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- PDB-2g9j: Complex of TM1a(1-14)Zip with TM9a(251-284): a model for the poly... -

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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 / regulation of ATP-dependent activity / positive regulation of heart rate by epinephrine / Activation of the AP-1 family of transcription factors / protein localization to nuclear periphery / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / response to amino acid starvation / mediator complex binding ...Striated Muscle Contraction / Smooth Muscle Contraction / regulation of ATP-dependent activity / positive regulation of heart rate by epinephrine / Activation of the AP-1 family of transcription factors / protein localization to nuclear periphery / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / response to amino acid starvation / mediator complex binding / bleb / ruffle organization / positive regulation of ATP-dependent activity / actin filament capping / muscle filament sliding / sarcomere organization / ventricular cardiac muscle tissue morphogenesis / negative regulation of vascular associated smooth muscle cell migration / amino acid biosynthetic process / myofibril / TFIID-class transcription factor complex binding / 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 / positive regulation of stress fiber assembly / cardiac muscle contraction / cellular response to nutrient levels / cytoskeletal protein binding / stress fiber / in utero embryonic development / muscle contraction / positive regulation of cell adhesion / negative regulation of cell migration / cellular response to amino acid starvation / actin filament organization / wound healing / actin filament / RNA polymerase II transcription regulator complex / cellular response to reactive oxygen species / ruffle membrane / disordered domain specific binding / regulation of cell shape / actin filament binding / actin cytoskeleton / transcription regulator complex / actin binding / DNA-binding transcription activator activity, RNA polymerase II-specific / 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 / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / protein-containing complex / DNA-templated transcription / 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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Experimental details

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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

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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

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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

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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

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