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- PDB-8bxr: Titin FnIII-domain I109-I111 (I/A4-A/A6) from the MIR region -

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Basic information

Entry
Database: PDB / ID: 8bxr
TitleTitin FnIII-domain I109-I111 (I/A4-A/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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 9, 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
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)33,6837
Polymers33,3111
Non-polymers3726
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint14 kcal/mol
Surface area17450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.360, 89.110, 128.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 33310.680 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.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.61 Å3/Da / Density % sol: 52.9 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.1M MES pH 6, 10% [w/v] PEG 6000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.7→36.57 Å / Num. obs: 8696 / % possible obs: 85.3 % / Redundancy: 1.17 % / Biso Wilson estimate: 68.11 Å2 / CC1/2: 0.992 / Rrim(I) all: 0.207 / Net I/σ(I): 8.32
Reflection shellResolution: 2.7→2.8 Å / Mean I/σ(I) obs: 1.18 / Num. unique obs: 893 / CC1/2: 0.515

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→36.57 Å / SU ML: 0.5544 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.0988
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2714 435 5.02 %
Rwork0.2254 8235 -
obs0.2277 8670 85.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.26 Å2
Refinement stepCycle: LAST / Resolution: 2.7→36.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2326 0 24 37 2387
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00282400
X-RAY DIFFRACTIONf_angle_d0.53173254
X-RAY DIFFRACTIONf_chiral_restr0.0427358
X-RAY DIFFRACTIONf_plane_restr0.0051423
X-RAY DIFFRACTIONf_dihedral_angle_d13.8413913
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-3.090.4081440.3462742X-RAY DIFFRACTION87.67
3.09-3.890.32841450.26282736X-RAY DIFFRACTION86.36
3.89-36.570.21851460.18112757X-RAY DIFFRACTION82.47
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.12601573714-2.21845458756-0.6352579974914.464727436941.925610366920.9737811023670.06575397571820.275720068292-0.220126612847-0.0180073524936-0.110104467701-0.182537699234-0.0643368097501-0.0830123373629-3.02663228682E-50.588851395006-0.0243910599685-0.01311921240250.7005172855280.01153702707380.7684461009-21.460530920630.532850360922.7797541222
24.69884014767-0.312817267905-0.06259382794943.589753945020.05800032711942.57834198029-0.007762708144180.1759258383220.0441256321879-0.0985102802424-0.162876275463-0.06021973103260.255494123109-0.07071529696223.26870218777E-50.663477633311-0.0452733883583-0.02598919603930.671211216817-0.02837172772980.6084613617867.24995334773-0.60261847926715.676294206
32.055724333751.69184996336-2.625159540662.62731637372-2.673807884735.0962191845-0.04358463002180.0218549237688-0.1129624554390.3410698235540.00381724394125-0.09696336226670.168417708279-0.16053303903-1.13741067064E-50.839856652123-0.0157449241424-0.0924305043140.717210366351-0.01202327386830.62106082789939.2169136419-12.0004421117-14.7959294377
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 97 )0 - 971 - 98
22chain 'A' and (resid 98 through 193)98 - 19399 - 194
33chain 'A' and (resid 194 through 297)194 - 297195 - 298

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