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- PDB-2k8x: GlyTM1b(1-19)zip: A Chimeric Peptide Model of the N-Terminus of a... -

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Basic information

Entry
Database: PDB / ID: 2k8x
TitleGlyTM1b(1-19)zip: A Chimeric Peptide Model of the N-Terminus of a Rat Short Alpha-Tropomyosin with the N-Terminus Encoded by Exon 1b in Complex with TM9d(252-284), a Peptide Model Containing the C Terminus of Alpha-Tropomyosin Encoded by Exon 9d
ComponentsTM1b(1-19)Zip
KeywordsACTIN-BINDING PROTEIN / tropomyosin / N terminus / protein complex / C terminus / tropomodulin binding protein / overlap complex / coiled coil / cytoskeletal regulatory protein
Function / homology
Function and homology information


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 / nitrogen catabolite activation of transcription from RNA polymerase II promoter / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding ...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 / nitrogen catabolite activation of transcription from RNA polymerase II promoter / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding / positive regulation of transcription initiation by RNA polymerase II / positive regulation of RNA polymerase II transcription preinitiation complex assembly / amino acid biosynthetic process / cellular response to amino acid starvation / RNA polymerase II transcription regulator complex / : / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / intracellular signal transduction / 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 / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus
Similarity search - Function
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
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailsThe structure of TM1b(1-19)Zip labeled with 13C and 15N in the presence of unlabeled TM9d(252-284)
AuthorsGreenfield, N.J. / Kotylanskaya, L. / Hitchcock-DeGregori, S.E.
CitationJournal: Biochemistry / Year: 2009
Title: Structure of the N terminus of a nonmuscle alpha-tropomyosin in complex with the C terminus: implications for actin binding.
Authors: Greenfield, N.J. / Kotlyanskaya, L. / Hitchcock-DeGregori, S.E.
History
DepositionSep 25, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 3, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation
Category: database_2 / pdbx_nmr_exptl_sample ...database_2 / pdbx_nmr_exptl_sample / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_exptl_sample.isotopic_labeling / _pdbx_nmr_sample_details.label / _pdbx_nmr_sample_details.type / _pdbx_nmr_software.name
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TM1b(1-19)Zip
B: TM1b(1-19)Zip


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_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200target function
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide TM1b(1-19)Zip


Mass: 4331.915 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: TPM1 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P03069*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: The structure of TM1b(1-19)Zip labeled with 13C and 15N in the presence of unlabeled TM9d(252-284)
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1222D 1H-15N HSQC
1313D CBCA(CO)NH
1413D HNCO
1512D 1H-15N HSQC
1613D HNCA
1713D HN(CA)CB
1813D HBHA(CO)NH
1913D HN(CO)CA
11013D 1H-13C NOESY
111113C 15N X-filtered NOESY
112313C 15N X-filtered NOESY
11312D 1H-13C HSQC
11413D (H)CCH-COSY
11513D 1H-15N NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM [U-99% 13C; U-99% 15N] TM1b(1-19)Zip, 1 mM TM9d(252-284), 90% H2O/10% D2Osample_190% H2O/10% D2O
solution21 mM [U-15N] TM1b(1-19)Zip, 1 mM TM9d(252-284), 90% H2O/10% D2Osample_290% H2O/10% D2O
solution30.5 mM [U-99% 13C; U-99% 15N] TM1b(1-19)Zip, 0.5 mM TM1b(1-19)Zip, 1 mM TM9d(252-284), 90% H2O/10% D2Osample_390% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMTM1b(1-19)Zip[U-99% 13C; U-99% 15N]1
1 mMTM9d(252-284)natural abundance1
1 mMTM1b(1-19)Zip[U-15N]2
1 mMTM9d(252-284)natural abundance2
0.5 mMTM1b(1-19)Zip[U-99% 13C; U-99% 15N]3
1 mMTM9d(252-284)natural abundance3
Sample conditionsIonic strength: 0.14 / pH: 6.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
AutoStructure1.12Huang, Y. et al.structure solution
CNS1.1Brunger, A.T. et al.refinement
Sparky3.111Goddard, T. et al.peak picking
NMRPipe1.1Delaglio, F. et al.processing
NMRDrawDelaglio, F. et al.processing
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
Details: The structures obtained using AutoStructure were refined using CNS and included a term for explicit solvent in the refinement protocol
NMR constraintsNA alpha-angle constraints total count: 0 / NA beta-angle constraints total count: 0 / NA chi-angle constraints total count: 0 / NA epsilon-angle constraints total count: 0 / NA gamma-angle constraints total count: 0 / NA other-angle constraints total count: 0 / NOE constraints total: 3276 / NOE intraresidue total count: 1544 / NOE long range total count: 128 / NOE medium range total count: 864 / NOE sequential total count: 740 / Disulfide bond constraints total count: 0 / Hydrogen bond constraints total count: 112 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 128 / Protein psi angle constraints total count: 128
NMR representativeSelection criteria: fewest violations
NMR ensembleAverage constraint violations per residue: 0 / Average constraints per residue: 0 / Average distance constraint violation: 0 Å / Conformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 10 / Maximum distance constraint violation: 0 Å / Maximum upper distance constraint violation: 0 Å
NMR ensemble rmsDistance rms dev: 0 Å / Distance rms dev error: 0 Å

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