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- PDB-5kht: Crystal structure of the N-terminal fragment of tropomyosin isofo... -

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Basic information

Entry
Database: PDB / ID: 5kht
TitleCrystal structure of the N-terminal fragment of tropomyosin isoform Tpm1.1 at 1.5 A resolution
ComponentsTropomyosin alpha-1 chain,General control protein GCN4
Keywordsactin-binding protein / tropomyosin / coiled coil
Function / homology
Function and homology information


positive regulation of heart rate by epinephrine / muscle thin filament tropomyosin / bleb / negative regulation of vascular associated smooth muscle cell migration / regulation of muscle contraction / 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 ...positive regulation of heart rate by epinephrine / muscle thin filament tropomyosin / bleb / negative regulation of vascular associated smooth muscle cell migration / regulation of muscle contraction / 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 / ruffle organization / nitrogen catabolite activation of transcription from RNA polymerase II promoter / Oxidative Stress Induced Senescence / positive regulation of ATP-dependent activity / Striated Muscle Contraction / ventricular cardiac muscle tissue morphogenesis / structural constituent of muscle / regulation of heart contraction / sarcomere organization / negative regulation of vascular associated smooth muscle cell proliferation / TFIID-class transcription factor complex binding / positive regulation of cell adhesion / Smooth Muscle Contraction / 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 / cytoskeleton organization / cytoskeletal protein binding / cellular response to amino acid starvation / sarcomere / negative regulation of cell migration / actin filament / actin filament organization / wound healing / structural constituent of cytoskeleton / ruffle membrane / cellular response to reactive oxygen species / RNA polymerase II transcription regulator complex / : / actin filament binding / actin cytoskeleton / actin binding / regulation of cell shape / 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 / cytoskeleton / 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 / identical protein binding / nucleus / cytosol
Similarity search - Function
Vasodilator-stimulated phosphoprotein / 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 ...Vasodilator-stimulated phosphoprotein / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / General control transcription factor GCN4 / Tropomyosin alpha-1 chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4964 Å
AuthorsKostyukova, A.S. / Krieger, I. / Yoon, Y.-H. / Tolkatchev, D. / Samatey, F.A.
CitationJournal: Protein Sci. / Year: 2018
Title: Structural destabilization of tropomyosin induced by the cardiomyopathy-linked mutation R21H.
Authors: Ly, T. / Krieger, I. / Tolkatchev, D. / Krone, C. / Moural, T. / Samatey, F.A. / Kang, C. / Kostyukova, A.S.
History
DepositionJun 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.2Jan 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tropomyosin alpha-1 chain,General control protein GCN4
B: Tropomyosin alpha-1 chain,General control protein GCN4
C: Tropomyosin alpha-1 chain,General control protein GCN4
D: Tropomyosin alpha-1 chain,General control protein GCN4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2388
Polymers21,8134
Non-polymers4244
Water3,045169
1
A: Tropomyosin alpha-1 chain,General control protein GCN4
C: Tropomyosin alpha-1 chain,General control protein GCN4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1194
Polymers10,9072
Non-polymers2122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-22 kcal/mol
Surface area7180 Å2
MethodPISA
2
B: Tropomyosin alpha-1 chain,General control protein GCN4
D: Tropomyosin alpha-1 chain,General control protein GCN4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1194
Polymers10,9072
Non-polymers2122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-17 kcal/mol
Surface area7460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.970, 36.470, 36.710
Angle α, β, γ (deg.)65.21, 74.71, 78.98
Int Tables number1
Space group name H-MP1

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Components

#1: Protein/peptide
Tropomyosin alpha-1 chain,General control protein GCN4 / Alpha-tropomyosin / Tropomyosin-1 / Amino acid biosynthesis regulatory protein


Mass: 5453.298 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TPM1, C15orf13, TMSA, GCN4, AAS3, ARG9, YEL009C / Strain: ATCC 204508 / S288c / Production host: Escherichia coli (E. coli) / References: UniProt: P09493, UniProt: P03069
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 8000, Hepes/sodium hydroxide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4964→34.549 Å / Num. obs: 21841 / % possible obs: 83.11 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 13.1
Reflection shellResolution: 1.4964→1.5338 Å / Rmerge(I) obs: 0.412

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSv.2015data reduction
XSCALENovember 3, 2014data scaling
PHASERv2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Chimeric model built by Phyre

Resolution: 1.4964→34.549 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 2.07 / Phase error: 31.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.249 1986 9.1 %
Rwork0.2055 --
obs0.2094 21830 83.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4964→34.549 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1512 0 28 169 1709
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071608
X-RAY DIFFRACTIONf_angle_d1.0112122
X-RAY DIFFRACTIONf_dihedral_angle_d16.934686
X-RAY DIFFRACTIONf_chiral_restr0.066225
X-RAY DIFFRACTIONf_plane_restr0.004279
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4964-1.53380.4028810.2833702X-RAY DIFFRACTION41
1.5338-1.57530.2946900.2702938X-RAY DIFFRACTION55
1.5753-1.62170.33431180.25941208X-RAY DIFFRACTION72
1.6217-1.6740.36841530.24991556X-RAY DIFFRACTION91
1.674-1.73380.34081610.24531545X-RAY DIFFRACTION91
1.7338-1.80330.2661500.24371528X-RAY DIFFRACTION89
1.8033-1.88530.29071550.24731469X-RAY DIFFRACTION87
1.8853-1.98470.31521560.24251587X-RAY DIFFRACTION93
1.9847-2.1090.29041540.20591540X-RAY DIFFRACTION91
2.109-2.27180.22321490.19311500X-RAY DIFFRACTION88
2.2718-2.50040.23621550.20031573X-RAY DIFFRACTION93
2.5004-2.86210.27551600.20641533X-RAY DIFFRACTION90
2.8621-3.60530.25121470.19031597X-RAY DIFFRACTION93
3.6053-34.55830.18061570.18371568X-RAY DIFFRACTION92

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