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- PDB-8fms: Complex structure of K210 deletion Troponin complex with neridronate -

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Basic information

Entry
Database: PDB / ID: 8fms
TitleComplex structure of K210 deletion Troponin complex with neridronate
Components
  • Troponin C, slow skeletal and cardiac muscles
  • Troponin I, cardiac muscle
  • Troponin T, cardiac muscle
KeywordsSTRUCTURAL PROTEIN / Ca sensing complex / troponin complex / K210 deletion / neridronate
Function / homology
Function and homology information


regulation of systemic arterial blood pressure by ischemic conditions / troponin C binding / diaphragm contraction / regulation of ATP-dependent activity / regulation of muscle filament sliding speed / troponin T binding / cardiac Troponin complex / cardiac myofibril / troponin complex / regulation of smooth muscle contraction ...regulation of systemic arterial blood pressure by ischemic conditions / troponin C binding / diaphragm contraction / regulation of ATP-dependent activity / regulation of muscle filament sliding speed / troponin T binding / cardiac Troponin complex / cardiac myofibril / troponin complex / regulation of smooth muscle contraction / regulation of muscle contraction / muscle filament sliding / negative regulation of ATP-dependent activity / transition between fast and slow fiber / positive regulation of ATP-dependent activity / Striated Muscle Contraction / response to metal ion / regulation of cardiac muscle contraction by calcium ion signaling / ventricular cardiac muscle tissue morphogenesis / sarcomere organization / regulation of heart contraction / heart contraction / tropomyosin binding / troponin I binding / striated muscle thin filament / skeletal muscle contraction / calcium channel inhibitor activity / vasculogenesis / Ion homeostasis / cardiac muscle contraction / sarcomere / response to calcium ion / intracellular calcium ion homeostasis / calcium-dependent protein binding / actin filament binding / actin binding / heart development / protein domain specific binding / calcium ion binding / protein kinase binding / protein homodimerization activity / identical protein binding / cytosol
Similarity search - Function
Troponin T / Troponin I residues 1-32 / Troponin I residues 1-32 / : / Troponin / Troponin domain superfamily / Troponin / EF-hand domain pair / : / EF-hand domain pair ...Troponin T / Troponin I residues 1-32 / Troponin I residues 1-32 / : / Troponin / Troponin domain superfamily / Troponin / 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 I, cardiac muscle / Troponin T, cardiac muscle / Troponin C, slow skeletal and cardiac muscles
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.435 Å
AuthorsWang, P. / Ahmed, M. / Sadek, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) United States
CitationJournal: To Be Published
Title: Structural and Phenotypic Correction of K210del Genetic Cardiomyopathy by an FDA Approved drug
Authors: Wang, P. / Ahmed, M. / Sadek, H.
History
DepositionDec 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Troponin C, slow skeletal and cardiac muscles
B: Troponin T, cardiac muscle
C: Troponin I, cardiac muscle
D: Troponin C, slow skeletal and cardiac muscles
E: Troponin T, cardiac muscle
F: Troponin I, cardiac muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,34312
Polymers94,1036
Non-polymers2406
Water00
1
A: Troponin C, slow skeletal and cardiac muscles
B: Troponin T, cardiac muscle
C: Troponin I, cardiac muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1726
Polymers47,0513
Non-polymers1203
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8390 Å2
ΔGint-102 kcal/mol
Surface area20120 Å2
MethodPISA
2
D: Troponin C, slow skeletal and cardiac muscles
E: Troponin T, cardiac muscle
F: Troponin I, cardiac muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1726
Polymers47,0513
Non-polymers1203
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8660 Å2
ΔGint-88 kcal/mol
Surface area20350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.763, 170.378, 69.709
Angle α, β, γ (deg.)90.00, 101.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Troponin C, slow skeletal and cardiac muscles / TN-C


Mass: 18673.635 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNNC1, TNNC / Production host: Escherichia coli (E. coli) / References: UniProt: P63316
#2: Protein Troponin T, cardiac muscle / TnTc / Cardiac muscle troponin T / cTnT


Mass: 12971.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNNT2 / Production host: Escherichia coli (E. coli) / References: UniProt: P45379
#3: Protein Troponin I, cardiac muscle / Cardiac troponin I


Mass: 15405.877 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNNI3, TNNC1 / Production host: Escherichia coli (E. coli) / References: UniProt: P19429
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.51 Å3/Da / Density % sol: 51.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2M Sodium Acetate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 11980 / % possible obs: 97.8 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.171 / Net I/σ(I): 10
Reflection shellResolution: 3.4→3.52 Å / Rmerge(I) obs: 1.002 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1113

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.435→43.655 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 31.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2842 462 4.96 %
Rwork0.2553 --
obs0.2568 9319 75.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.435→43.655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5373 0 6 0 5379
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025416
X-RAY DIFFRACTIONf_angle_d0.457229
X-RAY DIFFRACTIONf_dihedral_angle_d6.5343411
X-RAY DIFFRACTIONf_chiral_restr0.033798
X-RAY DIFFRACTIONf_plane_restr0.003958
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4353-3.93210.3438690.28151423X-RAY DIFFRACTION36
3.9321-4.95290.2952050.25373537X-RAY DIFFRACTION90
4.9529-43.60.2511880.24693897X-RAY DIFFRACTION98

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