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- PDB-8osd: Crystal structure of the titin domain Fn3-49 -

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Basic information

Entry
Database: PDB / ID: 8osd
TitleCrystal structure of the titin domain Fn3-49
ComponentsTitin
KeywordsSTRUCTURAL PROTEIN / Titin Fibronectin type III A-band STRUCTURAL PROTEIN
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: 1.7 Å
AuthorsNikoopour, R. / Rees, 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 18, 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


Theoretical massNumber of molelcules
Total (without water)24,5092
Polymers24,5092
Non-polymers00
Water1,49583
1
A: Titin


Theoretical massNumber of molelcules
Total (without water)12,2551
Polymers12,2551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Titin


Theoretical massNumber of molelcules
Total (without water)12,2551
Polymers12,2551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.460, 66.810, 52.810
Angle α, β, γ (deg.)90.000, 102.330, 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 / Titin domain Fn3-49


Mass: 12254.647 Da / Num. of mol.: 2
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


Mass: 18.015 Da / Num. of mol.: 83 / 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: 1.72 Å3/Da / Density % sol: 28.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 30mM HEPES pH 7.5 150mM NaCl 1mM DTT 100mM Potassium thiocyanate 30% w/v PEG MME2000

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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: 1.7→40.83 Å / Num. obs: 17148 / % possible obs: 93.6 % / Redundancy: 3 % / Biso Wilson estimate: 19.41 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.1106 / Net I/σ(I): 6.83
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.561 / Num. unique obs: 1663 / CC1/2: 0.77

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→40.83 Å / SU ML: 0.2271 / Cross valid method: FREE R-VALUE / σ(F): 1.47 / Phase error: 32.7106
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2602 900 5.25 %
Rwork0.2171 16244 -
obs0.2193 17144 93.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.06 Å2
Refinement stepCycle: LAST / Resolution: 1.7→40.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1620 0 0 83 1703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00651687
X-RAY DIFFRACTIONf_angle_d0.89882309
X-RAY DIFFRACTIONf_chiral_restr0.0556239
X-RAY DIFFRACTIONf_plane_restr0.0066303
X-RAY DIFFRACTIONf_dihedral_angle_d12.947629
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.810.34821600.29892591X-RAY DIFFRACTION91.09
1.81-1.950.30041740.26142577X-RAY DIFFRACTION90.26
1.95-2.140.31951250.22742702X-RAY DIFFRACTION93.24
2.14-2.450.29551340.22742798X-RAY DIFFRACTION95.26
2.45-3.090.28871570.23382773X-RAY DIFFRACTION96.35
3.09-40.830.2021500.18562803X-RAY DIFFRACTION95.38
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)
10.6076304293620.17450341463-0.2074032693660.913372840378-0.1379370721742.21083210037-0.001889131885870.0382651143786-0.0295343178811-0.0913154756352-0.000905015414439-0.05421767181280.0584822703005-0.2807845402840.03019400373230.16490052426-0.003440685136690.002223860250440.2162702053860.005649099361840.17674582082814.405108888428.457231596927.1748325546
22.607508834630.126147102818-0.8260737534811.348845120330.4317464485752.20392691517-0.0607043776170.3399357298560.1797262584410.0888708662942-0.01755017251330.00704764236055-0.378154033171-0.4387854688020.05724547718930.2429440990010.0421310818034-0.002224776918580.2653779200330.002092852516140.16774582188511.839092699241.152817669724.840665122
32.22878843937-0.448212738607-1.541741340681.72169237434-0.1389245915854.1215174610.195649822920.06643728791410.5215967890060.1776811856360.0745090052215-0.155903287283-0.5116712187720.0403967156332-0.08921168139320.0586298937155-0.00844981022094-0.05020299920610.193725444397-0.02117426010670.22246375614219.664282732138.101893425530.9991547336
40.2255482581030.4759739246350.06055681998292.572806190592.420213896534.004588977950.0885390456901-0.04891049618650.0374378098453-0.30275689523-0.2386155874650.154278306375-0.493123661681-0.5150181197630.140239357430.1185755561550.0178767143158-0.02373638336650.265383474636-0.01226332247580.1967294635079.4705955241233.175253242224.5874928898
53.51598783120.767987555275-0.02774576467194.558453401960.03756539884083.513061674950.221630525172-0.554242978760.3514143092340.665024202349-0.2252832309180.383044428496-0.568955397738-0.3511067119110.003366034471240.3466862072150.0270132568079-0.02936951796670.4349552109890.00458321033890.22105176962112.871399129741.160843992140.97081632
61.33441221910.2993500206690.3150083262330.73802463261-0.3111599047752.481497626850.178112021547-0.0599131544779-0.291014563203-0.01585731538080.135311790668-0.143600242344-0.189319328417-0.183369902658-0.2501665647030.172749868175-0.01515545435210.02390969412980.2694055520720.01023490950310.1982010705472.7906278309127.725007651949.5836760857
71.13082081897-0.5519860980280.3706305696781.00887694452-0.2524865572072.80678184613-0.0455190290983-0.04857312695150.09134453561020.0415210138930.07928591009470.0976886449846-0.5840250246020.0301334047633-0.08812495491050.20146518125-0.01988273102550.01287226018120.196345262182-0.004701433304440.1877273350334.1669244264233.691976051356.7421570538
82.614996653290.4714678624310.5964983240611.60505339420.3747351312971.905831448280.02062336282980.0756113808552-0.2078131037440.0453234166466-0.02423972839180.0826055716772-0.1156984394030.04129800497950.008299445931620.185328351862-0.0276959400710.0255705083910.2660529113280.002155119191670.1829928696668.8616548075427.801355766744.3329752855
91.8968555413-0.07270557128730.417201296261.451556188661.115643012773.08006556316-0.09349078361610.0640753629129-0.0656058007408-0.1822199491550.2143033834930.0054869742038-0.3183489210830.268020908115-0.1477349954080.209438762205-0.0421115878124-0.003610593576730.2369893789140.03244559256530.1819220698018.7531395100824.333648790347.6268424189
102.15219382617-0.035784768352-0.4804551914533.220362714510.3260346965083.107492504630.352155932705-0.297586304555-0.2740171420880.17769196903-0.3717818302740.2526847728660.622159248017-0.1729441195540.006409718120490.240751996506-0.0457712727653-0.01363233755350.227812824314-0.01296086434240.318457417188-0.74629859358917.243985474441.7797734648
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 41 )
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 60 )
3X-RAY DIFFRACTION3chain 'A' and (resid 61 through 75 )
4X-RAY DIFFRACTION4chain 'A' and (resid 76 through 95 )
5X-RAY DIFFRACTION5chain 'A' and (resid 96 through 104 )
6X-RAY DIFFRACTION6chain 'B' and (resid 2 through 23 )
7X-RAY DIFFRACTION7chain 'B' and (resid 24 through 36 )
8X-RAY DIFFRACTION8chain 'B' and (resid 37 through 71 )
9X-RAY DIFFRACTION9chain 'B' and (resid 72 through 93 )
10X-RAY DIFFRACTION10chain 'B' and (resid 94 through 104 )

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