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- PDB-4c4k: Crystal structure of the titin M10-Obscurin Ig domain 1 complex -

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Basic information

Entry
Database: PDB / ID: 4c4k
TitleCrystal structure of the titin M10-Obscurin Ig domain 1 complex
Components
  • OBSCURIN
  • TITIN
KeywordsTRANSFERASE / SARCOMERE / IMMUNOGLOBULIN DOMAIN / LIMB-GIRDLE MUSCULAR DYSTROPHY
Function / homology
Function and homology information


protein localization to M-band / sarcomerogenesis / titin-telethonin complex / structural molecule activity conferring elasticity / skeletal muscle myosin thick filament assembly / telethonin binding / phosphatidylinositol-5-phosphate binding / detection of muscle stretch / muscle alpha-actinin binding / : ...protein localization to M-band / sarcomerogenesis / titin-telethonin complex / structural molecule activity conferring elasticity / skeletal muscle myosin thick filament assembly / telethonin binding / phosphatidylinositol-5-phosphate binding / detection of muscle stretch / muscle alpha-actinin binding / : / cardiac myofibril assembly / phosphatidylinositol-3-phosphate binding / cardiac muscle hypertrophy / mitotic chromosome condensation / phosphatidylinositol-3,4-bisphosphate binding / cardiac muscle tissue morphogenesis / Striated Muscle Contraction / muscle filament sliding / protein kinase regulator activity / phosphatidylinositol-4-phosphate binding / actinin binding / M band / regulation of small GTPase mediated signal transduction / I band / cardiac muscle cell development / structural constituent of muscle / ankyrin binding / sarcomere organization / NRAGE signals death through JNK / RHOQ GTPase cycle / myofibril / phosphatidylinositol-3,4,5-trisphosphate binding / striated muscle thin filament / skeletal muscle thin filament assembly / RHOA GTPase cycle / skeletal muscle contraction / striated muscle contraction / cardiac muscle contraction / titin binding / phosphatidylinositol-4,5-bisphosphate binding / muscle contraction / guanyl-nucleotide exchange factor activity / condensed nuclear chromosome / positive regulation of protein secretion / response to calcium ion / sarcolemma / Z disc / actin filament binding / Platelet degranulation / G alpha (12/13) signalling events / protease binding / protein tyrosine kinase activity / calmodulin binding / non-specific serine/threonine protein kinase / protein kinase activity / nuclear body / 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 / metal ion binding / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Obscurin, SH3 domain / : / PPAK motif / PPAK motif / Titin, Z repeat / Titin Z / MyBP-C, tri-helix bundle domain / Tri-helix bundle domain / : / SOS1/NGEF-like PH domain ...Obscurin, SH3 domain / : / PPAK motif / PPAK motif / Titin, Z repeat / Titin Z / MyBP-C, tri-helix bundle domain / Tri-helix bundle domain / : / SOS1/NGEF-like PH domain / IQ calmodulin-binding motif / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / IQ motif profile. / Immunoglobulin I-set / Immunoglobulin I-set domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology 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 / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine protein kinases specific active-site signature. / PH-like domain superfamily / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / 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: 1.95 Å
AuthorsPernigo, S. / Fukuzawa, A. / Gautel, M. / Steiner, R.A.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: The Crystal Structure of the Human Titin:Obscurin Complex Reveals a Conserved Yet Specific Muscle M-Band Zipper Module.
Authors: Pernigo, S. / Fukuzawa, A. / Pandini, A. / Holt, M. / Kleinjung, J. / Gautel, M. / Steiner, R.A.
History
DepositionSep 5, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Mar 4, 2015Group: Database references
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
O: OBSCURIN
T: TITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,10014
Polymers21,3552
Non-polymers74512
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-7.6 kcal/mol
Surface area11790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.940, 66.880, 72.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein OBSCURIN / OBSCURIN-RHOGEF / OBSCURIN-MYOSIN LIGHT CHAIN KINASE / OBSCURIN-MLCK


Mass: 10373.669 Da / Num. of mol.: 1 / Fragment: FIRST IG DOMAIN, RESIDUES 9-103
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2
References: UniProt: Q5VST9, non-specific serine/threonine protein kinase
#2: Protein TITIN / CONNECTIN / RHABDOMYOSARCOMA ANTIGEN MU-RMS-40.14


Mass: 10981.231 Da / Num. of mol.: 1 / Fragment: M10 DOMAIN, 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): BL21(DE3) / Variant (production host): ROSETTA 2
References: UniProt: Q8WZ42, non-specific serine/threonine protein kinase
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsINITIAL GSS IS DERIVED FROM VECTOR AFTER TEV CLEAVAGE

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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: 2.34 Å3/Da / Density % sol: 47.5 % / Description: NONE
Crystal growpH: 8.5
Details: 0.1 M TRIS-HCL PH 8.5, 0.2 M SODIUM ACETATE, 30% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2012 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.95→35.7 Å / Num. obs: 15005 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 31.76 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.8
Reflection shellResolution: 1.95→2 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2 / % possible all: 98.5

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WP3

2wp3


Resolution: 1.95→17.48 Å / Cor.coef. Fo:Fc: 0.9549 / Cor.coef. Fo:Fc free: 0.9429 / SU R Cruickshank DPI: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.155 / SU Rfree Blow DPI: 0.138 / SU Rfree Cruickshank DPI: 0.135
RfactorNum. reflection% reflectionSelection details
Rfree0.2096 756 5.06 %RANDOM
Rwork0.1711 ---
obs0.173 14950 98.83 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.9583 Å20 Å20 Å2
2--1.864 Å20 Å2
3---4.0943 Å2
Refine analyzeLuzzati coordinate error obs: 0.222 Å
Refinement stepCycle: LAST / Resolution: 1.95→17.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1440 0 48 103 1591
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011523HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.122045HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d528SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes39HARMONIC2
X-RAY DIFFRACTIONt_gen_planes221HARMONIC5
X-RAY DIFFRACTIONt_it1523HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.6
X-RAY DIFFRACTIONt_other_torsion15.91
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion201SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1765SEMIHARMONIC4
LS refinement shellResolution: 1.95→2.08 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2495 137 5.18 %
Rwork0.1922 2506 -
all0.195 2643 -
obs--98.83 %
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)
13.223-1.46810.70427.67671.07270.5118-0.2449-0.0466-0.60650.34330.21610.55690.52910.09820.02880.07050.02060.0308-0.05760.00980.0324-16.2391-0.5562-4.7806
20.2107-2.246-0.48360.02111.46742.53920.1941-0.0957-0.12320.035-0.17520.02490.03740.2224-0.0188-0.1419-0.0223-0.0251-0.12580.0178-0.0725-17.163811.5513-11.7935
33.59092.84920.4131.3763-5.36932.3984-0.119-0.2312-0.54960.1812-0.01160.25020.2228-0.42050.13050.0422-0.09740.12620.05340.00970.2821-28.5375-2.1439-0.0586
43.2325-3.28842.92446.88652.9885.9279-0.256-0.07410.26910.07680.0005-0.11470.00910.24950.2554-0.0180.0111-0.0030.0051-0.0030.0241-20.641412.32272.3007
50.52265.3657-4.69425.1794-3.82112.59220.0832-0.1516-0.05120.04980.0690.1169-0.521-0.4513-0.1521-0.15040.04140.0077-0.05560.0171-0.0004-25.215719.1283-4.4577
60.6093-1.6921-2.67012.3624-0.76864.13350.08440.0709-1.0022-0.13420.17660.4330.3304-0.5523-0.2611-0.1359-0.0264-0.1202-0.1356-0.00160.2617-28.37644.5595-8.3114
74.14921.3014-1.31659.3644-2.23370.8958-0.03990.03290.2603-0.33570.0010.1834-0.01060.02670.0389-0.10910.003-0.0173-0.16160.0015-0.1284-19.72116.5302-9.9557
83.57741.2128-1.43698.7329-0.19733.3588-0.0431-0.2945-0.03680.34940.0893-0.07860.1229-0.0281-0.0462-0.15820.0205-0.0303-0.0705-0.0097-0.1239-17.448810.4099-0.9693
91.1606-3.16234.76349.2391-0.61792.1413-0.1905-0.9258-0.83290.6330.43880.50470.62630.0305-0.24830.20390.08050.07520.09790.12120.1659-19.7279-0.96562.6652
101.03083.84581.96521.25321.81812.56110.00120.0230.0183-0.30230.1892-0.0981-0.18470.3143-0.1905-0.01710.00840.02130.0527-0.01990.1387-8.178617.7504-9.4108
110.1892-3.30923.61760-2.13473.65770.05890.5008-0.87550.22410.21330.52790.0585-0.082-0.27210.03640.08170.0752-0.15820.01810.1929-23.36777.9881-19.106
122.72193.8722-2.29941.68540.41182.81610.0372-0.20750.2086-0.1739-0.1701-0.2330.10950.00660.1329-0.11-0.00610.0104-0.1843-0.0127-0.0522-14.4522-11.5658-19.3251
133.7023-2.1662-2.3154.1463-0.58113.40650.14730.8448-1.01-0.4265-0.09120.5432-0.3213-0.2598-0.0560.00760.0264-0.05440.0417-0.08830.2167-21.49439.3143-25.3624
1411.2459-4.2908-2.81448.72480.68443.3760.0318-0.0477-0.1970.62710.3643-0.1434-0.54850.8431-0.3961-0.0534-0.0330.0128-0.0663-0.1047-0.0669-6.95064.1521-19.1037
152.1966-0.17160.32933.96520.96296.2090.1352-0.0278-0.0002-0.6646-0.0397-0.116-0.26120.2524-0.0955-0.05860.00030.0294-0.1035-0.024-0.0356-6.6142-3.0238-27.3464
161.02980.7837-1.31030.03922.65473.7006-0.03360.0955-0.1693-0.1945-0.03370.42130.1759-0.24510.06730.07440.0409-0.1187-0.0696-0.08710.268-20.76641.7561-28.1896
179.2975-1.2858-1.04599.41191.66921.8587-0.2258-0.2933-0.35360.28940.11980.02340.44980.51050.106-0.02540.09350.0178-0.0477-0.02920.0019-7.0177-9.4377-21.4942
180.25050.7354-4.42194.51864.42233.34640.1109-0.0069-0.04980.04990.1280.0990.34940.6985-0.2390.01620.03530.0087-0.0248-0.0647-0.0024-9.43480.931-15.545
193.41562.0729-2.97120.40660.70355.3617-0.0070.4668-0.0836-0.1291-0.0093-0.0412-0.31920.05360.01630.0537-0.0030.013-0.05930.0248-0.0401-15.745815.1842-21.4997
201.40750.96-1.21991.4012-0.49081.6467-0.017-0.1328-0.25340.1831-0.2010.05930.6930.36510.21810.14940.11870.014-0.08070.0067-0.0068-11.0465-4.8562-13.1446
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN T AND RESID 2 - 14
2X-RAY DIFFRACTION2CHAIN T AND RESID 15 - 30
3X-RAY DIFFRACTION3CHAIN T AND RESID 31 - 36
4X-RAY DIFFRACTION4CHAIN T AND RESID 37 - 44
5X-RAY DIFFRACTION5CHAIN T AND RESID 45 - 54
6X-RAY DIFFRACTION6CHAIN T AND RESID 55 - 60
7X-RAY DIFFRACTION7CHAIN T AND RESID 61 - 71
8X-RAY DIFFRACTION8CHAIN T AND RESID 72 -83
9X-RAY DIFFRACTION9CHAIN T AND RESID 84 - 92
10X-RAY DIFFRACTION10CHAIN T AND RESID 93 -98
11X-RAY DIFFRACTION11CHAIN O AND RESID 7 - 15
12X-RAY DIFFRACTION12CHAIN O AND RESID 16 -30
13X-RAY DIFFRACTION13CHAIN O AND RESID 31 - 39
14X-RAY DIFFRACTION14CHAIN O AND RESID 40 - 48
15X-RAY DIFFRACTION15CHAIN O AND RESID 49 - 60
16X-RAY DIFFRACTION16CHAIN O AND RESID 61 - 65
17X-RAY DIFFRACTION17CHAIN O AND RESID 66 - 76
18X-RAY DIFFRACTION18CHAIN O AND RESID 77 -83
19X-RAY DIFFRACTION19CHAIN O AND RESID 84 -91
20X-RAY DIFFRACTION20CHAIN O AND RESID 92-100

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