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- PDB-8bw6: Titin FnIII-domain I110 (I/A6) from the MIR region -

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Basic information

Entry
Database: PDB / ID: 8bw6
TitleTitin FnIII-domain I110 (I/A6) from the MIR region
ComponentsTitin
KeywordsSTRUCTURAL PROTEIN / titin / MIR / I-band / I/A junction / FnIII
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 / actinin binding / M band / I band / cardiac muscle cell development / regulation of protein kinase activity / structural constituent of muscle / sarcomere organization / skeletal muscle thin filament assembly / striated muscle thin filament / striated muscle contraction / cardiac muscle contraction / protein kinase A signaling / condensed nuclear chromosome / muscle contraction / positive regulation of protein secretion / Z disc / response to calcium ion / : / actin filament binding / Platelet degranulation / protein tyrosine kinase activity / protease binding / non-specific serine/threonine protein kinase / calmodulin binding / 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
DI(HYDROXYETHYL)ETHER / Titin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMayans, O. / Fleming, J.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 6, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,61610
Polymers11,0351
Non-polymers5819
Water64936
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint1 kcal/mol
Surface area6250 Å2
Unit cell
Length a, b, c (Å)45.860, 45.860, 112.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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


Mass: 11035.440 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: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.67 Å3/Da / Density % sol: 53.91 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.1M Tris pH8 30% PEG 300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.95→42.44 Å / Num. obs: 9305 / % possible obs: 100 % / Redundancy: 12.36 % / CC1/2: 1 / Rsym value: 0.046 / Net I/σ(I): 23.09
Reflection shellResolution: 1.95→2 Å / Redundancy: 12.43 % / Mean I/σ(I) obs: 0.93 / Num. unique obs: 651 / CC1/2: 1 / Rsym value: 240.3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→42.44 Å / SU ML: 0.3068 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 38.5755
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2539 466 5.01 %
Rwork0.2174 8834 -
obs0.2194 9300 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.89 Å2
Refinement stepCycle: LAST / Resolution: 1.95→42.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms773 0 36 36 845
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077844
X-RAY DIFFRACTIONf_angle_d0.97511133
X-RAY DIFFRACTIONf_chiral_restr0.0542119
X-RAY DIFFRACTIONf_plane_restr0.0073148
X-RAY DIFFRACTIONf_dihedral_angle_d15.7335325
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.230.31671500.30432853X-RAY DIFFRACTION99.93
2.23-2.810.35621530.33762906X-RAY DIFFRACTION99.9
2.81-42.440.23131630.18863075X-RAY DIFFRACTION99.97
Refinement TLS params.Method: refined / Origin x: 10.2063015497 Å / Origin y: 5.18083112146 Å / Origin z: 17.5025802777 Å
111213212223313233
T0.482044621282 Å20.0113374947214 Å20.118186221001 Å2-0.261916737254 Å20.0183696000926 Å2--0.385068701511 Å2
L4.80809320877 °21.90132024217 °20.658626142597 °2-4.95392144961 °2-0.257542842022 °2--5.03938446632 °2
S0.148382176676 Å °-0.218552626233 Å °-0.0637708948397 Å °0.231835138857 Å °-0.22506958097 Å °-0.144483065152 Å °-0.151297683264 Å °0.0480363809053 Å °0.0885373412224 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 1 through 99)

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