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- PDB-8bvo: Titin I110-I111 FnIII tandem from the MIR region (I/A5-I/A6) -

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Basic information

Entry
Database: PDB / ID: 8bvo
TitleTitin I110-I111 FnIII tandem from the MIR region (I/A5-I/A6)
ComponentsTitin
KeywordsSTRUCTURAL PROTEIN / titin / MIR / I-band / I/A junction / FnIII / Ig
Function / homology
Function and homology information


sarcomerogenesis / structural molecule activity conferring elasticity / telethonin binding / skeletal muscle myosin thick filament assembly / cardiac myofibril assembly / muscle alpha-actinin binding / detection of muscle stretch / cardiac muscle tissue morphogenesis / regulation of catalytic activity / cardiac muscle hypertrophy ...sarcomerogenesis / structural molecule activity conferring elasticity / telethonin binding / skeletal muscle myosin thick filament assembly / cardiac myofibril assembly / muscle alpha-actinin binding / detection of muscle stretch / cardiac muscle tissue morphogenesis / regulation of catalytic activity / cardiac muscle hypertrophy / mitotic chromosome condensation / Striated Muscle Contraction / M band / actinin binding / I band / cardiac muscle cell development / regulation of protein kinase activity / sarcomere organization / structural constituent of muscle / skeletal muscle thin filament assembly / striated muscle thin filament / striated muscle contraction / protein kinase A signaling / cardiac muscle contraction / muscle contraction / condensed nuclear chromosome / positive regulation of protein secretion / Z disc / response to calcium ion / : / actin filament binding / Platelet degranulation / protein tyrosine kinase activity / 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 / extracellular exosome / extracellular region / ATP binding / identical protein binding / cytosol
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsMayans, O. / Fleming, J.R. / Williams, R.
Funding support United Kingdom, France, 2items
OrganizationGrant numberCountry
British Heart FoundationPG/13/21/3007 United Kingdom
Leducq FoundationTNE-13CVD04 France
CitationJournal: Biomedicines / Year: 2023
Title: Immunological and Structural Characterization of Titin Main Immunogenic Region; I110 Domain Is the Target of Titin Antibodies in Myasthenia Gravis.
Authors: Stergiou, C. / Williams, R. / Fleming, J.R. / Zouvelou, V. / Ninou, E. / Andreetta, F. / Rinaldi, E. / Simoncini, O. / Mantegazza, R. / Bogomolovas, J. / Tzartos, J. / Labeit, S. / Mayans, O. / Tzartos, S.
History
DepositionDec 5, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Titin


Theoretical massNumber of molelcules
Total (without water)22,2481
Polymers22,2481
Non-polymers00
Water79344
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11390 Å2
Unit cell
Length a, b, c (Å)34.287, 46.259, 71.345
Angle α, β, γ (deg.)90.000, 100.730, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Titin / / Connectin / Rhabdomyosarcoma antigen MU-RMS-40.14


Mass: 22248.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTN / Production host: Escherichia coli (E. coli)
References: UniProt: Q8WZ42, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

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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: 2.5 Å3/Da / Density % sol: 50.77 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 24% (w/v) PEG 1500, 20% (w/v) glycerol

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.55→38.61 Å / Num. obs: 7239 / % possible obs: 98.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 65.93 Å2 / CC1/2: 0.982 / Rrim(I) all: 0.192 / Net I/σ(I): 6.04
Reflection shellResolution: 2.55→2.6 Å / Num. unique obs: 401 / CC1/2: 0.424 / Rrim(I) all: 0.1828

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→38.61 Å / SU ML: 0.6479 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 39.8037
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2872 509 7.05 %
Rwork0.2235 6715 -
obs0.2283 7224 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 78.67 Å2
Refinement stepCycle: LAST / Resolution: 2.55→38.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1559 0 0 44 1603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00831601
X-RAY DIFFRACTIONf_angle_d1.01572179
X-RAY DIFFRACTIONf_chiral_restr0.0517230
X-RAY DIFFRACTIONf_plane_restr0.0092288
X-RAY DIFFRACTIONf_dihedral_angle_d15.6358611
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.810.49341250.41231656X-RAY DIFFRACTION99.33
2.81-3.210.40251310.31331669X-RAY DIFFRACTION99.01
3.21-4.050.29091230.22231682X-RAY DIFFRACTION98.85
4.05-38.610.2291300.1741708X-RAY DIFFRACTION98.29
Refinement TLS params.Method: refined / Origin x: 0.248237786025 Å / Origin y: 4.71987781321 Å / Origin z: -14.6338084419 Å
111213212223313233
T0.583852839874 Å20.00949738260837 Å2-0.00290738992507 Å2-0.515438813272 Å20.0863102690629 Å2--0.612590397631 Å2
L3.24606891008 °20.287964629741 °22.02740798128 °2-0.576016363962 °20.49142568867 °2--2.75242959333 °2
S0.151551469785 Å °-0.76610112097 Å °-0.276412175943 Å °0.177644434359 Å °-0.134393119527 Å °-0.133815593511 Å °0.0659300203007 Å °-0.347581782569 Å °-0.00325280290743 Å °
Refinement TLS groupSelection details: (chain 'A' and resid -1 through 196)

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