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- PDB-1mv4: TM9A251-284: A Peptide Model of the C-Terminus of a Rat Striated ... -

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Basic information

Entry
Database: PDB / ID: 1mv4
TitleTM9A251-284: A Peptide Model of the C-Terminus of a Rat Striated Alpha Tropomyosin
ComponentsTropomyosin 1 alpha chain
KeywordsDE NOVO PROTEIN / TROPOMYOSIN / EXON 9A / ACTIN-BINDING / TROPONIN BINDING / MUSCLE / ALPHA-HELIX / COILED-COIL / DIMER / PEPTIDE-MODEL / TWO-CHAINED / DISULFIDE CROSS-LINKED
Function / homology
Function and homology information


Striated Muscle Contraction / Smooth Muscle Contraction / positive regulation of heart rate by epinephrine / bleb / actin filament capping / ruffle organization / muscle filament sliding / sarcomere organization / ventricular cardiac muscle tissue morphogenesis / negative regulation of vascular associated smooth muscle cell migration ...Striated Muscle Contraction / Smooth Muscle Contraction / positive regulation of heart rate by epinephrine / bleb / actin filament capping / ruffle organization / muscle filament sliding / sarcomere organization / ventricular cardiac muscle tissue morphogenesis / negative regulation of vascular associated smooth muscle cell migration / myofibril / negative regulation of vascular associated smooth muscle cell proliferation / cytoskeletal protein binding / cardiac muscle contraction / stress fiber / positive regulation of stress fiber assembly / positive regulation of cell adhesion / muscle contraction / negative regulation of cell migration / actin filament organization / cellular response to reactive oxygen species / actin filament / wound healing / ruffle membrane / disordered domain specific binding / actin filament binding / regulation of cell shape / actin cytoskeleton / actin binding / in utero embryonic development / protein heterodimerization activity / protein homodimerization activity / protein-containing complex / identical protein binding / cytoplasm
Similarity search - Function
Tropomyosins signature. / Tropomyosin / Tropomyosin
Similarity search - Domain/homology
Tropomyosin alpha-1 chain
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / 1648 CONFORMATIONALLY- RESTRICTING NOE CONSTRAINTS (OUT OF A TOTAL OF 2036 NOE DERIVED DISTANCES) 52 LOOSE DIHEDRAL ANGLE CONSTRAINTS, 48 BACKBONE INTRA- HELICAL HYDROGEN BOND CONSTRAINTS WERE UTILILIZED.
AuthorsGreenfield, N.J. / Swapna, G.V.T. / Huang, Y. / Palm, T. / Graboski, S. / Montelione, G.T. / Hitchcock-Degregori, S.E.
CitationJournal: Biochemistry / Year: 2003
Title: The Structure of the Carboxyl Terminus of Striated alpha-Tropomyosin in Solution Reveals an Unusual Parallel Arrangement of Interacting alpha-Helices
Authors: Greenfield, N.J. / Swapna, G.V.T. / Huang, Y. / Palm, T. / Graboski, S. / Montelione, G.T. / Hitchcock-DeGregori, S.E.
History
DepositionSep 24, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2003Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: 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 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE THIS SEQUENCE HAS A SYNTHETIC GCG AT N-TERMINUS AND CONTAINS THE MUTATION N279K. THE ...SEQUENCE THIS SEQUENCE HAS A SYNTHETIC GCG AT N-TERMINUS AND CONTAINS THE MUTATION N279K. THE SEQUENCE DATABASE MATCH, HOWEVER, erroneously HAS A K AT THIS POSITION as well. The sequence in the database should have an ASN at position 279, which has been engineered to LYS in this entry.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tropomyosin 1 alpha chain
B: Tropomyosin 1 alpha chain


Theoretical massNumber of molelcules
Total (without water)8,3552
Polymers8,3552
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 COVALENT GEOMETRY, STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Tropomyosin 1 alpha chain / Alpha-tropomyosin


Mass: 4177.707 Da / Num. of mol.: 2 / Fragment: C-TERMINAL (RESIDUES 251-284)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Tissue: SKELETAL MUSCLE / Gene: TPM1 / Plasmid: PPROEX HTA / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 / References: UniProt: P04692
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
1313D 13C-X-FILTERED NOESY
NMR detailsText: THE RESONANCE ASSIGNMENTS WERE MADE USING THROUGH BOND TRIPLE RESONANCE EXPERIMENTS INCLUDING HN(CA)CO, HNCO, H(CA)(C0)NH, H(CA)NH, CA(CO)NH, CANH, CBCA(CO)NH, CBCANH, HCCH-COSY AND CCH-COSY

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Sample preparation

DetailsContents: 1-2 MM
Solvent system: 100 MM NACL, 20 MM POTASSIUM PHOSPHATE, 10% DUETERIUM OXIDE, 90% H20, PH 6.4
Sample conditionsIonic strength: 0.12 N / pH: 6.4 / Pressure: 1 atm / Temperature: 283.00 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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
DYANA1.5GUNTERT, WUTHRICHrefinement
VNMR5.3BVARIAN ASSOCIATESstructure solution
DYANA1.5GUNTERT, WUTHRICHstructure solution
AutoAssign1HUANG, MONTELIONEstructure solution
AutoStructure1HUANG, MONTELIONEstructure solution
Sparky3.74GODDARD, KNELLERstructure solution
RefinementMethod: 1648 CONFORMATIONALLY- RESTRICTING NOE CONSTRAINTS (OUT OF A TOTAL OF 2036 NOE DERIVED DISTANCES) 52 LOOSE DIHEDRAL ANGLE CONSTRAINTS, 48 BACKBONE INTRA- HELICAL HYDROGEN BOND CONSTRAINTS WERE UTILILIZED.
Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN REFERENCE CITED ABOVE
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: STRUCTURES WITH COVALENT GEOMETRY, STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS
Conformers calculated total number: 200 / Conformers submitted total number: 10

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