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- PDB-8bnq: Crystal structure of the FnIII-tandem A84-A86 from the A-band of titin -

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Basic information

Entry
Database: PDB / ID: 8bnq
TitleCrystal structure of the FnIII-tandem A84-A86 from the A-band of titin
ComponentsTitin
KeywordsSTRUCTURAL PROTEIN / titin / muscle / A-band
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: 2.3 Å
AuthorsZacharchenko, T. / Fleming, J.R. / Mayans, O.
Funding support United Kingdom, France, 3items
OrganizationGrant numberCountry
British Heart FoundationPG/13/21/3007 United Kingdom
The French Muscular Dystrophy Telethon (AFM-Telethon)21436 France
Leducq FoundationTNE-13CVD04 France
CitationJournal: J.Muscle Res.Cell.Motil. / Year: 2023
Title: Molecular insights into titin's A-band.
Authors: Fleming, J.R. / Muller, I. / Zacharchenko, T. / Diederichs, K. / Mayans, O.
History
DepositionNov 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 6, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Titin
B: Titin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2114
Polymers67,0862
Non-polymers1242
Water2,378132
1
A: Titin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6673
Polymers33,5431
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Titin


Theoretical massNumber of molelcules
Total (without water)33,5431
Polymers33,5431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.270, 75.000, 79.840
Angle α, β, γ (deg.)114.574, 92.503, 100.913
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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


Mass: 33543.184 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 / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.47 Å3/Da / Density % sol: 50.28 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 5% [v/v] polyethylene glycol 400 and 40% [v/v] 2-methyl-2,4-pentanediol (MPD)

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Data collection

DiffractionMean temperature: 293.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9725 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9725 Å / Relative weight: 1
ReflectionResolution: 2.3→29.5 Å / Num. obs: 27975 / % possible obs: 97.95 % / Redundancy: 3.6 % / Biso Wilson estimate: 45.69 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.121 / Net I/σ(I): 9.27
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.02 / Num. unique obs: 2819 / CC1/2: 0.492 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NZI

2nzi


Resolution: 2.3→29.5 Å / SU ML: 0.3396 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 32.6361
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2578 1001 3.58 %
Rwork0.1975 26953 -
obs0.1997 27954 97.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.34 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4699 0 8 132 4839
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00874817
X-RAY DIFFRACTIONf_angle_d1.1036558
X-RAY DIFFRACTIONf_chiral_restr0.0673731
X-RAY DIFFRACTIONf_plane_restr0.0074856
X-RAY DIFFRACTIONf_dihedral_angle_d18.87361822
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.420.34781430.3073881X-RAY DIFFRACTION97.34
2.42-2.570.32951260.29983821X-RAY DIFFRACTION97.72
2.57-2.770.32181380.28393830X-RAY DIFFRACTION97.81
2.77-3.050.34631360.25773861X-RAY DIFFRACTION98.18
3.05-3.490.31511560.21613875X-RAY DIFFRACTION98.2
3.49-4.40.24761550.16393843X-RAY DIFFRACTION98.64
4.4-29.50.16891470.143842X-RAY DIFFRACTION98.08

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