraction / Smooth Muscle Contraction / positive regulation of heart rate by epinephrine / regulation of ATP-dependent activity / : / bleb / negative regulation of vascular associated smooth muscle cell migration / muscle filament sliding / protein localization to nuclear periphery / FCERI mediated MAPK activation / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / actin filament capping / ruffle organization / nitrogen catabolite activation of transcription from RNA polymerase II promoter / Oxidative Stress Induced Senescence / positive regulation of ATP-dependent activity / ventricular cardiac muscle tissue morphogenesis / myofibril / sarcomere organization / negative regulation of vascular associated smooth muscle cell proliferation / TFIID-class transcription factor complex binding / positive regulation of cell adhesion / positive regulation of transcription initiation by RNA polymerase II / positive regulation of RNA polymerase II transcription preinitiation complex assembly / amino acid biosynthetic process / cardiac muscle contraction / stress fiber / positive regulation of stress fiber assembly / cytoskeletal protein binding / cellular response to amino acid starvation / negative regulation of cell migration / muscle contraction / actin filament / actin filament organization / wound healing / ruffle membrane / cellular response to reactive oxygen species / RNA polymerase II transcription regulator complex / : / disordered domain specific binding / actin filament binding / actin cytoskeleton / actin binding / regulation of cell shape / DNA-binding transcription activator activity, RNA polymerase II-specific / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription regulator complex / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / intracellular signal transduction / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor 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 superfamily / Basic-leucine zipper domain
Similarity search - Domain/homology
General control transcription factor GCN4 / Tropomyosin alpha-1 chain / Tropomyosin alpha-1 chain
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Saccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / Initail structure was calculated with Torsion Angle Dynamics, refined with simulated annealing, included a term for explicit solvent in the refinement protocol.
AuthorsGreenfield, N.J. / Huang, Y.J. / Swapna, G.V.T. / Bhattacharya, A. / Singh, A. / Montelione, G.T. / Hitchcock-DeGregori, S.E. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Solution NMR Structure of the Junction between Tropomyosin Molecules: Implications for Actin Binding and Regulation.
Authors: Greenfield, N.J. / Huang, Y.J. / Swapna, G.V. / Bhattacharya, A. / Rapp, B. / Singh, A. / Montelione, G.T. / Hitchcock-Degregori, S.E.
History
DepositionMar 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Tropomyosin 1 alpha chain
A: Tropomyosin 1 alpha chain/General control protein GCN4
D: Tropomyosin 1 alpha chain
B: Tropomyosin 1 alpha chain/General control protein GCN4


Theoretical massNumber of molelcules
Total (without water)16,1754
Polymers16,1754
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 19610 structures from initial DYANA calcultions with the lowest target functions were refined using CNS. The structures back calculated data agree with experimental NOESY spectra. The structures have acceptable covalent geometry, favorable non-bond energy, the lowest energy and the fewest restraint violations.
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide Tropomyosin 1 alpha chain


Mass: 4177.707 Da / Num. of mol.: 2 / Fragment: TM9a(251-284) / Mutation: N279K
Source method: isolated from a genetically manipulated source
Details: This peptide is the product of a synthetic gene. It contains GCG at the N terminus followed by residues 251-284 of rat striated tropomyosin. The peptide has the mutation N279K
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: TPM1 / Plasmid: Pproex Hta / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: Q63609, UniProt: P04692*PLUS
#2: Protein/peptide Tropomyosin 1 alpha chain/General control protein GCN4


Mass: 3909.709 Da / Num. of mol.: 2 / Fragment: TM1a(1-14)Zip
Source method: isolated from a genetically manipulated source
Details: This peptide is the product of a synthetic gene. It contains a gly at the N terminus followed by the first 14 residues of rat striated tropomyosin and the last 18 residues of yeast GCN4
Source: (gene. exp.) Rattus norvegicus, Saccharomyces cerevisiae
Genus: Rattus, Saccharomyces / Species: , / Strain: , / Gene: TPM1 / Plasmid: pSBETc, pET3a, and pET11a cut with NdeI and BamHI / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS
References: UniProt: Q63609, UniProt: P03069, UniProt: P04692*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 15N-separated NOESY
1323D 13C-separated NOESY
14313C X-filtered NOESY
1543D 15N-separated NOESY
1643D 13C-separated NOESY
17513C X-filtered NOESY
18613C X-filtered NOESY
19713C X-filtered NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
11mM complex of TM1a(1-14)Zip U-15N withTM9a(251-284)U15N, 100 mM NaCl, 10 mM sodium phospate 10% deuterium oxide pH 6.5100 mM NaCl, 10 mM sodium phospate 10% deuterium oxide pH 6.5
21mM complex of TM1a(1-14)Zip U15N/U13C with TM9a(251-284) unlabled, 100 mM NaCl, 10 mM sodium phospate 10% deuterium oxide pH 6.5100 mM NaCl, 10 mM sodium phospate 10% deuterium oxide pH 6.5
31mM complex of TM1a(1-14)Zip U15N/U13C with TM9a(251-284) unlabled, 100 mM NaCl, 10 mM sodium phospate 99.9% deuterium oxide pH 6.5100 mM NaCl, 10 mM sodium phospate 99.9% deuterium oxide pH 6.5
41mM complex of TM1a(1-14)Zip unlabeled with TM9a(251-284)U15N/U13C, 100 mM NaCl, 10 mM sodium phospate 10% deuterium oxide pH 6.5 or in 99.9% deuterium oxide100 mM NaCl, 10 mM sodium phospate 10% deuterium oxide pH 6.5 or in 99.9% deuterium oxide
51mM complex of TM1a(1-14)Zip unlabeled with TM9a(251-284)U15N/U13C, 100 mM NaCl, 10 mM sodium phospate 10% deuterium oxide 99.9% deuterium oxide, pH 6.5100 mM NaCl, 10 mM sodium phospate 10% deuterium oxide 99.9% deuterium oxide, pH 6.5
61mM complex of TM1a(1-14), one chain labeled U15N/U13C the other chain unlabeled, with unlabeled TM9a(251-284), 100 mM NaCl, 10 mM sodium phospate 10% deuterium oxide pH 6.5100 mM NaCl, 10 mM sodium phospate 10% deuterium oxide pH 6.5
71mM complex of TM9a(251-284), one chain labeled U15N/U13C the other chain unlabeled, with unlabele TM1a(1-14)Zip, 100 mM NaCl, 10 mM sodium phospate 10% deuterium oxide pH 6.5100 mM NaCl, 10 mM sodium phospate 10% deuterium oxide pH 6.5
Sample conditionsIonic strength: 0.14 / pH: 6.5 / Pressure: ambient / Temperature: 10 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002
Bruker AVANCEBrukerAVANCE6003

-
Processing

NMR software
NameVersionDeveloperClassification
AutoStructureCustomHuangdata analysis
DYANA1.5Guntertstructure solution
VNMR6.1 cVariancollection
NMRPipe2005Delaglioprocessing
CNS1.1Brungerrefinement
Sparky3.74Goddarddata analysis
XwinNMR3.5 pl 6Brukercollection
RefinementMethod: Initail structure was calculated with Torsion Angle Dynamics, refined with simulated annealing, included a term for explicit solvent in the refinement protocol.
Software ordinal: 1
Details: The structures were based on a total of 2630 restraints, 2198 conformationally restricting NOEs, 232 dihedral angle constraints and 200 hydrogen bond constraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: 10 structures from initial DYANA calcultions with the lowest target functions were refined using CNS. The structures back calculated data agree with experimental NOESY ...Conformer selection criteria: 10 structures from initial DYANA calcultions with the lowest target functions were refined using CNS. The structures back calculated data agree with experimental NOESY spectra. The structures have acceptable covalent geometry, favorable non-bond energy, the lowest energy and the fewest restraint violations.
Conformers calculated total number: 196 / 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://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