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- PDB-8oq9: Crystal structure of the titin domain Fn3-56 -

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Basic information

Entry
Database: PDB / ID: 8oq9
TitleCrystal structure of the titin domain Fn3-56
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 / M band / actinin binding / I band / cardiac muscle cell development / regulation of protein kinase activity / sarcomere organization / structural constituent of muscle / skeletal muscle thin filament assembly / striated muscle thin filament / striated muscle contraction / protein kinase A signaling / cardiac muscle contraction / muscle contraction / condensed nuclear chromosome / positive regulation of protein secretion / Z disc / response to calcium ion / : / actin filament binding / Platelet degranulation / protein tyrosine kinase activity / protease binding / calmodulin binding / non-specific serine/threonine protein kinase / 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: 1.65 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 11, 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)34,56311
Polymers34,1303
Non-polymers4338
Water6,557364
1
A: Titin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4422
Polymers11,3771
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Titin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6446
Polymers11,3771
Non-polymers2675
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Titin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4783
Polymers11,3771
Non-polymers1012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.530, 89.630, 97.110
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
11C-401-

HOH

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Components

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


Mass: 11376.671 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 / Chloride


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


Mass: 18.015 Da / Num. of mol.: 364 / 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: 45.29 %
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: I04 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.65→40.69 Å / Num. obs: 35650 / % possible obs: 95.44 % / Redundancy: 4.1 % / Biso Wilson estimate: 16.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0557 / Net I/σ(I): 17.16
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.395 / Num. unique obs: 2622 / CC1/2: 0.765 / % possible all: 71.37

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→40.69 Å / SU ML: 0.1735 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.1913
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1919 1791 5.02 %
Rwork0.1643 33859 -
obs0.1657 35650 95.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.51 Å2
Refinement stepCycle: LAST / Resolution: 1.65→40.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2258 0 8 364 2630
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01072400
X-RAY DIFFRACTIONf_angle_d1.08483296
X-RAY DIFFRACTIONf_chiral_restr0.0579372
X-RAY DIFFRACTIONf_plane_restr0.0082439
X-RAY DIFFRACTIONf_dihedral_angle_d6.0151363
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.690.23661010.25331884X-RAY DIFFRACTION69.94
1.69-1.740.35291050.25562167X-RAY DIFFRACTION80.37
1.74-1.80.29951360.22582509X-RAY DIFFRACTION93.13
1.8-1.870.25361470.1892678X-RAY DIFFRACTION99.37
1.87-1.940.22121380.16462686X-RAY DIFFRACTION99.37
1.94-2.030.20321300.16182703X-RAY DIFFRACTION99.68
2.03-2.140.19791530.1592718X-RAY DIFFRACTION99.9
2.14-2.270.20671210.15162735X-RAY DIFFRACTION99.93
2.27-2.440.19391500.15682707X-RAY DIFFRACTION99.65
2.44-2.690.17251680.16112706X-RAY DIFFRACTION99.83
2.69-3.080.21781390.16042744X-RAY DIFFRACTION99.86
3.08-3.880.16231370.14722777X-RAY DIFFRACTION99.76
3.88-40.690.15711660.16122845X-RAY DIFFRACTION99.31
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)
15.47000373334-1.538809985542.575234186073.57772574401-5.203560077298.37570846587-0.197664979923-0.114554942196-0.2925681567570.02738413373390.2808904026480.06685785088160.236336132883-0.439312026777-0.09354270653240.1423625149470.0009744616108810.01717812008870.110432516068-0.02996828952050.13433827969-11.6175867499-22.57537366990.00571148996565
22.372682990960.79159908572-0.379189210052.30393230763-0.0824289658222.4127971280.0220514492490.0937389102376-0.108656289198-0.1317976278660.00194392751381-0.07139482822570.008376246071830.0459226742355-0.0115154747830.07557345456960.00501651769175-0.01611051485210.0732222212281-0.00366666422390.0869077417496-2.95661455456-18.2114742617-4.9495079949
31.891011401030.846784901392-0.2730751245852.00664890834-0.3137127981682.32983140096-0.04136035849880.11969828735-0.0926433474833-0.1464988326430.0389498062238-0.0787891523917-0.00248554756220.07290543724220.0003787701452080.07572227003690.01413080962620.006481898223310.0970847524654-0.003972474955240.0984673175347-1.41856270141-18.0900148525-5.83828296348
41.10539514242-1.95576368126-0.3893895281123.460571480690.688569478150.136896636624-0.1156380497-0.0335310790291.62892819574-0.1823272873330.0171934369951-0.818068586406-1.378934438180.3161931622330.07213882136440.603538660856-0.1103521897910.04428961644660.2968654099440.05865405497720.5287800506874.02714234728-4.55159873398-18.5059190576
50.6521725406591.107398143361.681184201736.518261396440.7153897793295.31796383315-0.1427419573830.6890841210440.5280165021050.006252496929530.3043012049710.0145233517274-0.306981525751-0.167602557114-0.1558981990120.1474249603390.0234649028898-0.01572035472790.07456245747830.04004625841110.0888358364822-7.62537435744-1.8606511403210.5991269053
62.727839950331.52788314553-2.642181738441.4680065502-1.832459073524.09320097233-0.06068839431850.0501692938297-0.0689840326834-0.03606431837080.0202381138784-0.1440272509270.00649527504141-0.1200724787880.05769450262070.09549202576050.0256372521205-0.01659487046070.0664993513240.006896288857150.108707419607-10.9001898729-10.094836275415.2393080023
73.31829982406-0.698317041467-2.685911956653.86953131671.999701947466.327834800390.017364160598-0.06166012763970.08543999629220.053825006345-0.081271938738-0.0966500160717-0.09328311266380.1360536141010.08130993935770.1029401764980.00506595756783-0.02259831589830.1067540329960.02770861583770.108563991241-10.3344805627-10.769092898521.3011330269
83.310394889030.725227417067-2.726774313811.84659579127-2.073626465053.864549606780.08681762183010.0829473884664-0.04550228575640.1630532527260.03821000097230.0368304113744-0.148937489535-0.301824395222-0.1083146254160.124480859396-0.00113484936641-0.02626614604970.0870720468101-0.02805313325330.0909174368765-15.1528747458-8.6878434503621.271529513
96.148918041534.03021723248-2.201496481067.18330942702-0.4890713870626.053406715960.07918680725160.05466130452740.5524724314510.238750376180.2100412924260.479952835609-0.211309312431-0.331326420717-0.3547899749780.08945277141470.0484110657144-0.04263652262420.09616811866950.0150680706290.1249065625219.96506760351-18.544458109813.5030560254
102.087273117221.31275738599-0.389559971734.78205584171-1.507295794982.51793676042-0.0653297109613-0.00489938879813-0.0712560324209-0.1574554712310.1293138448860.3769603324440.142068489968-0.147791475923-0.1033803679810.08442721851860.0173199237762-0.02858962911910.09776110300050.0001958174185890.1469935674295.25709514228-27.479872876810.5908074319
111.90083549484-0.1491725229730.2455991332033.81389471752-2.111815375934.42497516030.0259975938405-0.106216323842-0.3368608726130.0995741203526-0.0329670497393-0.1067501451910.2309094616740.09825676484060.0030024362550.1265387440930.002449395295660.00609608017670.09746645251370.01511080077370.17405452138512.055760719-32.611078276113.1472989942
121.40391765040.366055689896-0.5706141698652.99391003486-1.38566686812.45128501451-0.0465756308164-0.00621120378479-0.2309329269680.1198790544520.1484619822020.1926395669050.159021784149-0.00915355722313-0.07156703729560.08812106808250.0140734489513-0.02046335800880.08335252366840.009302350950490.1452764988369.76192326751-32.004811139816.8692740349
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 12 )AA3 - 121 - 10
22chain 'A' and (resid 13 through 56 )AA13 - 5611 - 54
33chain 'A' and (resid 57 through 98 )AA57 - 9855 - 96
44chain 'A' and (resid 99 through 105 )AA99 - 10597 - 103
55chain 'B' and (resid 3 through 12 )BB3 - 121 - 10
66chain 'B' and (resid 13 through 46 )BB13 - 4611 - 44
77chain 'B' and (resid 47 through 67 )BB47 - 6745 - 65
88chain 'B' and (resid 68 through 104 )BB68 - 10466 - 102
99chain 'C' and (resid 3 through 12 )CC3 - 121 - 10
1010chain 'C' and (resid 13 through 38 )CC13 - 3811 - 36
1111chain 'C' and (resid 39 through 67 )CC39 - 6737 - 65
1212chain 'C' and (resid 68 through 102 )CC68 - 10266 - 100

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