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- PDB-1yv0: Crystal structure of skeletal muscle troponin in the Ca2+-free state -

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Basic information

Entry
Database: PDB / ID: 1yv0
TitleCrystal structure of skeletal muscle troponin in the Ca2+-free state
Components
  • Troponin C, skeletal muscle
  • Troponin I, fast skeletal muscle
  • Troponin T, fast skeletal muscle isoforms
KeywordsCONTRACTILE PROTEIN / troponin / off state / thin filament / actin binding / muscle
Function / homology
Function and homology information


troponin C binding / troponin complex / Striated Muscle Contraction / regulation of muscle contraction / sarcomere organization / tropomyosin binding / troponin I binding / skeletal muscle contraction / cardiac muscle contraction / actin binding / calcium ion binding
Similarity search - Function
Troponin T / : / Troponin / Troponin domain superfamily / Troponin / EF hand / EF-hand domain pair / : / EF-hand domain pair / EF-hand, calcium binding motif ...Troponin T / : / Troponin / Troponin domain superfamily / Troponin / EF hand / EF-hand domain pair / : / 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
Similarity search - Domain/homology
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: 7 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 14, 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 1.3Mar 7, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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.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 1.5Feb 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, fast skeletal muscle isoforms
I: Troponin I, fast skeletal muscle
C: Troponin C, skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8585
Polymers46,8093
Non-polymers492
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6910 Å2
ΔGint-58 kcal/mol
Surface area24960 Å2
MethodPISA
2
T: Troponin T, fast skeletal muscle isoforms
I: Troponin I, fast skeletal muscle
C: Troponin C, skeletal muscle
hetero molecules

T: Troponin T, fast skeletal muscle isoforms
I: Troponin I, fast skeletal muscle
C: Troponin C, skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,71610
Polymers93,6186
Non-polymers974
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_645y+1,x-1,-z1
Buried area17090 Å2
ΔGint-132 kcal/mol
Surface area46630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.662, 134.662, 102.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Troponin T, fast skeletal muscle isoforms / Troponin T2


Mass: 12694.692 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Escherichia coli (E. coli) / References: UniProt: P12620
#2: Protein Troponin I, fast skeletal muscle / Troponin I / fast-twitch isoform


Mass: 15853.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Escherichia coli (E. coli) / References: UniProt: P68246
#3: Protein Troponin C, skeletal muscle


Mass: 18261.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: TNNC2 / Production host: Escherichia coli (E. coli) / References: UniProt: P02588
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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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: 4.871 Å3/Da / Density % sol: 74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.6 M tri-Sodium Citrate dihydrate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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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: Mar 9, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 7→25 Å / Num. all: 1622 / Num. obs: 1541 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 7→7.24 Å / Rmerge(I) obs: 0.067 / % possible all: 84.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 7→25 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.359 78 random
Rwork0.3579 --
all0.3579 1616 -
obs0.3579 1529 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2842 0 2 0 2844
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONrmsd bonds0.012423
X-RAY DIFFRACTIONrmsd angles1.86454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs
7-7.310.525790.6071X-RAY DIFFRACTION160
7.31-7.690.483190.6242X-RAY DIFFRACTION164
7.69-8.150.4931100.4524X-RAY DIFFRACTION166
8.15-8.760.427290.5506X-RAY DIFFRACTION185
8.76-9.590.333290.4355X-RAY DIFFRACTION190
9.59-10.880.2576110.2602X-RAY DIFFRACTION183
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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