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- PDB-5jde: Crystal structure of I9-I11 tandem from titin (P1) -

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Basic information

Entry
Database: PDB / ID: 5jde
TitleCrystal structure of I9-I11 tandem from titin (P1)
ComponentsTitin
KeywordsSTRUCTURAL PROTEIN / titin
Function / homology
Function and homology information


sarcomerogenesis / structural molecule activity conferring elasticity / telethonin binding / skeletal muscle myosin thick filament assembly / cardiac myofibril assembly / detection of muscle stretch / muscle alpha-actinin binding / cardiac muscle tissue morphogenesis / regulation of catalytic activity / Striated Muscle Contraction ...sarcomerogenesis / structural molecule activity conferring elasticity / telethonin binding / skeletal muscle myosin thick filament assembly / cardiac myofibril assembly / detection of muscle stretch / muscle alpha-actinin binding / cardiac muscle tissue morphogenesis / regulation of catalytic activity / Striated Muscle Contraction / mitotic chromosome condensation / cardiac muscle hypertrophy / M band / actinin binding / 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 / 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: 1.9 Å
AuthorsWilliams, R. / Bogomolovas, J. / Labiet, S. / Mayans, O.
CitationJournal: Open Biology / Year: 2016
Title: Exploration of pathomechanisms triggered by a single-nucleotide polymorphism in titin's I-band: the cardiomyopathy-linked mutation T2580I.
Authors: Bogomolovas, J. / Fleming, J.R. / Anderson, B.R. / Williams, R. / Lange, S. / Simon, B. / Khan, M.M. / Rudolf, R. / Franke, B. / Bullard, B. / Rigden, D.J. / Granzier, H. / Labeit, S. / Mayans, O.
History
DepositionApr 16, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Titin
B: Titin


Theoretical massNumber of molelcules
Total (without water)59,4102
Polymers59,4102
Non-polymers00
Water5,044280
1
A: Titin


Theoretical massNumber of molelcules
Total (without water)29,7051
Polymers29,7051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Titin


Theoretical massNumber of molelcules
Total (without water)29,7051
Polymers29,7051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.725, 42.397, 83.529
Angle α, β, γ (deg.)85.18, 79.76, 87.05
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 29705.213 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTN / Plasmid: pETM11 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8WZ42, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.2 Å3/Da / Density % sol: 44.18 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris HCl pH 8.5, 30% [w/v] PEG 4000, 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→19.42 Å / Num. obs: 38254 / % possible obs: 96.61 % / Redundancy: 3.5 % / Rsym value: 0.076 / Net I/σ(I): 11.3
Reflection shellHighest resolution: 1.9 Å / Rsym value: 0.645

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QEG

4qeg


Resolution: 1.9→19.42 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 25
RfactorNum. reflection% reflection
Rfree0.2189 1196 3.13 %
Rwork0.1714 --
obs0.1729 38227 96.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4089 0 0 280 4369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084163
X-RAY DIFFRACTIONf_angle_d1.0795633
X-RAY DIFFRACTIONf_dihedral_angle_d13.8851535
X-RAY DIFFRACTIONf_chiral_restr0.045676
X-RAY DIFFRACTIONf_plane_restr0.004696
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9038-1.980.29671240.26933849X-RAY DIFFRACTION89
1.98-2.07010.30081180.23934127X-RAY DIFFRACTION96
2.0701-2.17920.28411300.21724131X-RAY DIFFRACTION97
2.1792-2.31570.23771190.20374198X-RAY DIFFRACTION97
2.3157-2.49440.28041520.20744192X-RAY DIFFRACTION98
2.4944-2.74520.24321440.19154154X-RAY DIFFRACTION98
2.7452-3.1420.24611310.1864216X-RAY DIFFRACTION98
3.142-3.95690.19021380.14474128X-RAY DIFFRACTION97
3.9569-28.51370.17561400.1354036X-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)
13.31540.6760.3192.6491-0.61792.0101-0.16280.3403-0.1117-0.06740.0578-0.1220.00450.1830.07620.2687-0.03870.02660.2117-0.03680.271950.129233.64484.2625
22.356-0.144-0.77711.19820.35671.6603-0.1244-0.286-0.15320.09530.03450.00150.0101-0.04790.06680.20090.04240.00910.21960.02180.186416.828836.564329.6241
32.49591.0291-1.85391.4139-0.84823.89730.4291-0.07480.25120.19840.09160.2882-0.1353-0.1353-0.50370.3696-0.02410.04950.47990.04920.423-7.872530.01455.9476
41.57480.048-0.86112.184-0.19432.89210.0350.04330.0358-0.01220.00980.1878-0.2844-0.2643-0.07320.32230.03310.04290.3225-0.01810.2312-28.900655.161946.3358
52.38890.7055-1.0041.57670.18231.57160.0495-0.0785-0.06530.0382-0.00420.0102-0.0207-0.0357-0.04610.14160.007-0.02540.12440.00360.18682.865357.153718.5216
62.35080.4268-0.80181.67620.18853.8196-0.12430.21820.0088-0.18890.1071-0.0620.29980.08920.01650.2275-0.0033-0.01840.21990.01580.216930.628849.3836-4.9474
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 4 through 90)
2X-RAY DIFFRACTION2(chain 'A' and resid 91 through 177)
3X-RAY DIFFRACTION3(chain 'A' and resid 178 through 263 )
4X-RAY DIFFRACTION4(chain 'B' and resid 6 through 90)
5X-RAY DIFFRACTION5(chain 'B' and resid 91 through 177)
6X-RAY DIFFRACTION6(chain 'B' and resid 178 through 264 )

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