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- PDB-3knb: Crystal structure of the titin C-terminus in complex with obscuri... -

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Basic information

Entry
Database: PDB / ID: 3knb
TitleCrystal structure of the titin C-terminus in complex with obscurin-like 1
Components
  • Obscurin-like protein 1
  • Titin
KeywordsSTRUCTURAL PROTEIN/STRUCTURAL PROTEIN / Ig-like / titin / obscurin / obsl1 / ATP-binding / Calmodulin-binding / Cardiomyopathy / Disease mutation / Immunoglobulin domain / Kinase / Limb-girdle muscular dystrophy / Magnesium / Nucleotide-binding / Nucleus / Phosphoprotein / Serine/threonine-protein kinase / Transferase / STRUCTURAL PROTEIN-STRUCTURAL PROTEIN complex
Function / homology
Function and homology information


3M complex / sarcomerogenesis / structural molecule activity conferring elasticity / telethonin binding / skeletal muscle myosin thick filament assembly / protein localization to Golgi apparatus / cardiac myofibril assembly / muscle alpha-actinin binding / detection of muscle stretch / cytoskeletal anchor activity ...3M complex / sarcomerogenesis / structural molecule activity conferring elasticity / telethonin binding / skeletal muscle myosin thick filament assembly / protein localization to Golgi apparatus / cardiac myofibril assembly / muscle alpha-actinin binding / detection of muscle stretch / cytoskeletal anchor activity / cardiac muscle tissue morphogenesis / regulation of catalytic activity / cardiac muscle hypertrophy / mitotic chromosome condensation / Striated Muscle Contraction / actinin binding / M band / I band / cardiac muscle cell development / regulation of protein kinase activity / positive regulation of dendrite morphogenesis / structural constituent of muscle / regulation of mitotic nuclear division / sarcomere organization / Golgi organization / skeletal muscle thin filament assembly / striated muscle thin filament / intercalated disc / striated muscle contraction / cardiac muscle contraction / cytoskeleton organization / protein kinase A signaling / condensed nuclear chromosome / muscle contraction / positive regulation of protein secretion / Z disc / microtubule cytoskeleton organization / response to calcium ion / : / actin filament binding / Platelet degranulation / Neddylation / protein tyrosine kinase activity / protease binding / non-specific serine/threonine protein kinase / calmodulin binding / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / calcium ion binding / positive regulation of gene expression / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / enzyme binding / extracellular exosome / extracellular region / ATP binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
PPAK motif / PPAK motif / Titin, Z repeat / Titin Z / MyBP-C, tri-helix bundle domain / Tri-helix bundle domain / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain ...PPAK motif / PPAK motif / Titin, Z repeat / Titin Z / MyBP-C, tri-helix bundle domain / Tri-helix bundle domain / Immunoglobulin 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 / Immunoglobulins / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Obscurin-like protein 1 / Titin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å
AuthorsSauer, F. / Vahokoski, J. / Wilmanns, M.
CitationJournal: Embo Rep. / Year: 2010
Title: Molecular basis of the head-to-tail assembly of giant muscle proteins obscurin-like 1 and titin.
Authors: Sauer, F. / Vahokoski, J. / Song, Y.H. / Wilmanns, M.
History
DepositionNov 12, 2009Deposition site: RCSB / Processing site: RCSB
SupersessionDec 1, 2009ID: 3IRG
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Feb 21, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_unobs_or_zero_occ_atoms / 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 / _diffrn_source.pdbx_synchrotron_site / _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: Obscurin-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8213
Polymers21,7242
Non-polymers961
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-17 kcal/mol
Surface area9560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.910, 60.910, 42.050
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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


Mass: 10746.997 Da / Num. of mol.: 1
Fragment: titin, C-terminal domain M10, resideus 34253-34350
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTN / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q8WZ42, non-specific serine/threonine protein kinase
#2: Protein Obscurin-like protein 1


Mass: 10977.501 Da / Num. of mol.: 1
Fragment: obscurin-like 1, N-terminal domain, residues 1-105
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA0657, OBSL1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O75147
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.07 Å3/Da / Density % sol: 40.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: ammonium sulfate, imidazole, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.99184, 0.91740, 0.91706
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 25, 2009
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.991841
20.91741
30.917061
ReflectionResolution: 1.4→19.53 Å / Num. all: 34358 / Num. obs: 34179 / % possible obs: 99.5 %
Reflection shellResolution: 1.4→1.44 Å / Num. unique all: 2514 / % possible all: 99.6

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Processing

Software
NameVersionClassification
MAR345data collection
SHELXSphasing
PHENIX(phenix.refine: 1.5_2)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.4→19.53 Å / SU ML: 0.18 / σ(F): 1.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1949 1711 5.01 %RANDOM
Rwork0.1637 ---
obs0.1653 34177 99.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.43 Å2 / ksol: 0.397 e/Å3
Refinement stepCycle: LAST / Resolution: 1.4→19.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1413 0 5 266 1684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061644
X-RAY DIFFRACTIONf_angle_d1.0862280
X-RAY DIFFRACTIONf_dihedral_angle_d15.584609
X-RAY DIFFRACTIONf_chiral_restr0.068263
X-RAY DIFFRACTIONf_plane_restr0.005310
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4001-1.45010.28021710.22793270X-RAY DIFFRACTION100
1.4501-1.50810.27391840.20593213X-RAY DIFFRACTION100
1.5081-1.57670.28311700.1913263X-RAY DIFFRACTION100
1.5767-1.65980.21851730.1753212X-RAY DIFFRACTION100
1.6598-1.76380.24261640.16883292X-RAY DIFFRACTION99
1.7638-1.89980.22991740.16433219X-RAY DIFFRACTION99
1.8998-2.09080.19881660.14953251X-RAY DIFFRACTION100
2.0908-2.39290.18671460.1553266X-RAY DIFFRACTION99
2.3929-3.0130.19381730.16723243X-RAY DIFFRACTION99
3.013-19.53270.16181900.15073237X-RAY DIFFRACTION100

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