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- PDB-8omw: Crystal structure of the titin domain Fn3-20 -

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Basic information

Entry
Database: PDB / ID: 8omw
TitleCrystal structure of the titin domain Fn3-20
ComponentsTitin
KeywordsSTRUCTURAL PROTEIN / Titin Fibronectin type III A-band STRUCTURAL PROTEIN
Function / homology
Function and homology information


sarcomerogenesis / titin-telethonin complex / structural molecule activity conferring elasticity / skeletal muscle myosin thick filament assembly / telethonin binding / detection of muscle stretch / muscle alpha-actinin binding / : / cardiac myofibril assembly / cardiac muscle hypertrophy ...sarcomerogenesis / titin-telethonin complex / structural molecule activity conferring elasticity / skeletal muscle myosin thick filament assembly / telethonin binding / detection of muscle stretch / muscle alpha-actinin binding / : / cardiac myofibril assembly / cardiac muscle hypertrophy / mitotic chromosome condensation / cardiac muscle tissue morphogenesis / Striated Muscle Contraction / muscle filament sliding / protein kinase regulator activity / actinin binding / M band / I band / cardiac muscle cell development / structural constituent of muscle / sarcomere organization / striated muscle thin filament / skeletal muscle thin filament assembly / skeletal muscle contraction / striated muscle contraction / cardiac muscle contraction / muscle contraction / condensed nuclear chromosome / positive regulation of protein secretion / response to calcium ion / Z disc / actin filament binding / Platelet degranulation / protease binding / protein tyrosine kinase activity / calmodulin binding / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / calcium ion binding / positive regulation of gene expression / protein kinase binding / enzyme binding / protein homodimerization activity / 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 / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsRees, M. / Gautel, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
British Heart FoundationRG/15/8/31480 United Kingdom
CitationJournal: J.Struct.Biol. / Year: 2023
Title: Structure determination and analysis of titin A-band fibronectin type III domains provides insights for disease-linked variants and protein oligomerisation.
Authors: Rees, M. / Nikoopour, R. / Alexandrovich, A. / Pfuhl, M. / Lopes, L.R. / Akhtar, M.M. / Syrris, P. / Elliott, P. / Carr-White, G. / Gautel, M.
History
DepositionMar 31, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Titin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6652
Polymers11,6291
Non-polymers351
Water4,486249
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-7 kcal/mol
Surface area6250 Å2
Unit cell
Length a, b, c (Å)49.034, 34.263, 63.081
Angle α, β, γ (deg.)90.000, 99.680, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-201-

CL

21A-325-

HOH

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Components

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


Mass: 11629.278 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 BL21 (bacteria)
References: UniProt: Q8WZ42, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.25 Å3/Da / Density % sol: 45.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10mM Tris-HCl pH 7.5 50mM NaCl 0.5mM DTT 0.1M TBG pH 9.0 25% w/v PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.05→31.09 Å / Num. obs: 47937 / % possible obs: 97.99 % / Redundancy: 14 % / Biso Wilson estimate: 6.98 Å2 / CC1/2: 0.774 / Rmerge(I) obs: 0.6268 / Net I/σ(I): 163.69
Reflection shellResolution: 1.05→1.09 Å / Redundancy: 14 % / Num. unique obs: 4253 / CC1/2: 0.612 / % possible all: 88.64

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.05→31.09 Å / SU ML: 0.0781 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 14.211
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1775 2014 4.24 %
Rwork0.149 45507 -
obs0.1501 47521 97.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.65 Å2
Refinement stepCycle: LAST / Resolution: 1.05→31.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms811 0 1 249 1061
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01888
X-RAY DIFFRACTIONf_angle_d1.2731224
X-RAY DIFFRACTIONf_chiral_restr0.0974128
X-RAY DIFFRACTIONf_plane_restr0.0104164
X-RAY DIFFRACTIONf_dihedral_angle_d6.8373131
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.05-1.070.20741260.1812786X-RAY DIFFRACTION84.75
1.07-1.10.17651410.12773227X-RAY DIFFRACTION97.51
1.1-1.140.13621440.11983252X-RAY DIFFRACTION98.55
1.14-1.170.14821450.12383232X-RAY DIFFRACTION98.43
1.17-1.220.15211440.11913232X-RAY DIFFRACTION98.68
1.22-1.260.13191470.12173292X-RAY DIFFRACTION98.94
1.26-1.320.15671420.12493274X-RAY DIFFRACTION98.96
1.32-1.390.13141430.1243265X-RAY DIFFRACTION98.75
1.39-1.480.15031460.12333285X-RAY DIFFRACTION99.31
1.48-1.590.16971460.12983294X-RAY DIFFRACTION99.34
1.59-1.750.15151470.13493317X-RAY DIFFRACTION99.11
1.75-2.010.16151460.14463323X-RAY DIFFRACTION99.91
2.01-2.530.20111460.15973324X-RAY DIFFRACTION99.4
2.53-31.090.22191510.18863404X-RAY DIFFRACTION99.36

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