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- PDB-6fwx: Chimeric titin Z1Z2-Z1Z2 tandem (Z1212) functionalized with a GRG... -

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Basic information

Entry
Database: PDB / ID: 6fwx
TitleChimeric titin Z1Z2-Z1Z2 tandem (Z1212) functionalized with a GRGDS exogenous peptide from fibronectin
ComponentsTitin,Titin,Titin
KeywordsSTRUCTURAL PROTEIN / titin / Z1Z2
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 / muscle alpha-actinin binding / : / cardiac myofibril assembly / cardiac muscle hypertrophy ...sarcomerogenesis / titin-telethonin complex / structural molecule activity conferring elasticity / skeletal muscle myosin thick filament assembly / telethonin binding / detection of muscle stretch / muscle alpha-actinin binding / : / cardiac myofibril assembly / cardiac muscle hypertrophy / protein kinase regulator activity / mitotic chromosome condensation / cardiac muscle tissue morphogenesis / Striated Muscle Contraction / muscle filament sliding / actinin binding / 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 / response to calcium ion / Z disc / actin filament binding / Platelet degranulation / protease binding / protein tyrosine kinase activity / calmodulin binding / non-specific serine/threonine protein kinase / protein kinase activity / 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 / 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 / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMayans, O. / Fleming, J. / Hill, C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
BBRSC and JRI OrthopaedicsBB/I01666X/1 United Kingdom
Citation
Journal: Adv. Mater. Weinheim / Year: 2019
Title: Self-Assembling Proteins as High-Performance Substrates for Embryonic Stem Cell Self-Renewal.
Authors: Hill, C.J. / Fleming, J.R. / Mousavinejad, M. / Nicholson, R. / Tzokov, S.B. / Bullough, P.A. / Bogomolovas, J. / Morgan, M.R. / Mayans, O. / Murray, P.
#1: Journal: Int J Mol Sci / Year: 2019
Title: The ZT Biopolymer: A Self-Assembling Protein Scaffold for Stem Cell Applications.
Authors: Nesterenko, Y. / Hill, C.J. / Fleming, J.R. / Murray, P. / Mayans, O.
History
DepositionMar 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation / citation_author / reflns / Item: _reflns.percent_possible_obs
Revision 1.2Apr 8, 2020Group: Database references / Category: citation / citation_author
Revision 1.3Jan 17, 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

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Assembly

Deposited unit
A: Titin,Titin,Titin
B: Titin,Titin,Titin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,9934
Polymers83,8692
Non-polymers1242
Water00
1
A: Titin,Titin,Titin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0593
Polymers41,9341
Non-polymers1242
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Titin,Titin,Titin


Theoretical massNumber of molelcules
Total (without water)41,9341
Polymers41,9341
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)134.400, 134.400, 134.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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


Mass: 41934.480 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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2

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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: 2.78 Å3/Da / Density % sol: 55.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10% [v/v] isopropanol, 100 mM Na2HPO4 pH 4.2, 200 mM LiSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.974 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.974 Å / Relative weight: 1
ReflectionResolution: 3→41.8 Å / Num. obs: 17993 / % possible obs: 99 % / Redundancy: 4.1 % / Net I/σ(I): 9.26
Reflection shellResolution: 3→3.108 Å / Rmerge(I) obs: 1.803 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 1813 / CC1/2: 0.162 / Rrim(I) all: 2.079

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A38

2a38


Resolution: 3→41.798 Å / SU ML: 0.69 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 30.67
RfactorNum. reflection% reflection
Rfree0.2255 910 5.06 %
Rwork0.1995 --
obs0.2008 17985 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3→41.798 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2918 0 8 0 2926
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022976
X-RAY DIFFRACTIONf_angle_d0.4614050
X-RAY DIFFRACTIONf_dihedral_angle_d14.3131791
X-RAY DIFFRACTIONf_chiral_restr0.041479
X-RAY DIFFRACTIONf_plane_restr0.003531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0003-3.18820.48021520.42552878X-RAY DIFFRACTION100
3.1882-3.43430.31671500.31652819X-RAY DIFFRACTION99
3.4343-3.77970.31081540.26612833X-RAY DIFFRACTION100
3.7797-4.32610.21821490.18582863X-RAY DIFFRACTION99
4.3261-5.44860.19411500.16112833X-RAY DIFFRACTION100
5.4486-41.80180.19361550.1812849X-RAY DIFFRACTION99

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