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- PDB-4jnw: Bacterially expressed Titin Kinase -

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Basic information

Entry
Database: PDB / ID: 4jnw
TitleBacterially expressed Titin Kinase
ComponentsTitin
KeywordsTRANSFERASE / muscle cytoskeleton
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 / protein kinase A signaling / muscle alpha-actinin binding / cardiac myofibril assembly / mitotic chromosome condensation ...sarcomerogenesis / titin-telethonin complex / structural molecule activity conferring elasticity / skeletal muscle myosin thick filament assembly / telethonin binding / detection of muscle stretch / protein kinase A signaling / muscle alpha-actinin binding / cardiac myofibril assembly / mitotic chromosome condensation / cardiac muscle hypertrophy / cardiac muscle tissue morphogenesis / actinin binding / Striated Muscle Contraction / muscle filament sliding / protein kinase regulator activity / 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 / Z disc / response to calcium ion / actin filament binding / Platelet degranulation / protease binding / protein tyrosine kinase activity / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / calmodulin binding / 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 / Tyrosine-protein kinase, active site / Immunoglobulin subtype / Immunoglobulin / Phosphorylase Kinase; domain 1 / Ig-like domain profile. / Immunoglobulin-like domain / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Immunoglobulin-like domain superfamily / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsBogomolovas, J. / Labeit, S. / Mayans, O.
Citation
Journal: Open Biol / Year: 2014
Title: Titin kinase is an inactive pseudokinase scaffold that supports MuRF1 recruitment to the sarcomeric M-line.
Authors: Bogomolovas, J. / Gasch, A. / Simkovic, F. / Rigden, D.J. / Labeit, S. / Mayans, O.
#1: Journal: Nature / Year: 1998
Title: Structural basis for activation of the titin kinase domain during myofibrillogenesis.
Authors: Mayans, O. / van der Ven, P.F. / Wilm, M. / Mues, A. / Young, P. / Furst, D.O. / Wilmanns, M. / Gautel, M.
#2: Journal: J.Synchrotron Radia. / Year: 1999
Title: X-ray analysis of protein crystals with thin-plate morphology
Authors: Mayans, O. / Wilmanns, M.
History
DepositionMar 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Titin
B: Titin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0414
Polymers74,8562
Non-polymers1842
Water8,449469
1
A: Titin


Theoretical massNumber of molelcules
Total (without water)37,4281
Polymers37,4281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Titin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6123
Polymers37,4281
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.860, 89.730, 113.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 37428.219 Da / Num. of mol.: 2 / Fragment: titin kinase: unp residues 32172-32492
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 469 / 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: 2.69 Å3/Da / Density % sol: 54.3 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.06→28.979 Å / Num. obs: 49576 / % possible obs: 97.9 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 13.9
Reflection shellResolution: 2.06→2.1 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.562 / Mean I/σ(I) obs: 3.6 / % possible all: 95.4

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TKI

1tki


Resolution: 2.06→28.979 Å / SU ML: 0.21 / σ(F): 2 / Phase error: 24.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2037 1488 3 %FREERFLAG
Rwork0.1663 ---
obs0.1674 49576 97.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.06→28.979 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5216 0 12 469 5697
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075348
X-RAY DIFFRACTIONf_angle_d17207
X-RAY DIFFRACTIONf_dihedral_angle_d15.1522023
X-RAY DIFFRACTIONf_chiral_restr0.072816
X-RAY DIFFRACTIONf_plane_restr0.003910
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.12650.25851320.20834266X-RAY DIFFRACTION97
2.1265-2.20250.22861360.18914381X-RAY DIFFRACTION99
2.2025-2.29060.23141340.17524371X-RAY DIFFRACTION99
2.2906-2.39480.22531350.17244375X-RAY DIFFRACTION99
2.3948-2.5210.23621360.17624391X-RAY DIFFRACTION99
2.521-2.67880.23341360.17584359X-RAY DIFFRACTION99
2.6788-2.88550.21361350.17494384X-RAY DIFFRACTION98
2.8855-3.17560.20991350.1774351X-RAY DIFFRACTION98
3.1756-3.63430.20131340.16284368X-RAY DIFFRACTION97
3.6343-4.57590.17871370.13514379X-RAY DIFFRACTION97
4.5759-28.98190.15971380.16074463X-RAY DIFFRACTION95
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)
13.9140.45860.65290.5991-0.01651.457-0.0328-0.43660.01840.0967-0.02090.00350.0268-0.1350.01080.08210.0080.01380.0196-0.01550.017617.3915-2.4815-7.1488
23.1690.3096-0.68740.55370.05840.7149-0.0056-0.25870.07690.04730.00160.04750.0140.0456-0.00340.0792-0.0001-0.00890.0771-0.00280.045422.028-42.0517-27.9689
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 338 )
2X-RAY DIFFRACTION2chain 'B' and (resid 18 through 338 )

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