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- PDB-8fmo: Complex structure of K210 deletion Troponin complex with risedronate -

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Basic information

Entry
Database: PDB / ID: 8fmo
TitleComplex structure of K210 deletion Troponin complex with risedronate
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 / risedronate
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 myofibril / cardiac Troponin complex / troponin complex / regulation of 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 myofibril / cardiac Troponin complex / troponin complex / regulation of muscle contraction / regulation of smooth muscle contraction / negative regulation of ATP-dependent activity / transition between fast and slow fiber / positive regulation of ATP-dependent activity / Striated Muscle Contraction / muscle filament sliding / response to metal ion / regulation of cardiac muscle contraction by calcium ion signaling / ventricular cardiac muscle tissue morphogenesis / heart contraction / regulation of 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 / intracellular calcium ion homeostasis / response to calcium ion / 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: 2.612 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
Water99155
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
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8560 Å2
ΔGint-103 kcal/mol
Surface area19640 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
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8680 Å2
ΔGint-99 kcal/mol
Surface area20150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.379, 169.297, 69.414
Angle α, β, γ (deg.)90.00, 102.12, 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
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: 2.4 Å3/Da / Density % sol: 48.7 %
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: 0.97973 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97973 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 26261 / % possible obs: 98.4 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 20.3
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 2421

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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: 2.612→43.391 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2616 1127 4.77 %
Rwork0.2148 --
obs0.2171 23629 87.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.612→43.391 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5364 0 6 55 5425
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055407
X-RAY DIFFRACTIONf_angle_d0.9227215
X-RAY DIFFRACTIONf_dihedral_angle_d8.6363409
X-RAY DIFFRACTIONf_chiral_restr0.042796
X-RAY DIFFRACTIONf_plane_restr0.005955
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.612-2.73060.3493820.28041808X-RAY DIFFRACTION57
2.7306-2.87450.393890.27852243X-RAY DIFFRACTION69
2.8745-3.05460.32031310.28222656X-RAY DIFFRACTION83
3.0546-3.29040.34811530.26733092X-RAY DIFFRACTION96
3.2904-3.62130.30321600.23143157X-RAY DIFFRACTION99
3.6213-4.1450.26171820.19813144X-RAY DIFFRACTION100
4.145-5.22080.20381780.17023167X-RAY DIFFRACTION99
5.2208-43.3910.19811520.18463235X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -2.4341 Å / Origin y: -39.4947 Å / Origin z: 17.2529 Å
111213212223313233
T0.2707 Å2-0.086 Å20.0228 Å2-0.247 Å20.0199 Å2--0.2169 Å2
L0.1111 °2-0.1885 °20.1241 °2-0.1423 °20.3176 °2---0.1704 °2
S0.0274 Å °0.0471 Å °0.0019 Å °0.0379 Å °-0.0516 Å °-0.0295 Å °-0.048 Å °-0.0275 Å °0.0063 Å °
Refinement TLS groupSelection details: all

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