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- PDB-2wp3: Crystal structure of the Titin M10-Obscurin like 1 Ig complex -

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Basic information

Entry
Database: PDB / ID: 2wp3
TitleCrystal structure of the Titin M10-Obscurin like 1 Ig complex
Components
  • OBSCURIN-LIKE PROTEIN 1
  • TITIN
KeywordsTRANSFERASE/STRUCTURAL PROTEIN / TRANSFERASE-STRUCTURAL PROTEIN COMPLEX / SARCOMERE / IMMUNOGLOBULIN DOMAIN / LIMB-GIRDLE MUSCULAR DYSTROPHY / SERINE/THREONINE-PROTEIN KINASE / ATP-BINDING / KELCH REPEAT / CARDIOMYOPATHY / CALMODULIN-BINDING
Function / homology
Function and homology information


3M complex / sarcomerogenesis / titin-telethonin complex / structural molecule activity conferring elasticity / skeletal muscle myosin thick filament assembly / telethonin binding / protein localization to Golgi apparatus / detection of muscle stretch / protein kinase A signaling / muscle alpha-actinin binding ...3M complex / sarcomerogenesis / titin-telethonin complex / structural molecule activity conferring elasticity / skeletal muscle myosin thick filament assembly / telethonin binding / protein localization to Golgi apparatus / detection of muscle stretch / protein kinase A signaling / muscle alpha-actinin binding / cytoskeletal anchor activity / cardiac myofibril assembly / positive regulation of dendrite morphogenesis / mitotic chromosome condensation / cardiac muscle hypertrophy / cardiac muscle tissue morphogenesis / actinin binding / Striated Muscle Contraction / muscle filament sliding / protein kinase regulator activity / M band / I band / cardiac muscle cell development / structural constituent of muscle / sarcomere organization / regulation of mitotic nuclear division / Golgi organization / striated muscle thin filament / skeletal muscle thin filament assembly / intercalated disc / skeletal muscle contraction / striated muscle contraction / cardiac muscle contraction / muscle contraction / cytoskeleton organization / condensed nuclear chromosome / positive regulation of protein secretion / microtubule cytoskeleton organization / Z disc / response to calcium ion / actin filament binding / Platelet degranulation / Neddylation / protease binding / protein tyrosine kinase activity / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / 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 / enzyme binding / Golgi apparatus / 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 / 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
Obscurin-like protein 1 / Titin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsPernigo, S. / Fuzukawa, 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
DepositionAug 2, 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 1.3May 1, 2024Group: 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,5717
Polymers22,1072
Non-polymers4645
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-17.4 kcal/mol
Surface area10040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.674, 61.674, 42.347
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 OBSCURIN-LIKE PROTEIN 1


Mass: 11125.619 Da / Num. of mol.: 1 / Fragment: IG1, RESIDUES 1-106
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 / RHABDOMYSARCOMA 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.: 4 / 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.: 233 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 2.1 Å3/Da / Density % sol: 41.5 % / Description: NONE
Crystal growpH: 7
Details: PROTEIN COMPLEX AT 13 MG/ML 2M AMM SULPHATE, 0.1 M BIS-TRIS PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9745
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 21, 2009 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9745 Å / Relative weight: 1
ReflectionResolution: 1.48→53.38 Å / Num. obs: 30142 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 19.38 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.9
Reflection shellResolution: 1.48→1.56 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4.6 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0070refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PREVIOUSLY SOLVED STRUCTURE FROM IN-HOUSE DATA

Resolution: 1.48→33.19 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.202 / SU ML: 0.07 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.084 / 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
Rfree0.21741 1470 5 %RANDOM
Rwork0.1755 ---
obs0.17754 28138 98.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.578 Å2
Baniso -1Baniso -2Baniso -3
1--1.5 Å2-0.75 Å20 Å2
2---1.5 Å20 Å2
3---2.25 Å2
Refinement stepCycle: LAST / Resolution: 1.48→33.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1459 0 29 233 1721
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221632
X-RAY DIFFRACTIONr_bond_other_d0.0010.021108
X-RAY DIFFRACTIONr_angle_refined_deg1.781.9882235
X-RAY DIFFRACTIONr_angle_other_deg0.9243.0012726
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4315221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.56224.15465
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.11215257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2031511
X-RAY DIFFRACTIONr_chiral_restr0.1020.2256
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211833
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02304
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_it1.0721.51047
X-RAY DIFFRACTIONr_mcbond_other0.3381.5420
X-RAY DIFFRACTIONr_mcangle_it1.74221702
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7233585
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.274.5525
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: 1.479→1.517 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 98 -
Rwork0.313 1991 -
obs--93.8 %
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)
13.2386-0.78450.7221.38490.32935.401-0.0685-0.02180.0330.41670.05920.2532-0.4375-0.14110.00920.21810.0360.07230.06430.00330.1183-27.909511.9452.0119
23.93551.44650.73258.9982-0.23561.5250.0072-0.44440.17680.2486-0.0719-0.1972-0.0439-0.02920.06480.1268-0.03270.00480.10120.00420.0421-26.7975-8.35135.713
31.96352.4874-0.05444.4448-3.33188.23950.0791-0.08210.01620.16430.03510.073-0.1582-0.3769-0.11420.0540.0265-0.02380.0647-0.01040.1308-33.56512.02-1.4899
42.68993.08352.69649.36242.52213.5107-0.22860.49890.114-0.25670.0839-0.4036-0.08330.44130.14470.1203-0.0312-0.01930.1640.05740.1119-27.2552-2.9708-8.9777
51.5099-0.2490.87619.9551-0.65460.6013-0.0441-0.10750.21470.3482-0.1240.47640.0381-0.1140.16820.1415-0.07350.07020.0718-0.07850.155-34.7645-5.7215-2.2875
60.5078-1.1105-0.24739.3653-0.80370.79750.06110.0893-0.0788-0.4297-0.2183-0.21440.11530.07890.15720.06820.0223-0.02650.06010.01390.1084-24.42470.9354-5.313
74.2904-0.24691.42628.6773-8.81989.37680.0077-0.3261-0.4286-0.1652-0.0479-0.23760.3267-0.04270.04020.29330.0074-0.07320.05560.01240.2302-21.8463-14.46374.0035
83.2933-1.19643.48044.6131-4.46669.5070.1495-0.1187-0.34690.05470.16190.03750.3284-0.2813-0.31150.03780.0015-0.0180.01930.01060.0387-11.9522-0.5936.4432
92.6701-1.86521.58245.5406-3.98895.82310.02530.27780.1791-0.2438-0.18150.0354-0.0310.20250.15610.0308-0.0037-0.02420.03650.02070.0386-18.684611.6654-2.2714
105.732.1888-3.4248.3281-5.10417.28890.1051-0.31930.01160.7129-0.0123-0.2279-0.52410.1724-0.09270.06670.0026-0.01330.0198-0.00630.0197-7.37638.13138.1048
119.4777-6.7335-0.973710.38625.70564.5919-0.0978-0.06460.5254-0.11210.1716-0.3921-0.16330.138-0.07380.039-0.04490.00060.0706-0.0080.0307-5.406717.8112.8097
123.16981.71550.00139.4742-2.64362.5019-0.0213-0.18090.30330.3030.08180.2007-0.1869-0.1001-0.06050.01720.01220.00140.0205-0.01670.031-15.32116.63944.0684
135.1438-2.10731.38938.1341-3.76624.47730.03180.76730.3795-0.7012-0.1652-0.0918-0.09590.18490.13340.1268-0.0159-0.01260.11820.05890.0298-11.014715.1787-7.4477
142.9199-1.93023.95193.5402-4.107110.47070.03860.1651-0.0418-0.1450.0028-0.03610.05670.0728-0.04140.0084-0.00260.00350.0165-0.00520.0027-9.7255.7811-0.298
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 - 104
8X-RAY DIFFRACTION8T1 - 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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