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- PDB-5jdd: Crystal structure of I9-I11 tandem from titin (P212121) -

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Basic information

Entry
Database: PDB / ID: 5jdd
TitleCrystal structure of I9-I11 tandem from titin (P212121)
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: 1.53 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Titin


Theoretical massNumber of molelcules
Total (without water)29,7051
Polymers29,7051
Non-polymers00
Water9,764542
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.340, 65.800, 108.390
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: 29705.213 Da / Num. of mol.: 1
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.: 542 / 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: 2.54 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-Tris Propane pH 8.5, 20% [w/v] PEG 3350, 0.2 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.53→41.83 Å / Num. obs: 45488 / % possible obs: 97.5 % / Redundancy: 5.5 % / Rsym value: 0.058 / Net I/σ(I): 12.6
Reflection shellResolution: 1.53→1.61 Å / Rsym value: 0.414

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→41.83 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 0.06 / Phase error: 18.01
RfactorNum. reflection% reflection
Rfree0.1965 2687 3.12 %
Rwork0.1615 --
obs0.1625 45171 97.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.53→41.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2068 0 0 542 2610
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062183
X-RAY DIFFRACTIONf_angle_d1.0942980
X-RAY DIFFRACTIONf_dihedral_angle_d12.962830
X-RAY DIFFRACTIONf_chiral_restr0.075362
X-RAY DIFFRACTIONf_plane_restr0.005371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.55780.24621590.22674211X-RAY DIFFRACTION94
1.5578-1.58780.2291300.2184353X-RAY DIFFRACTION97
1.5878-1.62020.25081270.2014358X-RAY DIFFRACTION96
1.6202-1.65540.22391670.19094347X-RAY DIFFRACTION98
1.6554-1.69390.211420.17994385X-RAY DIFFRACTION96
1.6939-1.73630.19051590.18374388X-RAY DIFFRACTION98
1.7363-1.78320.19551340.17314354X-RAY DIFFRACTION97
1.7832-1.83570.2281510.17064396X-RAY DIFFRACTION97
1.8357-1.8950.18151440.16854381X-RAY DIFFRACTION99
1.895-1.96270.19111440.1564412X-RAY DIFFRACTION97
1.9627-2.04130.20051410.15834420X-RAY DIFFRACTION98
2.0413-2.13420.19551390.15794416X-RAY DIFFRACTION98
2.1342-2.24670.21851350.16634436X-RAY DIFFRACTION98
2.2467-2.38740.21481460.16844357X-RAY DIFFRACTION97
2.3874-2.57180.221180.16994394X-RAY DIFFRACTION98
2.5718-2.83050.19381530.16924475X-RAY DIFFRACTION99
2.8305-3.240.2251330.15324471X-RAY DIFFRACTION99
3.24-4.08150.16031410.13814401X-RAY DIFFRACTION98
4.0815-41.84830.15721240.14214386X-RAY DIFFRACTION97
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)
10.65540.28230.12480.3729-0.03490.364-0.03860.0411-0.02010.07980.024-0.030.07-0.06190.00130.10640.0034-0.00180.1072-0.0230.1043-20.914-44.7008-9.58
20.22260.0292-0.1420.21910.07650.13220.00060.04190.002-0.0189-0.0061-0.0092-0.0131-0.0073-0.00520.05440.006300.0522-0.01760.0582-22.3289-6.07497.3799
30.43540.3658-0.04451.08460.12450.6130.0434-0.0135-0.01330.0089-0.1028-0.0463-0.0222-0.0026-0.12010.07170.00290.00020.0878-0.00010.0679-17.279728.398318.4345
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 91 )
2X-RAY DIFFRACTION2chain 'A' and (resid 92 through 177 )
3X-RAY DIFFRACTION3chain 'A' and (resid 178 through 265 )

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