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- PDB-6yj0: Solution NMR structure of titin N2A region Ig domain I83 -

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Basic information

Entry
Database: PDB / ID: 6yj0
TitleSolution NMR structure of titin N2A region Ig domain I83
ComponentsTitin
KeywordsPROTEIN BINDING / calcium binding actin binding muscle I-band
Function / homology
Function and homology information


forward locomotion / heart growth / striated muscle cell development / regulation of relaxation of cardiac muscle / sarcomerogenesis / structural molecule activity conferring elasticity / telethonin binding / skeletal muscle myosin thick filament assembly / cardiac myofibril assembly / muscle myosin complex ...forward locomotion / heart growth / striated muscle cell development / regulation of relaxation of cardiac muscle / sarcomerogenesis / structural molecule activity conferring elasticity / telethonin binding / skeletal muscle myosin thick filament assembly / cardiac myofibril assembly / muscle myosin complex / muscle alpha-actinin binding / ventricular system development / detection of muscle stretch / cardiac muscle tissue morphogenesis / adult heart development / cardiac muscle tissue development / cardiac muscle hypertrophy / M band / actinin binding / I band / cardiac muscle cell development / A band / structural constituent of muscle / ankyrin binding / sarcomere organization / skeletal muscle thin filament assembly / striated muscle thin filament / somitogenesis / heart morphogenesis / cardiac muscle contraction / protein kinase A signaling / sarcomere / condensed nuclear chromosome / muscle contraction / positive regulation of protein secretion / structural constituent of cytoskeleton / Z disc / response to calcium ion / : / actin filament binding / heart development / protein tyrosine kinase activity / in utero embryonic development / protease binding / calmodulin binding / non-specific serine/threonine protein kinase / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / calcium ion binding / positive regulation of gene expression / protein kinase binding / enzyme binding / ATP binding / identical protein binding
Similarity search - Function
PPAK motif / PPAK motif / Titin, Z repeat / Titin Z / MyBP-C, tri-helix bundle domain / Tri-helix bundle domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain ...PPAK motif / PPAK motif / Titin, Z repeat / Titin Z / MyBP-C, tri-helix bundle domain / Tri-helix bundle domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase domain / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsPfuhl, M. / Gage, M.
CitationJournal: J.Mol.Biol. / Year: 2021
Title: Solution NMR Structure of Titin N2A Region Ig Domain I83 and Its Interaction with Metal Ions.
Authors: Kelly, C. / Pace, N. / Gage, M. / Pfuhl, M.
History
DepositionApr 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Titin


Theoretical massNumber of molelcules
Total (without water)11,9141
Polymers11,9141
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, NMR 15N relaxation result is in good agreement with a monomer
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7330 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)40 / 400structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Titin / / Connectin


Mass: 11914.169 Da / Num. of mol.: 1 / Mutation: N.A.
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Tissue: muscleSkeletal muscle / Cell: myocyte / Gene: Ttn / Variant: N2A / Plasmid: pET151/D-TOPO / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): BL21*
References: UniProt: A2ASS6, non-specific serine/threonine protein kinase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-15N NOESY
122isotropic23D 1H-13C NOESY aliphatic
132isotropic23D 1H-13C NOESY aromatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.8 mM [U-95% 15N] domain I83 from mouse titin, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution20.8 mM [U-95% 13C; U-95% 15N] domain I83 from mouse titin, 90% H2O/10% D2O15N_13C_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMdomain I83 from mouse titin[U-95% 15N]1
0.8 mMdomain I83 from mouse titin[U-95% 13C; U-95% 15N]2
Sample conditionsDetails: 20 mM Hepes, pH 7.2, 100 mM sodium chloride, 2 mM DTT and 0.02% NaN3
Ionic strength: 100 mM / Ionic strength err: 0.1 / Label: conditions_1 / pH: 7.2 / PH err: 0.02 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 298 K / Temperature err: 0.1

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III7001
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis2.4CCPNdata analysis
ARIA2.3.2Linge, O'Donoghue and Nilgesstructure calculation
X-PLOR NIH2.35Schwieters, Kuszewski, Tjandra and Clorestructure calculation
RefinementMethod: simulated annealing / Software ordinal: 3 / Details: standard simulated annealing
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 40

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