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- PDB-8orl: Crystal structure of the S23226G missense variant of titin domain... -

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Basic information

Entry
Database: PDB / ID: 8orl
TitleCrystal structure of the S23226G missense variant of titin domain Fn3-56
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 / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 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
DepositionApr 14, 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
B: Titin
C: Titin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,54413
Polymers34,0403
Non-polymers50410
Water7,981443
1
A: Titin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4483
Polymers11,3471
Non-polymers1012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Titin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5785
Polymers11,3471
Non-polymers2324
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Titin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5185
Polymers11,3471
Non-polymers1724
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.348, 89.862, 98.309
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-439-

HOH

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Components

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


Mass: 11346.646 Da / Num. of mol.: 3
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 443 / 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: 2.28 Å3/Da / Density % sol: 46.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10mM Tris-HCl pH 7.5 50mM NaCl 0.5mM DTT 0.1M MES 10mM ZnCl2 20% (w/v) PEG6000

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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: 1.43→55.39 Å / Num. obs: 57214 / % possible obs: 99.09 % / Redundancy: 6.5 % / Biso Wilson estimate: 15.09 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.09748 / Rpim(I) all: 0.04119 / Net I/σ(I): 11.25
Reflection shellResolution: 1.43→1.48 Å / Rmerge(I) obs: 0.7034 / Num. unique obs: 5192 / CC1/2: 0.703

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.43→55.39 Å / SU ML: 0.1556 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.1796
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1941 2870 5.02 %
Rwork0.1587 54344 -
obs0.1604 57214 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.88 Å2
Refinement stepCycle: LAST / Resolution: 1.43→55.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2273 0 10 443 2726
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712412
X-RAY DIFFRACTIONf_angle_d0.98213303
X-RAY DIFFRACTIONf_chiral_restr0.0761367
X-RAY DIFFRACTIONf_plane_restr0.0088439
X-RAY DIFFRACTIONf_dihedral_angle_d5.6971362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.43-1.450.29781210.25762294X-RAY DIFFRACTION85.1
1.45-1.480.29961400.22642638X-RAY DIFFRACTION97.41
1.48-1.510.22021430.19862713X-RAY DIFFRACTION99.96
1.51-1.540.24621430.18212718X-RAY DIFFRACTION99.9
1.54-1.570.24621430.16322711X-RAY DIFFRACTION100
1.57-1.610.20971430.15872694X-RAY DIFFRACTION99.96
1.61-1.650.19371450.15182729X-RAY DIFFRACTION99.86
1.65-1.70.20221380.15372733X-RAY DIFFRACTION100
1.7-1.750.20781480.15342707X-RAY DIFFRACTION100
1.75-1.80.17421440.15742741X-RAY DIFFRACTION99.97
1.8-1.870.20931520.15822711X-RAY DIFFRACTION100
1.87-1.940.18221310.14142735X-RAY DIFFRACTION99.86
1.94-2.030.18511320.14432755X-RAY DIFFRACTION100
2.03-2.140.19841610.14332727X-RAY DIFFRACTION99.93
2.14-2.270.17641110.14232784X-RAY DIFFRACTION100
2.27-2.450.20211540.15152721X-RAY DIFFRACTION99.97
2.45-2.690.18371710.16032743X-RAY DIFFRACTION100
2.69-3.080.21671420.16192792X-RAY DIFFRACTION99.93
3.08-3.880.17881400.15332808X-RAY DIFFRACTION99.8
3.88-55.390.17371680.16762890X-RAY DIFFRACTION99.84

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