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- PDB-7sc2: CRYSTAL STRUCTURE OF THE N-DOMAIN OF CARDIAC MUSCLE TROPONIN C TE... -

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Basic information

Entry
Database: PDB / ID: 7sc2
TitleCRYSTAL STRUCTURE OF THE N-DOMAIN OF CARDIAC MUSCLE TROPONIN C TETHERED TO THE SWITCH REGION OF CARDIAC MUSCLE TROPONIN I (TETRAGONAL FORM)
ComponentsTroponin C, slow skeletal and cardiac muscles,Troponin I, cardiac muscle chimera
KeywordsCONTRACTILE PROTEIN / CALCIUM SENSITIZER / CONTRACTION REGULATION / CARDIAC TROPONIN / MUSCLE REGULATION / CALCIUM-BINDING / EF-HAND
Function / homology
Function and homology information


regulation of systemic arterial blood pressure by ischemic conditions / troponin C binding / regulation of muscle filament sliding speed / troponin T binding / diaphragm contraction / regulation of ATP-dependent activity / cardiac Troponin complex / cardiac myofibril / troponin complex / regulation of smooth muscle contraction ...regulation of systemic arterial blood pressure by ischemic conditions / troponin C binding / regulation of muscle filament sliding speed / troponin T binding / diaphragm contraction / regulation of ATP-dependent activity / cardiac Troponin complex / cardiac myofibril / troponin complex / regulation of smooth muscle contraction / regulation of muscle contraction / transition between fast and slow fiber / negative regulation of ATP-dependent activity / Striated Muscle Contraction / regulation of cardiac muscle contraction by calcium ion signaling / response to metal ion / ventricular cardiac muscle tissue morphogenesis / heart contraction / troponin I binding / skeletal muscle contraction / vasculogenesis / calcium channel inhibitor activity / cardiac muscle contraction / Ion homeostasis / sarcomere / intracellular calcium ion homeostasis / calcium-dependent protein binding / actin filament binding / heart development / actin binding / protein domain specific binding / calcium ion binding / protein kinase binding / protein homodimerization activity / cytosol
Similarity search - Function
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 ...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 C, slow skeletal and cardiac muscles
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.814 Å
AuthorsSack, J.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2022
Title: X-ray structure of a human cardiac muscle troponin C/troponin I chimera in two crystal forms.
Authors: Yan, C. / Sack, J.S.
History
DepositionSep 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 5, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 12, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3May 22, 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
A: Troponin C, slow skeletal and cardiac muscles,Troponin I, cardiac muscle chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3402
Polymers13,3001
Non-polymers401
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.935, 40.935, 128.932
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 C, slow skeletal and cardiac muscles,Troponin I, cardiac muscle chimera / TN-C / Cardiac troponin I


Mass: 13300.194 Da / Num. of mol.: 1 / Mutation: C35S, C84S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNNC1, TNNC, TNNI3, TNNC1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P63316, UniProt: P19429
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.03 Å3/Da / Density % sol: 39.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 22% PEG 4000, 0.1M NA ACETATE PH 4.5, 0.2M NAH4-ACETATE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.81→39.02 Å / Num. obs: 8344 / % possible obs: 78.5 % / Observed criterion σ(I): 0 / Redundancy: 12.3 % / Biso Wilson estimate: 48.41 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.4
Reflection shellResolution: 1.81→1.95 Å / Redundancy: 12.5 % / Rmerge(I) obs: 2.347 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 384 / % possible all: 21.2

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
BUSTER2.11.7 (6-FEB-2020)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.814→39.02 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.944 / SU R Cruickshank DPI: 0.177 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.189 / SU Rfree Blow DPI: 0.153 / SU Rfree Cruickshank DPI: 0.148
RfactorNum. reflection% reflectionSelection details
Rfree0.2391 422 5.06 %RANDOM
Rwork0.2222 ---
obs0.223 8344 78.5 %-
Displacement parametersBiso mean: 50.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.3138 Å20 Å20 Å2
2---0.3138 Å20 Å2
3---0.6276 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 1.814→39.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms803 0 1 29 833
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.008810HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.831090HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d281SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes139HARMONIC5
X-RAY DIFFRACTIONt_it810HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.32
X-RAY DIFFRACTIONt_other_torsion15
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion113SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact712SEMIHARMONIC4
LS refinement shellResolution: 1.814→1.94 Å
RfactorNum. reflection% reflection
Rfree0.2069 -3.52 %
Rwork0.2337 384 -
obs--20.92 %

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