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- PDB-1kql: Crystal structure of the C-terminal region of striated muscle alp... -

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Basic information

Entry
Database: PDB / ID: 1kql
TitleCrystal structure of the C-terminal region of striated muscle alpha-tropomyosin at 2.7 angstrom resolution
ComponentsFusion Protein of and striated muscle alpha-tropomyosin and the GCN4 leucine zipper
KeywordsCONTRACTILE PROTEIN / thin filament / tropomyosin / muscle regulation / coiled coil / four-helix bundle
Function / homology
Function and homology information


Striated Muscle Contraction / Smooth Muscle Contraction / positive regulation of heart rate by epinephrine / bleb / FCERI mediated MAPK activation / protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation ...Striated Muscle Contraction / Smooth Muscle Contraction / positive regulation of heart rate by epinephrine / bleb / FCERI mediated MAPK activation / protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / mediator complex binding / actin filament capping / ruffle organization / Oxidative Stress Induced Senescence / positive regulation of ATP-dependent activity / 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 / TFIID-class transcription factor complex binding / amino acid biosynthetic process / positive regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of transcription initiation by RNA polymerase II / cellular response to nutrient levels / stress fiber / cytoskeletal protein binding / cardiac muscle contraction / positive regulation of stress fiber assembly / muscle contraction / positive regulation of cell adhesion / cellular response to amino acid starvation / negative regulation of cell migration / actin filament organization / cellular response to reactive oxygen species / actin filament / wound healing / RNA polymerase II transcription regulator complex / ruffle membrane / actin filament binding / disordered domain specific binding / actin cytoskeleton / regulation of cell shape / 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 / in utero embryonic development / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / 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 / protein-containing complex / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Tropomyosins signature. / Tropomyosin / Tropomyosin / : / Basic region leucine zipper / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain ...Tropomyosins signature. / Tropomyosin / Tropomyosin / : / Basic region leucine zipper / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / General control transcription factor GCN4 / Tropomyosin alpha-1 chain
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Molecular replacement using a specially built model / Resolution: 2.7 Å
AuthorsLi, Y. / Mui, S. / Brown, J.H. / Strand, J. / Reshetnikova, L. / Tobacman, L.S. / Cohen, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: The crystal structure of the C-terminal fragment of striated-muscle alpha-tropomyosin reveals a key troponin T recognition site.
Authors: Li, Y. / Mui, S. / Brown, J.H. / Strand, J. / Reshetnikova, L. / Tobacman, L.S. / Cohen, C.
History
DepositionJan 7, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Dec 21, 2022Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Mar 13, 2024Group: Data collection / Source and taxonomy / Category: chem_comp_atom / chem_comp_bond / entity_src_gen
Revision 1.6Apr 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: Fusion Protein of and striated muscle alpha-tropomyosin and the GCN4 leucine zipper
B: Fusion Protein of and striated muscle alpha-tropomyosin and the GCN4 leucine zipper


Theoretical massNumber of molelcules
Total (without water)13,2072
Polymers13,2072
Non-polymers00
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-21 kcal/mol
Surface area8630 Å2
MethodPISA
2
A: Fusion Protein of and striated muscle alpha-tropomyosin and the GCN4 leucine zipper
B: Fusion Protein of and striated muscle alpha-tropomyosin and the GCN4 leucine zipper

A: Fusion Protein of and striated muscle alpha-tropomyosin and the GCN4 leucine zipper
B: Fusion Protein of and striated muscle alpha-tropomyosin and the GCN4 leucine zipper


Theoretical massNumber of molelcules
Total (without water)26,4144
Polymers26,4144
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+2/31
Buried area7310 Å2
ΔGint-71 kcal/mol
Surface area14630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.202, 137.202, 40.071
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11B-4-

HOH

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Components

#1: Protein Fusion Protein of and striated muscle alpha-tropomyosin and the GCN4 leucine zipper


Mass: 6603.480 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal methionine followed by sequence database residues 255-278 of GCN4 leucine zipper and then C-terminal sequence database residues 254-284 of rat striated muscle alpha-tropomyosin
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast), (gene. exp.) Rattus norvegicus (Norway rat)
Genus: Saccharomyces, Rattus / Species: , / Strain: , / Plasmid: pET3d / Gene (production host): GCN4, ARG9 / Production host: Escherichia coli (E. coli) / Strain (production host): DE3
References: UniProt: P03069, GenBank: 207514, UniProt: P04692*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 4.12 Å3/Da / Density % sol: 70 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: PEG 550 monomethylether, glycerol, sodium chloride, magnesium acetate, bicine, tris buffer, dithiothreitol, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mg/mlprotein1drop
220 %glycerol1drop
31 mMdithiothreitol1drop
410 mMTris1droppH7.5
512 %PEG550MME1drop
660 mMBicine1droppH9.0
7300 mM1dropNaCl
860 mM1dropMg(Ac)2
94 %PEG550 MME1reservoir
10100 mM1reservoirNaCl
1120 mM1reservoirMg(Ac)2
12200 mMbicine1reservoirpH8.3

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.909 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 20, 2001 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.909 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 7229 / Num. obs: 7221 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 12 % / Biso Wilson estimate: 82.3 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 34.9
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 9.14 / Num. unique all: 708 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 9999 Å / Num. measured all: 86920 / Rmerge(I) obs: 0.052
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.217

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: Molecular replacement using a specially built model
Starting model: a specially built 56-residue two-stranded coiled-coil that contains a 24 residue fragment from the high resolution structure of the GCN4 leucine zipper

Resolution: 2.7→44.91 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2889 508 -RANDOM
Rwork0.2523 ---
all0.2551 6469 --
obs0.2551 6469 99.6 %-
Displacement parametersBiso mean: 93.4 Å2
Baniso -1Baniso -2Baniso -3
1-2.22 Å215.96 Å20 Å2
2--2.22 Å20 Å2
3----4.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.7→44.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms892 0 0 27 919
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d15.6
X-RAY DIFFRACTIONc_improper_angle_d0.64
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection obs
2.7-2.80.3353490.32955680.04617
2.8-2.910.3547450.3134621
2.91-3.040.3658530.2986636
3.04-3.20.3673490.2696628
3.2-3.40.277500.2628636
3.4-3.660.2816600.297644
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 9999 Å / Num. reflection obs: 6498 / % reflection Rfree: 8 % / Rfactor all: 0.2551 / Rfactor obs: 0.251 / Rfactor Rfree: 0.289 / Rfactor Rwork: 0.251
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.012
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg15.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.64
LS refinement shell
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 2.69 Å / Rfactor Rfree: 0.3353 / Rfactor Rwork: 0.3295 / Rfactor obs: 0.3295

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