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- PDB-3azd: Crystal structure of tropomyosin N-terminal fragment at 0.98A res... -

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Basic information

Entry
Database: PDB / ID: 3azd
TitleCrystal structure of tropomyosin N-terminal fragment at 0.98A resolution
Componentsshort alpha-tropomyosin,transcription factor GCN4
KeywordsACTIN-BINDING PROTEIN / coiled-coil / muscle protein
Function / homology
Function and homology information


protein localization to nuclear periphery / 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 / TFIID-class transcription factor complex binding / amino acid biosynthetic process / positive regulation of transcription initiation by RNA polymerase II ...protein localization to nuclear periphery / 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 / TFIID-class transcription factor complex binding / amino acid biosynthetic process / positive regulation of transcription initiation by RNA polymerase II / positive regulation of RNA polymerase II transcription preinitiation complex assembly / cellular response to amino acid starvation / RNA polymerase II transcription regulator complex / : / actin binding / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / cytoskeleton / 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 / 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
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 1, alpha
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Saccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.98 Å
AuthorsMeshcheryakov, V.A. / Krieger, I. / Kostyukova, A.S. / Samatey, F.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Structure of a tropomyosin N-terminal fragment at 0.98 A resolution
Authors: Meshcheryakov, V.A. / Krieger, I. / Kostyukova, A.S. / Samatey, F.A.
History
DepositionMay 23, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.pdbx_description
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: short alpha-tropomyosin,transcription factor GCN4
B: short alpha-tropomyosin,transcription factor GCN4


Theoretical massNumber of molelcules
Total (without water)8,5502
Polymers8,5502
Non-polymers00
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-15 kcal/mol
Surface area5230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.000, 33.000, 52.030
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein/peptide short alpha-tropomyosin,transcription factor GCN4


Mass: 4274.863 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized tropomyosin fragment
Source: (synth.) Rattus norvegicus (Norway rat), (synth.) Saccharomyces cerevisiae S288c (yeast)
References: UniProt: Q6AZ25, UniProt: P03069
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 1.91 Å3/Da / Density % sol: 35.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.17M ammonium sulfate, 10% PEG 4000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 18, 2009
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 0.98→15.73 Å / Num. all: 34162 / Num. obs: 34162 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 0.98→1.03 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IHQ model1

1ihq


Resolution: 0.98→14.29 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.961 / SU B: 0.144 / SU ML: 0.008 / Cross valid method: THROUGHOUT / ESU R Free: 0.005 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17084 1799 5 %RANDOM
Rwork0.16737 ---
obs0.16753 34162 98.74 %-
all-34162 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 0.98→14.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms504 0 0 91 595
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022506
X-RAY DIFFRACTIONr_angle_refined_deg2.4151.983672
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.904558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.52722.85728
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.1815112
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.712158
X-RAY DIFFRACTIONr_chiral_restr0.130.276
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02364
X-RAY DIFFRACTIONr_mcbond_it1.4031.5296
X-RAY DIFFRACTIONr_mcangle_it1.8752472
X-RAY DIFFRACTIONr_scbond_it2.7443210
X-RAY DIFFRACTIONr_scangle_it3.0174.5200
LS refinement shellResolution: 0.98→1.005 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 135 -
Rwork0.319 2554 -
obs--99.26 %

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