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- PDB-6zva: Crystal structure of My5 -

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Basic information

Entry
Database: PDB / ID: 6zva
TitleCrystal structure of My5
ComponentsMyomesin-1
KeywordsSTRUCTURAL PROTEIN / myomesin / muscle / sarcomere / fn3
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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsSauer, F. / Wilmanns, M.
CitationJournal: To Be Published
Title: Crystal structure of Myomesin-1
Authors: Sauer, F. / Wilmanns, M.
History
DepositionJul 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Myomesin-1
A: Myomesin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4769
Polymers22,8032
Non-polymers6727
Water41423
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-85 kcal/mol
Surface area10960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.820, 97.820, 111.690
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-801-

SO4

21B-801-

SO4

31A-804-

SO4

41A-804-

SO4

51A-806-

SO4

61A-806-

SO4

71A-912-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 637 through 658 or (resid 659...
21(chain B and ((resid 637 and (name N or name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALTRPTRP(chain A and (resid 637 through 658 or (resid 659...AB637 - 6587 - 28
12LYSLYSLYSLYS(chain A and (resid 637 through 658 or (resid 659...AB65929
13VALVALVALVAL(chain A and (resid 637 through 658 or (resid 659...AB637 - 7317 - 101
14VALVALVALVAL(chain A and (resid 637 through 658 or (resid 659...AB637 - 7317 - 101
15VALVALVALVAL(chain A and (resid 637 through 658 or (resid 659...AB637 - 7317 - 101
16VALVALVALVAL(chain A and (resid 637 through 658 or (resid 659...AB637 - 7317 - 101
21VALVALVALVAL(chain B and ((resid 637 and (name N or name...BA6377
22GLYGLYVALVAL(chain B and ((resid 637 and (name N or name...BA635 - 7315 - 101
23GLYGLYVALVAL(chain B and ((resid 637 and (name N or name...BA635 - 7315 - 101
24GLYGLYVALVAL(chain B and ((resid 637 and (name N or name...BA635 - 7315 - 101
25GLYGLYVALVAL(chain B and ((resid 637 and (name N or name...BA635 - 7315 - 101

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Components

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


Mass: 11401.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYOM1 / Production host: Escherichia coli (E. coli) / References: UniProt: P52179
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.25 Å3/Da / Density % sol: 45.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.9M ammonium sulfate 0.3M trisodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.68→48.91 Å / Num. obs: 5931 / % possible obs: 100 % / Redundancy: 5 % / CC1/2: 0.992 / Rmerge(I) obs: 0.093 / Net I/σ(I): 12.9
Reflection shellResolution: 2.68→2.81 Å / Rmerge(I) obs: 0.453 / Num. unique obs: 782 / CC1/2: 0.799

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BPV

1bpv


Resolution: 2.68→46.63 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2512 582 9.82 %
Rwork0.1986 5345 -
obs0.204 5927 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.01 Å2 / Biso mean: 40.4278 Å2 / Biso min: 19.68 Å2
Refinement stepCycle: final / Resolution: 2.68→46.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1427 0 35 23 1485
Biso mean--87.9 30.09 -
Num. residues----189
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A756X-RAY DIFFRACTION18.052TORSIONAL
12B756X-RAY DIFFRACTION18.052TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.68-2.950.34751410.268713231464
2.95-3.380.26621400.217913241464
3.38-4.260.24251390.180713361475
4.26-46.630.22181620.180113621524
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)
11.47360.1052-0.95112.1265-1.6433.48890.183-0.16240.4118-0.2150.25490.3271-0.09280.2701-0.19750.26310.0863-0.06730.3627-0.08050.2935-4.91348.509729.886
22.6634-1.457-0.39186.5002-1.19451.7318-0.1687-0.23040.14650.01210.1887-0.31810.0551-0.17640.03580.22640.0784-0.00210.32180.06410.3359-12.5288-8.150943.2283
31.52040.4281-2.47850.40920.24317.1025-0.05670.22810.31650.0642-0.81541.5619-0.4-1.43990.25150.29460.05160.05560.2898-0.11260.7172-27.4086-1.19638.6546
43.9664-1.0760.76262.9756-1.49085.47370.0943-0.05080.1795-0.2053-0.1587-0.18730.62550.09280.03120.19090.0237-0.00310.27710.04220.273-8.8495-4.446236.7985
53.9121.7396-3.20021.5655-0.71243.25210.21220.53221.03470.35490.50331.1234-0.8084-0.6433-0.02460.25910.1158-0.01730.65720.03330.6085-15.64958.354331.0834
62.113-1.6007-0.34036.895-1.20523.1680.0967-0.24310.07230.4231-0.02070.4334-0.12350.0122-0.01580.1275-0.0882-0.01290.38810.05380.2364-18.531-1.764643.278
71.73670.2282-0.63631.8669-0.68051.7369-0.0298-0.20780.17480.2810.09620.1197-0.3490.0571-0.07730.16380.0098-0.06590.34640.02510.2512-10.54335.054339.1589
83.43160.3796-0.96122.63780.40893.6295-0.15870.1774-0.0841-0.07290.09490.0073-0.18350.1779-0.06230.23460.04250.07330.28430.02980.24658.66511.862817.7844
98.2755-4.75013.99393.7565-1.60742.3850.2875-0.96851.5188-0.0967-0.1699-0.6558-0.5468-0.692-0.82630.08250.02570.15340.49450.06930.52048.603827.542722.9564
108.21291.2414-1.86155.5816-6.56397.7380.5827-0.5997-0.17670.6927-1.1165-0.5351-0.18660.3936-0.29330.13750.003-0.02860.35510.14360.33287.881410.74428.1549
116.89-5.3309-7.25715.02264.96928.18740.0651-0.0384-0.882-0.280.3491-0.46810.2613-0.89010.02340.3450.0369-0.01390.4229-0.09420.2831.42677.731520.1117
122.12181.84050.49812.0653-0.62484.1737-0.011-0.04510.37870.20420.32140.174-0.2870.0943-0.26670.26220.06090.03920.1873-0.01340.34733.574118.104923.8476
133.3804-3.951-4.21797.65743.18677.95080.49730.09860.4148-0.7551-0.0473-1.4196-0.1036-0.0622-0.1920.3654-0.05280.06360.25670.01310.47856.193119.59317.0504
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 637:663)A637 - 663
2X-RAY DIFFRACTION2(chain A and resid 664:677)A664 - 677
3X-RAY DIFFRACTION3(chain A and resid 678:684)A678 - 684
4X-RAY DIFFRACTION4(chain A and resid 685:697)A685 - 697
5X-RAY DIFFRACTION5(chain A and resid 698:704)A698 - 704
6X-RAY DIFFRACTION6(chain A and resid 705:731)A705 - 731
7X-RAY DIFFRACTION7(chain B and resid 635:657)B635 - 657
8X-RAY DIFFRACTION8(chain B and resid 658:677)B658 - 677
9X-RAY DIFFRACTION9(chain B and resid 678:683)B678 - 683
10X-RAY DIFFRACTION10(chain B and resid 684:692)B684 - 692
11X-RAY DIFFRACTION11(chain B and resid 693:698)B693 - 698
12X-RAY DIFFRACTION12(chain B and resid 699:717)B699 - 717
13X-RAY DIFFRACTION13(chain B and resid 718:731)B718 - 731

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