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- PDB-5fm5: Crystal structure of the myomesin:obscurin-like-1 complex -

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Basic information

Entry
Database: PDB / ID: 5fm5
TitleCrystal structure of the myomesin:obscurin-like-1 complex
Components
  • MYOMESIN-1
  • OBSCURIN-LIKE-1
KeywordsSTRUCTURAL PROTEIN / SARCOMERE / M-BAND / CYTOSKELETAL PROTEIN / PROTEIN COMPLEX / IMMUNOGLOBULIN-LIKE DOMAIN / FIBRONECTIN DOMAIN
Function / homology
Function and homology information


3M complex / extraocular skeletal muscle development / striated muscle myosin thick filament / protein localization to Golgi apparatus / cardiac myofibril assembly / cytoskeletal anchor activity / M band / positive regulation of dendrite morphogenesis / structural constituent of muscle / regulation of mitotic nuclear division ...3M complex / extraocular skeletal muscle development / striated muscle myosin thick filament / protein localization to Golgi apparatus / cardiac myofibril assembly / cytoskeletal anchor activity / M band / positive regulation of dendrite morphogenesis / structural constituent of muscle / regulation of mitotic nuclear division / Golgi organization / intercalated disc / protein kinase A signaling / cytoskeleton organization / positive regulation of protein secretion / microtubule cytoskeleton organization / Z disc / kinase binding / Neddylation / centrosome / positive regulation of gene expression / perinuclear region of cytoplasm / Golgi apparatus / protein homodimerization activity / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Immunoglobulin domain / 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 domain / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Obscurin-like protein 1 / Myomesin-1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsPernigo, S. / Steiner, R.A.
CitationJournal: Structure / Year: 2017
Title: Binding of Myomesin to Obscurin-Like-1 at the Muscle M-Band Provides a Strategy for Isoform-Specific Mechanical Protection.
Authors: Pernigo, S. / Fukuzawa, A. / Beedle, A.E. / Holt, M. / Round, A. / Pandini, A. / Garcia-Manyes, S. / Gautel, M. / Steiner, R.A.
History
DepositionNov 1, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2016Group: Database references
Revision 1.2Dec 28, 2016Group: Database references
Revision 1.3Mar 1, 2017Group: Database references
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
M: MYOMESIN-1
N: MYOMESIN-1
O: OBSCURIN-LIKE-1
P: OBSCURIN-LIKE-1


Theoretical massNumber of molelcules
Total (without water)73,0224
Polymers73,0224
Non-polymers00
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9580 Å2
ΔGint-47.1 kcal/mol
Surface area22110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.180, 134.380, 68.390
Angle α, β, γ (deg.)90.00, 92.50, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein MYOMESIN-1 / / 190 KDA CONNECTIN-ASSOCIATED PROTEIN / 190 KDA TITIN-ASSOCIATED PROTEIN / MYOMESIN FAMILY MEMBER 1 / MYOMESIN


Mass: 25292.723 Da / Num. of mol.: 2 / Fragment: MY4-MY5, RESIDUES 510-739
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P52179
#2: Protein OBSCURIN-LIKE-1


Mass: 11218.062 Da / Num. of mol.: 2 / Fragment: OL3 (THIRD IG DOMAIN), RESIDUES 251-339
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O75147
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL M COMES FROM THE EXPRESSION VECTOR FIRST NINE RESIDUES COME 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: 2.87 Å3/Da / Density % sol: 57.2 % / Description: NONE
Crystal growpH: 8.5 / Details: 20% PEG8000, 0.2M MGCL2, 0.1M TRIS-HCL, PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9778
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 30, 2010 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 3.1→67.19 Å / Num. obs: 14811 / % possible obs: 99.1 % / Observed criterion σ(I): -1 / Redundancy: 4.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.7
Reflection shellResolution: 3.1→3.18 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.8 / % possible all: 98.2

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
MOLREPphasing
REFMAC5.8.0135refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2NZI,2WP3
Resolution: 3.1→75.4 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.886 / SU B: 42.922 / SU ML: 0.354 / Cross valid method: THROUGHOUT / ESU R Free: 0.413 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.25906 747 5 %RANDOM
Rwork0.21633 ---
obs0.21849 14049 98.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 85.542 Å2
Baniso -1Baniso -2Baniso -3
1-7.1 Å20 Å2-2.87 Å2
2---8.21 Å20 Å2
3---1.36 Å2
Refinement stepCycle: LAST / Resolution: 3.1→75.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3468 0 0 84 3552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193579
X-RAY DIFFRACTIONr_bond_other_d0.0050.023444
X-RAY DIFFRACTIONr_angle_refined_deg1.4641.9654852
X-RAY DIFFRACTIONr_angle_other_deg1.2337948
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.455441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.40722.662154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.77915599
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4671532
X-RAY DIFFRACTIONr_chiral_restr0.0840.2510
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213993
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02815
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_it1.3724.8961764
X-RAY DIFFRACTIONr_mcbond_other1.3734.8941763
X-RAY DIFFRACTIONr_mcangle_it2.3717.3382199
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.2215.0391815
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 3.1→3.181 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 43 -
Rwork0.332 1019 -
obs--98.15 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.6647-1.3535.96386.4021-5.225714.4604-0.1245-0.09350.4731-0.1302-0.1334-0.73990.17460.57870.25780.1420.05690.07720.2521-0.08370.3067-27.22045.6362-11.7495
25.9853-1.75370.81128.5826-0.70284.4646-0.32110.05470.5908-0.57520.321-0.2728-0.4451-0.14170.00020.13970.00240.04090.2127-0.05020.2619-34.29047.7771-13.405
314.5557-7.2009-3.741313.12295.4798.86450.29710.11761.8395-0.18890.19-0.6156-0.6589-0.0436-0.48710.41450.0128-0.03870.2486-0.09240.3212-35.915115.7453-8.4982
44.6921-3.1087-2.10737.9654.957411.3462-0.0317-0.8274-0.16680.54480.106-0.825-0.0803-0.6554-0.07430.10830.0042-0.09990.316-0.0310.3021-31.23340.4718-3.282
54.7765-4.63712.134712.8312-2.72212.5495-0.36340.0380.5555-0.0720.4663-0.9032-0.0704-0.3407-0.10290.136-0.03130.03980.17450.01680.2786-35.47424.5729-14.289
67.3171-4.14342.17846.46-0.22952.59530.16620.26990.0981-0.83010.1132-0.0507-0.35030.0551-0.27940.1872-0.02990.06410.2466-0.01750.1872-35.14716.1354-18.0737
72.20881.0562.413135.3981-0.90552.77730.05710.0375-0.46510.6590.4166-0.7190.07370.0941-0.47380.3360.10870.0140.3651-0.05970.2781-20.611-6.0332-1.679
820.7464-2.44354.57445.46615.53128.1323-0.0361-0.32320.59280.1110.0974-0.26540.1305-0.0452-0.06130.39530.04-0.06420.4107-0.04660.4202-16.5163-12.9618-3.7849
94.1541.4655-4.591111.99940.97826.19370.08690.59650.0091.6481-0.2513-0.87620.859-0.92210.16440.9793-0.0330.24380.5345-0.06930.4668-18.9025-30.9654-16.8086
1020.70335.8758-30.55937.9139-15.790953.2820.04880.04380.3319-0.7392-0.0313-0.32560.9080.1632-0.01740.49610.1799-0.01950.6718-0.07280.4492-17.9772-37.9182-38.7254
1112.8086-4.9975-5.11436.94387.260215.25240.10120.543-0.6548-0.3351-0.5670.524-0.4329-0.90450.46580.2574-0.0167-0.07240.10060.05370.3078-16.333-59.6542-15.7502
126.2398-1.7998-3.8197.64330.52218.22980.2122-0.0883-0.20760.1670.24840.2439-0.3221-0.1825-0.46070.07090.05880.00240.22980.08730.2981-18.1153-56.6595-6.7004
1324.30990.836511.092414.238911.833614.29110.9521.1754-2.5867-1.0829-0.69781.0441-0.4497-0.0502-0.25420.47990.14430.02930.449-0.00360.5705-9.2491-71.3351-22.9437
146.92631.1643-0.11998.9575.80134.04710.2868-0.12510.17940.5026-0.4185-0.17090.2099-0.15350.13160.15320.0023-0.11980.2930.13720.4132-6.9701-56.051-10.8087
1510.2555-3.3814-4.553511.7058-5.72766.9597-0.2428-0.5638-1.2075-0.38480.21761.10070.41090.20880.02520.30140.06050.06770.39670.07760.4815-9.0681-66.9762-6.8051
166.3116-4.0135-2.95566.71670.60586.6126-0.0586-0.3520.33990.34130.27380.1639-0.4089-0.151-0.21520.04770.03370.01820.14890.04540.1889-11.4762-53.8301-7.6479
178.1973-6.58530.13869.4176-0.76044.83690.71280.9323-0.2727-1.2826-0.69980.402-0.1647-0.0643-0.0130.24610.0029-0.04880.2333-0.02170.1858-9.4035-56.9516-16.2837
187.5888-5.0662-4.844719.9122-4.37386.6374-0.067-0.21350.170.63430.35820.3253-0.1751-0.0805-0.29120.3925-0.00150.01770.4150.02360.3277-26.6174-42.2448-2.6334
193.3564.6068-3.677122.1907-20.413620.22340.0911-0.0979-0.82721.1877-1.0349-1.0991-1.26380.71270.94380.32630.148-0.03170.3451-0.1090.3416-24.9263-21.713-15.3519
200.54960.58894.07840.63944.408530.4817-0.0067-0.16060.0174-0.0562-0.1410.0242-0.1857-0.91360.14770.47180.1137-0.00070.6245-0.00720.4862-24.0669-13.2007-38.9812
2115.039611.151513.360224.18166.807612.47470.2759-0.2746-0.39160.7367-0.0318-0.85980.1536-0.2415-0.24410.29380.14360.01160.47210.0070.3361-22.0076-13.0997-11.4305
225.2198-5.71110.46587.812-7.967932.33670.12390.32120.35060.00610.2927-1.08811.26621.9394-0.41660.16040.02860.0340.6412-0.06880.5407-19.599-6.0489-24.2969
234.22581.54012.64431.5711-0.382711.5582-0.0950.7079-0.3198-0.45010.61570.18780.69370.1905-0.52080.41380.02450.02590.52150.00830.3944-25.8608-11.8013-34.0331
249.03528.4782-7.97458.0559-7.47687.0449-1.27160.5251-0.7271-0.99080.6508-0.5631.1488-0.41420.62080.72310.31470.1080.5365-0.00360.6155-28.1901-27.9669-15.8006
254.10223.0881-4.802610.2395-3.91746.12970.23160.2499-0.13780.51880.03781.22820.0152-0.1536-0.26940.21510.0778-0.18360.3223-0.07740.5263-36.3885-12.8123-21.9856
2622.73610.21023.61646.8676-1.71555.4892-0.6116-0.17931.1965-0.01530.07350.3171-0.4876-0.36330.53820.43640.0863-0.00510.4402-0.12390.4522-37.8351-13.1105-33.7887
2710.8443-4.66747.905318.2066-4.11425.7970.1938-0.0928-0.2194-0.3301-0.0476-0.48440.1865-0.0333-0.14620.61750.1297-0.02710.6141-0.13080.3909-28.7574-26.7585-29.2185
282.16571.29521.59851.1802-0.900810.3069-0.42510.67680.2281-0.4560.46110.13910.22690.0838-0.0360.4338-0.01360.0460.4167-0.00560.3017-31.6982-9.7438-32.3283
292.3892-1.44361.6580.9263-0.97691.1948-0.1465-0.1705-0.20140.17370.24410.0935-0.1229-0.048-0.09760.31720.1834-0.00780.3949-0.11420.3447-30.7506-15.2466-15.7559
300.83242.30740.492716.3425-15.456829.7315-0.3720.08470.1041-0.92390.0453-0.1248-0.7749-0.10250.32660.3280.05660.16310.58550.01480.3496-24.2343-1.7376-32.3068
316.983913.1359-1.322124.9779-1.41135.75710.3482-0.26790.88260.6507-0.48451.6327-0.0175-0.46520.13630.30730.1090.02070.5354-0.06760.4836-22.4481-37.9954-11.4164
321.63840.0156.819612.3682.519328.96050.0804-0.15870.129-0.2701-0.86990.95170.3882-0.88940.78950.1966-0.0188-0.02870.4568-0.01630.3812-22.888-44.8481-26.5992
339.85154.3993-0.76754.0533.50387.25950.24150.8780.0896-0.64210.5001-0.3817-1.12110.2062-0.74170.84580.20780.06690.39760.17220.2831-16.8263-37.5306-32.2066
347.2812-2.89492.48692.23794.842432.1555-0.04020.15950.3719-0.17170.0352-0.1586-0.94480.60540.0050.39220.0666-0.0590.24640.09150.5729-13.4079-22.4506-14.0227
352.4830.51723.764522.5026.05576.9577-0.17530.16450.3016-0.222-0.0017-1.14-0.33390.24870.1770.1620.02110.10020.36470.04030.2763-8.9589-37.1675-19.5859
362.18470.3242.9061.0102-1.95039.773-0.16210.2353-0.0368-0.29120.0396-0.06440.41480.36370.12250.41750.03990.08810.46810.08330.4905-5.8921-37.1138-28.3234
3712.1786-0.194-0.31194.12350.29520.03090.18270.72030.2796-1.822-0.21560.9472-0.151-0.05490.03290.95890.1877-0.18650.53770.06390.573-14.2759-25.1749-27.7298
383.7859-1.4176-1.01284.6412-1.47429.71830.06620.9378-0.6008-1.2576-0.0804-0.5252-0.38721.54770.01410.6245-0.13880.27950.8577-0.16460.5182-11.2744-44.3342-31.2171
390.08630.52890.16895.81760.94483.8798-0.0247-0.00590.08930.83680.42810.36840.21920.3122-0.40340.42080.2565-0.09740.34080.0750.4466-12.2117-34.2107-13.6667
402.31592.3936-3.069410.9927.530917.9701-0.25830.4253-0.1463-0.42580.4244-0.36270.6293-0.4561-0.16610.55910.1399-0.090.54450.03450.3399-18.8232-48.4242-30.75
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1M510 - 524
2X-RAY DIFFRACTION2M525 - 560
3X-RAY DIFFRACTION3M561 - 567
4X-RAY DIFFRACTION4M568 - 578
5X-RAY DIFFRACTION5M579 - 588
6X-RAY DIFFRACTION6M589 - 603
7X-RAY DIFFRACTION7M604 - 610
8X-RAY DIFFRACTION8M611 - 616
9X-RAY DIFFRACTION9M617 - 627
10X-RAY DIFFRACTION10M628 - 632
11X-RAY DIFFRACTION11N510 - 520
12X-RAY DIFFRACTION12N521 - 532
13X-RAY DIFFRACTION13N533 - 539
14X-RAY DIFFRACTION14N540 - 560
15X-RAY DIFFRACTION15N561 - 567
16X-RAY DIFFRACTION16N568 - 588
17X-RAY DIFFRACTION17N589 - 604
18X-RAY DIFFRACTION18N605 - 615
19X-RAY DIFFRACTION19N616 - 627
20X-RAY DIFFRACTION20N628 - 632
21X-RAY DIFFRACTION21O243 - 250
22X-RAY DIFFRACTION22O251 - 256
23X-RAY DIFFRACTION23O257 - 267
24X-RAY DIFFRACTION24O268 - 274
25X-RAY DIFFRACTION25O275 - 288
26X-RAY DIFFRACTION26O289 - 294
27X-RAY DIFFRACTION27O295 - 301
28X-RAY DIFFRACTION28O302 - 314
29X-RAY DIFFRACTION29O315 - 332
30X-RAY DIFFRACTION30O333 - 339
31X-RAY DIFFRACTION31P242 - 251
32X-RAY DIFFRACTION32P252 - 257
33X-RAY DIFFRACTION33P258 - 268
34X-RAY DIFFRACTION34P269 - 274
35X-RAY DIFFRACTION35P275 - 283
36X-RAY DIFFRACTION36P284 - 297
37X-RAY DIFFRACTION37P298 - 303
38X-RAY DIFFRACTION38P304 - 316
39X-RAY DIFFRACTION39P317 - 331
40X-RAY DIFFRACTION40P332 - 339

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