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- PDB-2wwk: Crystal structure of the Titin M10-Obscurin like 1 Ig F17R mutant... -

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Basic information

Entry
Database: PDB / ID: 2wwk
TitleCrystal structure of the Titin M10-Obscurin like 1 Ig F17R mutant complex
Components
  • OBSCURIN-LIKE PROTEIN 1
  • TITIN
KeywordsTRANSFERASE/STRUCTURAL PROTEIN / TRANSFERASE-STRUCTURAL PROTEIN COMPLEX / SARCOMERE / IMMUNOGLOBULIN DOMAIN / LIMB-GIRDLE MUSCULAR DYSTROPHY / KELCH REPEAT / CARDIOMYOPATHY
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 / protein kinase regulator activity / cardiac muscle hypertrophy / mitotic chromosome condensation / actinin binding / Striated Muscle Contraction / M band / I band / positive regulation of dendrite morphogenesis / cardiac muscle cell development / structural constituent of muscle / regulation of mitotic nuclear division / sarcomere organization / Golgi organization / skeletal muscle thin filament assembly / striated muscle thin filament / intercalated disc / cardiac muscle contraction / striated muscle contraction / cytoskeleton organization / muscle contraction / protein kinase A signaling / condensed nuclear chromosome / 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 / 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 / protein homodimerization activity / extracellular exosome / extracellular region / ATP binding / identical protein binding / cytosol / cytoplasm
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 ...: / 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 / Tyrosine-protein kinase, active site / Immunoglobulin subtype / Immunoglobulin / 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 / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPernigo, S. / Fukuzawa, A. / Gautel, M. / Steiner, R.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural Insight Into M-Band Assembly and Mechanics from the Titin-Obscurin-Like-1 Complex.
Authors: Pernigo, S. / Fukuzawa, A. / Bertz, M. / Holt, M. / Rief, M. / Steiner, R.A. / Gautel, M.
History
DepositionOct 25, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 24, 2011Group: Derived calculations
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
O: OBSCURIN-LIKE PROTEIN 1
T: TITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3054
Polymers22,1172
Non-polymers1882
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-21.3 kcal/mol
Surface area10670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.010, 37.800, 68.490
Angle α, β, γ (deg.)90.00, 92.99, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11T-2076-

HOH

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Components

#1: Protein OBSCURIN-LIKE PROTEIN 1


Mass: 11135.640 Da / Num. of mol.: 1 / Fragment: IG1, RESIDUES 1-106 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA 2 / References: UniProt: O75147
#2: Protein TITIN / CONNECTIN / RHABDOMYOSARCOMA ANTIGEN MU-RMS-40.14


Mass: 10981.231 Da / Num. of mol.: 1 / Fragment: M10, RESIDUES 34252-34350
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA 2
References: UniProt: Q8WZ42, non-specific serine/threonine protein kinase
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN O, PHE 17 TO ARG
Sequence detailsINITIAL GSS ARE FROM THE EXPRESSION VECTOR

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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: 2.29 Å3/Da / Density % sol: 45.82 % / Description: NONE
Crystal growpH: 5.5
Details: 0.1 M BIS-TRIS PH 5.5, 0.2 M AMMONIUM SULPHATE, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 12, 2009 / Details: MIRRORS
RadiationMonochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.7→34.79 Å / Num. obs: 24975 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 20.95 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 20.6
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 8 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 6 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0093refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WP3

2wp3


Resolution: 1.7→31.27 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.891 / SU B: 5.219 / SU ML: 0.079 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25881 1224 4.9 %RANDOM
Rwork0.21884 ---
obs0.22073 23686 98.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.317 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å2-0 Å20.63 Å2
2---0.15 Å20 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 1.7→31.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1465 0 11 287 1763
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221542
X-RAY DIFFRACTIONr_bond_other_d0.0010.021050
X-RAY DIFFRACTIONr_angle_refined_deg1.5571.9842107
X-RAY DIFFRACTIONr_angle_other_deg0.83532572
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.795206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.77723.7564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.36315241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1711513
X-RAY DIFFRACTIONr_chiral_restr0.0830.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211739
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02292
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8131.51000
X-RAY DIFFRACTIONr_mcbond_other0.2471.5402
X-RAY DIFFRACTIONr_mcangle_it1.39221615
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2683542
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5334.5487
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 94 -
Rwork0.316 1761 -
obs--99.62 %
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)
18.42584.09225.75655.21624.64511.84780.07670.0189-0.58110.38880.0784-0.37230.65230.0211-0.15510.16240.02030.05170.08320.01710.130515.4013-8.535413.8742
25.41675.0883-0.351612.993-1.1293.62910.0057-0.1867-0.34180.1463-0.0263-0.67590.02420.32880.02060.0935-0.0026-0.02670.1017-0.0020.116324.2919.368318.1952
37.93461.1752.58162.9727-2.65399.2355-0.04460.3497-0.412-0.21750.2481-0.21660.19140.051-0.20350.17030.02820.03450.0675-0.03030.095716.6408-9.14716.6546
44.55631.0403-1.52636.5619-0.7587.17860.09240.12150.29340.0437-0.01820.4276-0.361-0.5153-0.07420.11630.01010.00160.10470.0060.075713.61618.40596.6341
51.86421.59140.113811.18880.37633.0237-0.01680.2895-0.033-0.3219-0.0075-0.5581-0.09470.2330.02430.1173-0.01150.02060.1384-0.00740.102724.03386.34226.7261
62.74545.65980.945816.81323.35531.8962-0.13520.17160.1646-0.3169-0.02130.4052-0.0995-0.12390.15650.04560.00190.00220.07510.01010.050712.06314.156310.7853
712.640118.37683.755133.62796.29813.81840.0124-0.1660.74060.4957-0.05390.4911-0.40790.13310.04160.1357-0.0184-0.02630.0772-0.02220.112921.635119.001320.9343
85.1371-0.04137.01951.4676-0.438218.7272-0.33520.10270.16460.0748-0.0309-0.1193-0.72940.46490.36610.0924-0.01240.02070.07740.01680.122811.07155.212128.9342
94.26022.39783.97593.74243.646210.3248-0.18180.2229-0.0875-0.2480.05040.1590.0703-0.19060.13140.0791-0.03070.04850.0827-0.01460.09325.6926-4.843916.0328
109.42511.53674.35382.96110.59525.35870.171-0.1263-0.34890.0853-0.0479-0.08540.14340.0972-0.1230.05860.00260.0340.09380.00480.04434.9054-3.031531.566
1133.33-13.6637-12.049411.19034.27734.4688-0.4531-0.5898-1.3875-0.03060.09490.90120.24310.18070.35820.2289-0.0876-0.05560.17250.05320.2568-3.8758-8.765428.0395
1211.78624.75898.68617.03924.599211.5440.4796-0.064-1.21720.47220.0443-0.27321.1211-0.1036-0.52380.1741-0.01560.03790.06760.01240.18095.1605-11.651622.3818
134.705-0.04414.14993.68544.347111.9562-0.06180.271-0.2024-0.3727-0.36620.66140.0107-0.69940.42810.151-0.0494-0.0560.2138-0.04490.1839-4.436-4.71216.1433
146.85840.464910.09651.86090.582622.5781-0.168-0.01460.022-0.09610.05040.127-0.5613-0.30880.11760.0326-0.00130.01370.0566-0.00090.07422.90061.767125.3635
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1O8 - 17
2X-RAY DIFFRACTION2O18 - 32
3X-RAY DIFFRACTION3O33 - 42
4X-RAY DIFFRACTION4O43 - 55
5X-RAY DIFFRACTION5O56 - 74
6X-RAY DIFFRACTION6O75 - 95
7X-RAY DIFFRACTION7O96 - 106
8X-RAY DIFFRACTION8T0 - 14
9X-RAY DIFFRACTION9T15 - 30
10X-RAY DIFFRACTION10T31 - 42
11X-RAY DIFFRACTION11T43 - 47
12X-RAY DIFFRACTION12T48 - 67
13X-RAY DIFFRACTION13T68 - 79
14X-RAY DIFFRACTION14T80 - 99

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