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- PDB-1ytz: Crystal structure of skeletal muscle troponin in the Ca2+-activat... -

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Basic information

Entry
Database: PDB / ID: 1ytz
TitleCrystal structure of skeletal muscle troponin in the Ca2+-activated state
Components
  • Troponin C
  • Troponin I
  • Troponin T
KeywordsCONTRACTILE PROTEIN / troponin / muscle / thin filament / actin binding / calcium
Function / homology
Function and homology information


troponin C binding / Striated Muscle Contraction / troponin complex / regulation of muscle contraction / tropomyosin binding / troponin I binding / skeletal muscle contraction / cardiac muscle contraction / actin binding / calcium ion binding
Similarity search - Function
Troponin complex, TnI/TnT subunit / Troponin T / : / Troponin / Troponin domain superfamily / Troponin / EF hand domain / EF-hand domain pair / EF-hand / : ...Troponin complex, TnI/TnT subunit / Troponin T / : / Troponin / Troponin domain superfamily / Troponin / EF hand domain / EF-hand domain pair / EF-hand / : / Recoverin; domain 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-DR6 / Troponin C, skeletal muscle / Troponin T, fast skeletal muscle isoforms / Troponin I, fast skeletal muscle
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsVinogradova, M.V. / Stone, D.B. / Malanina, G.G. / Karatzaferi, C. / Cooke, R. / Mendelson, R.A. / Fletterick, R.J.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Ca2+-regulated structural changes in troponin
Authors: Vinogradova, M.V. / Stone, D.B. / Malanina, G.G. / Karatzaferi, C. / Cooke, R. / Mendelson, R.A. / Fletterick, R.J.
History
DepositionFeb 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
T: Troponin T
I: Troponin I
C: Troponin C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,81610
Polymers52,0723
Non-polymers4,7447
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11400 Å2
ΔGint-109 kcal/mol
Surface area24960 Å2
MethodPISA
2
T: Troponin T
I: Troponin I
C: Troponin C
hetero molecules

T: Troponin T
I: Troponin I
C: Troponin C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,63220
Polymers104,1446
Non-polymers9,48814
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+3/21
Buried area25930 Å2
ΔGint-235 kcal/mol
Surface area46790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.608, 138.608, 83.676
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 3 types, 3 molecules TIC

#1: Protein Troponin T


Mass: 12694.692 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P12620
#2: Protein Troponin I / Troponin I / fast-twitch isoform


Mass: 21116.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P68246
#3: Protein Troponin C


Mass: 18261.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: TNNC2 / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P02588

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Non-polymers , 3 types, 40 molecules

#4: Chemical ChemComp-DR6 / ALPHA-[4-(1,1,3,3 - TETRAMETHYLBUTYL)PHENYL]-OMEGA-HYDROXY-POLY(OXY-1,2-ETHANEDIYL) / OCTYLPHENOXYPOLYETHOXYETHANOL / ALKYLPHENOL-HYDROXYPOLYOXYETHEYLENE / TRITON X-305 / ANAPOE-305


Mass: 1527.901 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C74H142O31
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 3.864 Å3/Da / Density % sol: 67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.4 M NaH2PO4/1.6 M K2HPO4, 200 mM NaCl, 0.1 M immidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 22, 2002
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3→25 Å / Num. all: 16801 / Num. obs: 16095 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.055
Reflection shellResolution: 3→3.11 Å / % possible all: 90.8

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→25 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.3375 785 Random
Rwork0.2893 --
all0.2893 16801 -
obs0.2893 16088 -
Refinement stepCycle: LAST / Resolution: 3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3164 0 85 33 3282
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.00909
X-RAY DIFFRACTIONx_angle_deg1.28568
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
3-3.140.4623890.4174X-RAY DIFFRACTION183489
3.14-3.30.4324820.385X-RAY DIFFRACTION191693
3.3-3.510.40591190.3415X-RAY DIFFRACTION194795
3.51-3.780.356800.2887X-RAY DIFFRACTION200196
3.78-4.160.3445990.2713X-RAY DIFFRACTION203198
4.16-4.760.28611030.2362X-RAY DIFFRACTION205698

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