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- PDB-2y25: Crystal structure of the myomesin domains My11-My13 -

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Basic information

Entry
Database: PDB / ID: 2y25
TitleCrystal structure of the myomesin domains My11-My13
ComponentsMYOMESIN
KeywordsSTRUCTURAL PROTEIN / SARCOMERE / M-BAND / IMMUNOGLOBULIN-LIKE DOMAIN
Function / homology
Function and homology information


extraocular skeletal muscle development / striated muscle myosin thick filament / M band / structural constituent of muscle / protein kinase A signaling / 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 subtype ...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
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsPinotsis, N. / Chatziefthimiou, S.D. / Wilmanns, M.
CitationJournal: Plos Biol. / Year: 2012
Title: Superhelical Architecture of the Myosin Filament-Linking Protein Myomesin with Unusual Elastic Properties.
Authors: Pinotsis, N. / Chatziefthimiou, S.D. / Berkemeier, F. / Beuron, F. / Mavridis, I.M. / Konarev, P.V. / Svergun, D.I. / Morris, E. / Rief, M. / Wilmanns, M.
History
DepositionDec 13, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2012Group: Other
Revision 1.2Dec 20, 2023Group: 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
A: MYOMESIN
B: MYOMESIN
C: MYOMESIN
D: MYOMESIN


Theoretical massNumber of molelcules
Total (without water)142,7734
Polymers142,7734
Non-polymers00
Water0
1
A: MYOMESIN
B: MYOMESIN

A: MYOMESIN
B: MYOMESIN


Theoretical massNumber of molelcules
Total (without water)142,7734
Polymers142,7734
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area4690 Å2
ΔGint-21.4 kcal/mol
Surface area66390 Å2
MethodPISA
2
C: MYOMESIN
D: MYOMESIN

C: MYOMESIN
D: MYOMESIN


Theoretical massNumber of molelcules
Total (without water)142,7734
Polymers142,7734
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area4680 Å2
ΔGint-21.4 kcal/mol
Surface area66440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.201, 155.201, 106.344
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24
15
25
16
26

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 1352:1403 OR RESSEQ 1409:1461)
211CHAIN C AND (RESSEQ 1352:1403 OR RESSEQ 1409:1461)
112CHAIN D AND (RESSEQ 1353:1461)
212CHAIN B AND (RESSEQ 1353:1461)
113CHAIN A AND (RESSEQ 1462:1570)
213CHAIN C AND (RESSEQ 1462:1570)
114CHAIN B AND (RESSEQ 1462:1570)
214CHAIN D AND (RESSEQ 1462:1570)
115CHAIN A AND (RESSEQ 1571:1666)
215CHAIN C AND (RESSEQ 1571:1666)
116CHAIN B AND (RESSEQ 1571:1666)
216CHAIN D AND (RESSEQ 1571:1666)

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 35693.348 Da / Num. of mol.: 4 / Fragment: DOMAINS MY11, MY12, MY13, RESIDUES 1357-1667
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: MUSCLESkeletal muscle / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P52179

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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: 4.59 Å3/Da / Density % sol: 73.22 % / Description: NONE
Crystal growpH: 6 / Details: MES PH 6, 220 MM LI2SO4, 13% PEG 8K.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0044
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Details: SILICON TOROIDAL MIRROR COATED WITH RHODIUM
RadiationMonochromator: SILICON (1 1 1) CHANNEL- CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0044 Å / Relative weight: 1
ReflectionResolution: 3.5→20 Å / Num. obs: 29917 / % possible obs: 93.8 % / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Biso Wilson estimate: 88.77 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.83
Reflection shellResolution: 3.5→3.58 Å / Redundancy: 2 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.4 / % possible all: 82

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2R15

2r15


Resolution: 3.5→19.95 Å / SU ML: 0.47 / σ(F): 0.06 / Phase error: 25.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2658 1234 4.1 %
Rwork0.2166 --
obs0.2186 29917 93.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.02 Å2 / ksol: 0.212 e/Å3
Displacement parametersBiso mean: 128.18 Å2
Baniso -1Baniso -2Baniso -3
1-2.5304 Å20 Å20 Å2
2--2.5304 Å20 Å2
3----10.0781 Å2
Refinement stepCycle: LAST / Resolution: 3.5→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9534 0 0 0 9534
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0149732
X-RAY DIFFRACTIONf_angle_d1.56713226
X-RAY DIFFRACTIONf_dihedral_angle_d19.7253394
X-RAY DIFFRACTIONf_chiral_restr0.0961514
X-RAY DIFFRACTIONf_plane_restr0.0091700
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A784X-RAY DIFFRACTIONPOSITIONAL
12C784X-RAY DIFFRACTIONPOSITIONAL0.009
21D839X-RAY DIFFRACTIONPOSITIONAL
22B839X-RAY DIFFRACTIONPOSITIONAL0.021
31A836X-RAY DIFFRACTIONPOSITIONAL
32C836X-RAY DIFFRACTIONPOSITIONAL0.019
41B846X-RAY DIFFRACTIONPOSITIONAL
42D846X-RAY DIFFRACTIONPOSITIONAL0.026
51A733X-RAY DIFFRACTIONPOSITIONAL
52C733X-RAY DIFFRACTIONPOSITIONAL0.033
61B733X-RAY DIFFRACTIONPOSITIONAL
62D733X-RAY DIFFRACTIONPOSITIONAL0.034
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.63940.35971210.31352852X-RAY DIFFRACTION84
3.6394-3.80390.331130.28683038X-RAY DIFFRACTION89
3.8039-4.0030.28481430.24013100X-RAY DIFFRACTION92
4.003-4.25150.25061390.20083180X-RAY DIFFRACTION94
4.2515-4.57610.22651470.16213285X-RAY DIFFRACTION97
4.5761-5.02990.1871570.15123292X-RAY DIFFRACTION98
5.0299-5.74250.23561570.17583299X-RAY DIFFRACTION98
5.7425-7.17850.30481330.21763334X-RAY DIFFRACTION97
7.1785-19.95050.27771240.21963303X-RAY DIFFRACTION95
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)
1-1.1871.5452-0.696-0.49281.7021-1.71760.5778-0.25010.38440.1986-0.6026-0.2539-0.6229-0.1898-0.00021.9520.52180.27371.7313-0.19371.824112.4498106.5427-20.2255
23.5598-3.2825-1.45586.623-0.88142.54490.37651.63330.2661-2.0227-0.74181.5036-1.2096-1.77520.1771.15330.6223-0.41441.6465-0.29160.905535.590677.9265-37.0053
32.8098-1.68012.00882.6210.63115.8230.35870.1605-0.6898-0.67340.0209-0.06370.7635-0.54160.25020.4919-0.01250.13050.32670.07030.417572.578163.4225-9.2926
41.7058-1.0009-0.10571.0101-1.72621.3170.08670.2448-0.461-0.1366-0.0430.7452-0.02940.13950.01250.52130.12840.01470.91320.22051.0623124.554728.894415.1685
55.6493-2.1127-0.03711.95641.01541.3651-0.3777-1.4984-0.72840.8197-0.0037-0.22740.7251-0.1275-0.81320.4429-0.02630.12691.0310.48270.654790.854438.433235.9924
63.7743-0.8442-0.8862.8608-1.71154.07330.0424-0.3991-0.1223-0.3382-0.0310.48670.434-0.28320.09880.2602-0.0701-0.04860.4817-0.17360.389865.555968.52198.4677
7-0.53541.08191.8118-0.8575-0.9997-1.6085-0.51590.2685-0.4702-0.80990.49230.14840.021-0.13340.00061.82610.4436-0.1681.84760.21141.8321-28.908565.1335113.7984
86.924-3.639-0.17633.5633-2.61612.8406-0.8323-2.2651.71951.42960.25880.2832-2.1704-1.3526-0.11941.59260.551-0.28931.0954-0.41250.8992-0.285142.0542130.5529
91.4377-1.17980.25842.72140.64145.044-0.0458-0.622-0.0330.09080.3711-0.5373-0.4470.86690.35550.37570.01890.10430.51870.11430.495414.19015.0157102.8641
101.3381-1.3804-2.18241.3007-0.95210.61550.0156-0.27120.80440.28810.1715-0.15590.2267-0.06920.01221.01270.10430.19620.49270.01990.997348.7116-46.979278.3749
112.0078-2.12940.44836.4414-0.74081.2051-0.03140.72040.0937-1.4184-0.3172-1.21730.11670.8245-0.99060.9898-0.02510.45060.35510.13080.62739.1535-13.244457.5625
122.5167-0.5775-2.20693.81-1.55652.95240.0846-0.24670.3801-0.19710.0543-0.1472-0.30160.23280.06150.4721-0.062-0.14620.348-0.040.39199.080612.050985.0854
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1352:1461)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 1462:1570)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 1571:1666)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 1353:1461)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 1462:1570)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 1571:1666)
7X-RAY DIFFRACTION7(CHAIN C AND RESID 1352:1461)
8X-RAY DIFFRACTION8(CHAIN C AND RESID 1462:1570)
9X-RAY DIFFRACTION9(CHAIN C AND RESID 1571:1666)
10X-RAY DIFFRACTION10(CHAIN D AND RESID 1353:1461)
11X-RAY DIFFRACTION11(CHAIN D AND RESID 1462:1570)
12X-RAY DIFFRACTION12(CHAIN D AND RESID 1571:1666)

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