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- PDB-2r15: Crystal structure of the myomesin domains 12 and 13 -

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Basic information

Entry
Database: PDB / ID: 2r15
TitleCrystal structure of the myomesin domains 12 and 13
ComponentsMyomesin-1
KeywordsCONTRACTILE PROTEIN / SARCOMERIC PROTEIN / IG-LIKE DOMAINS / HOMODIMER / Immunoglobulin domain / Muscle protein / Thick filament
Function / homology
Function and homology information


extraocular skeletal muscle development / striated muscle myosin thick filament / protein kinase A signaling / M band / structural constituent of muscle / sarcomere organization / positive regulation of protein secretion / kinase binding / positive regulation of gene expression / protein homodimerization activity / identical protein binding
Similarity search - Function
: / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily ...: / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Myomesin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.24 Å
AuthorsPinotsis, N. / Wilmanns, M. / Lange, S.
CitationJournal: EMBO J / Year: 2008
Title: Molecular basis of the C-terminal tail-to-tail assembly of the sarcomeric filament protein myomesin.
Authors: Nikos Pinotsis / Stephan Lange / Jean-Claude Perriard / Dmitri I Svergun / Matthias Wilmanns /
Abstract: Sarcomeric filament proteins display extraordinary properties in terms of protein length and mechanical elasticity, requiring specific anchoring and assembly mechanisms. To establish the molecular ...Sarcomeric filament proteins display extraordinary properties in terms of protein length and mechanical elasticity, requiring specific anchoring and assembly mechanisms. To establish the molecular basis of terminal filament assembly, we have selected the sarcomeric M-band protein myomesin as a prototypic filament model. The crystal structure of the myomesin C-terminus, comprising a tandem array of two immunoglobulin (Ig) domains My12 and My13, reveals a dimeric end-to-end filament of 14.3 nm length. Although the two domains share the same fold, an unexpected rearrangement of one beta-strand reveals how they are evolved into unrelated functions, terminal filament assembly (My13) and filament propagation (My12). The two domains are connected by a six-turn alpha-helix, of which two turns are void of any interactions with other protein parts. Thus, the overall structure of the assembled myomesin C-terminus resembles a three-body beads-on-the-string model with potentially elastic properties. We predict that the found My12-helix-My13 domain topology may provide a structural template for the filament architecture of the entire C-terminal Ig domain array My9-My13 of myomesin.
History
DepositionAug 22, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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: Myomesin-1
B: Myomesin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0916
Polymers46,7562
Non-polymers3354
Water4,450247
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.504, 87.870, 203.081
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Myomesin-1 / 190 kDa titin-associated protein / 190 kDa connectin-associated protein


Mass: 23378.072 Da / Num. of mol.: 2 / Fragment: DOMAINS 12 AND 13, UNP RESIDUES 1225-1443
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYOM1 / Plasmid: PET22B(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P52179
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.48 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.16M CH3COONH4, 14% (W/V) PEG 20000, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONEMBL/DESY, HAMBURG X1110.8126, 0.91837, 0.8126
SYNCHROTRONEMBL/DESY, HAMBURG BW7A20.98214, 0.98264, 0.91837
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 14, 2004
RadiationMonochromator: GE SINGLE CRYSTAL CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.81261
20.918371
30.982141
40.982641
ReflectionResolution: 2.24→20 Å / Num. obs: 25757 / % possible obs: 95.7 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 9.9
Reflection shellResolution: 2.24→2.28 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.382 / % possible all: 93.2

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Processing

Software
NameVersionClassification
CNSrefinement
REFMAC5.2.0005refinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.24→19.87 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.942 / SU B: 13.663 / SU ML: 0.167 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.249 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE MAD DATA SET WAS USED ONLY UP TO INITIAL DENSITY MODIFICATION
RfactorNum. reflection% reflectionSelection details
Rfree0.223 683 2.7 %RANDOM
Rwork0.196 ---
obs-25697 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.68 Å2
Baniso -1Baniso -2Baniso -3
1--1.58 Å20 Å20 Å2
2--2.09 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.24→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3209 0 22 247 3478
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223304
X-RAY DIFFRACTIONr_angle_refined_deg1.381.9514480
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4015414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.15525.4150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.33915551
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0871512
X-RAY DIFFRACTIONr_chiral_restr0.0960.2497
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022506
X-RAY DIFFRACTIONr_nbd_refined0.2190.21325
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22196
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2235
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2630.218
X-RAY DIFFRACTIONr_mcbond_it1.50632107
X-RAY DIFFRACTIONr_mcangle_it2.44253310
X-RAY DIFFRACTIONr_scbond_it4.09971368
X-RAY DIFFRACTIONr_scangle_it6.192101170
LS refinement shellResolution: 2.24→2.32 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.389 81 -
Rwork0.363 2266 -
obs--100 %
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)
19.9635-2.04850.09649.36041.161315.1981-0.44780.8098-1.38190.4437-0.04080.37551.3379-0.23480.48860.2899-0.06960.0623-0.1032-0.0513-0.0539.986.325190.8505
25.9755-4.0087-0.798910.22760.92716.26250.18030.62420.0418-0.0103-0.4809-0.06540.0988-0.33660.30060.0007-0.01220.0196-0.1001-0.0452-0.24367.008716.270490.5485
36.1538-5.1121.102511.8025-1.3455.28960.24930.2428-0.94960.5572-0.34560.10411.54910.170.09630.51360.0570.0728-0.07360.05470.00111.21823.541798.1488
40.05780.7435-1.85829.6467-24.121560.31760.22810.29220.37230.4928-0.02140.2176-0.34080.4795-0.20670.00390.08640.0481-0.03350.0495-0.0915.346728.405287.1571
56.96572.1815-2.22172.7764-2.1964.0286-0.0512-0.2230.0808-0.06630.0379-0.03950.1593-0.01140.0133-0.30280.0383-0.0138-0.28430.0009-0.241316.423642.210955.0016
63.86884.8926-3.42289.143-5.58953.56620.1914-0.65091.1940.54830.4740.4772-0.7455-0.5853-0.6654-0.06290.12060.0254-0.0975-0.03320.0613.14551.793461.1166
78.44972.5722-4.01543.4298-2.07993.6399-0.0453-0.06090.34160.18110.1417-0.0733-0.2495-0.2834-0.0963-0.27810.0429-0.0289-0.3225-0.0303-0.155216.38347.507257.275
812.7119-1.3236-2.01963.12951.74199.9029-0.0541-1.55361.75950.27290.19890.0623-1.37960.9017-0.14480.4449-0.0493-0.0370.0455-0.10510.130110.801283.121817.1042
91.63140.58492.36036.6672.24228.60850.0107-0.1520.08170.140.2053-0.3228-0.18970.1908-0.2160.1243-0.0361-0.0256-0.0453-0.0014-0.11467.347673.408615.0337
1018.650315.55357.214321.57521.963511.3935-0.47840.04262.0162-0.4926-0.09890.2813-2.38111.35730.57730.5895-0.2098-0.03570.07410.00560.329211.45687.724110.8252
118.1745-12.20113.923824.1312-29.360136.1449-0.1306-0.5899-0.166-0.66790.13830.48830.31890.4762-0.00770.14060.0137-0.1465-0.0980.0344-0.12225.892860.791114.3573
125.5815-1.18580.97873.0344-1.01093.0966-0.23860.44720.30840.0762-0.0272-0.2483-0.1972-0.22350.2658-0.3307-0.02640.0107-0.24090.0069-0.207917.204142.009844.2954
132.2404-2.38272.0016.8824-4.13268.16260.04920.8823-0.8139-0.54460.33390.06910.6562-0.2899-0.3831-0.1497-0.1018-0.016-0.0203-0.0594-0.016915.163132.440337.4675
148.7926-1.86233.21893.0477-0.8962.5782-0.08130.6037-0.2746-0.21140.1339-0.14590.0469-0.2696-0.0526-0.2924-0.04710.0042-0.1967-0.0497-0.194417.628636.933341.92
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1461 - 14666 - 11
2X-RAY DIFFRACTION1AA1479 - 151024 - 55
3X-RAY DIFFRACTION2AA1467 - 147812 - 23
4X-RAY DIFFRACTION2AA1511 - 152856 - 73
5X-RAY DIFFRACTION3AA1529 - 154674 - 91
6X-RAY DIFFRACTION4AA1547 - 157192 - 116
7X-RAY DIFFRACTION5AA1572 - 1599117 - 144
8X-RAY DIFFRACTION6AA1600 - 1620145 - 165
9X-RAY DIFFRACTION7AA1621 - 1667166 - 212
10X-RAY DIFFRACTION8BB1461 - 14666 - 11
11X-RAY DIFFRACTION8BB1479 - 151024 - 55
12X-RAY DIFFRACTION9BB1467 - 147812 - 23
13X-RAY DIFFRACTION9BB1511 - 152856 - 73
14X-RAY DIFFRACTION10BB1529 - 154674 - 91
15X-RAY DIFFRACTION11BB1547 - 157192 - 116
16X-RAY DIFFRACTION12BB1572 - 1599117 - 144
17X-RAY DIFFRACTION13BB1600 - 1620145 - 165
18X-RAY DIFFRACTION14BB1621 - 1667166 - 212

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