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- PDB-6qdj: Molecular features of the UNC-45 chaperone critical for binding a... -

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Basic information

Entry
Database: PDB / ID: 6qdj
TitleMolecular features of the UNC-45 chaperone critical for binding and folding muscle myosin
ComponentsMyosin-4
KeywordsMOTOR PROTEIN / MYOSIN / MHC-B / UNC-54
Function / homology
Function and homology information


egg-laying behavior / striated muscle myosin thick filament / skeletal muscle myosin thick filament assembly / muscle myosin complex / locomotion / A band / structural constituent of muscle / microfilament motor activity / muscle contraction / actin filament binding / ATP binding
Similarity search - Function
: / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. ...: / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / 1,4-BUTANEDIOL / HEXANE-1,6-DIOL / 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL / S-1,2-PROPANEDIOL / Myosin-4
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.884 Å
AuthorsMeinhart, A. / Clausen, T. / Arnese, R.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP 22570 Austria
CitationJournal: Nat Commun / Year: 2019
Title: Molecular features of the UNC-45 chaperone critical for binding and folding muscle myosin.
Authors: Hellerschmied, D. / Lehner, A. / Franicevic, N. / Arnese, R. / Johnson, C. / Vogel, A. / Meinhart, A. / Kurzbauer, R. / Deszcz, L. / Gazda, L. / Geeves, M. / Clausen, T.
History
DepositionJan 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myosin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,37717
Polymers90,3721
Non-polymers2,00516
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint5 kcal/mol
Surface area34280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.110, 111.960, 84.740
Angle α, β, γ (deg.)90.00, 97.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Myosin-4 / / Myosin heavy chain B / MHC B / Uncoordinated protein 54


Mass: 90372.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: unc-54, myo-4, F11C3.3 / Plasmid: bFastBac Dual / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P02566

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Non-polymers , 7 types, 253 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-BU1 / 1,4-BUTANEDIOL / 1,4-Butanediol


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#5: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL / Propanediol


Mass: 76.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O2
#6: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL / 1,6-Hexanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2
#7: Chemical ChemComp-P15 / 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL


Mass: 296.357 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H28O7
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM MES/imidazole pH 6.5 10 % PEG 4000 20 % glycerol 20 mM 1,6-hexandiol 20 mM 1-butanol 20 mM (RS)-1,2-propanediol 20 mM 2-propanol 20 mM 1,4-butanediol 20 mM 1,3-propandiol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 17, 2016
RadiationMonochromator: KB-mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.884→85 Å / Num. obs: 76208 / % possible obs: 93.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 37.5 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.045 / Net I/σ(I): 19.6
Reflection shellResolution: 1.884→2.05 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.9 / CC1/2: 0.866 / Rrim(I) all: 0.454 / % possible all: 78

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
Cootmodel building
PHENIXmodel building
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5m05

5m05


Resolution: 1.884→84.026 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.81
RfactorNum. reflection% reflectionSelection details
Rfree0.2128 3811 5 %Random
Rwork0.1845 ---
obs0.186 76204 94.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.884→84.026 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6126 0 131 237 6494
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126377
X-RAY DIFFRACTIONf_angle_d1.0578569
X-RAY DIFFRACTIONf_dihedral_angle_d15.8113862
X-RAY DIFFRACTIONf_chiral_restr0.065915
X-RAY DIFFRACTIONf_plane_restr0.0061097
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8839-1.90780.3379360.3244671X-RAY DIFFRACTION24
1.9078-1.93290.31951170.26662225X-RAY DIFFRACTION78
1.9329-1.95940.26021300.24182485X-RAY DIFFRACTION90
1.9594-1.98730.2451400.22662658X-RAY DIFFRACTION94
1.9873-2.0170.2751460.22252762X-RAY DIFFRACTION97
2.017-2.04850.23891470.21222791X-RAY DIFFRACTION99
2.0485-2.08210.25991490.20982838X-RAY DIFFRACTION99
2.0821-2.1180.26351460.19842781X-RAY DIFFRACTION99
2.118-2.15650.23331480.19132806X-RAY DIFFRACTION99
2.1565-2.1980.23541450.19082764X-RAY DIFFRACTION99
2.198-2.24290.25911500.1952832X-RAY DIFFRACTION99
2.2429-2.29170.21351460.19562781X-RAY DIFFRACTION99
2.2917-2.3450.23631480.19512815X-RAY DIFFRACTION99
2.345-2.40360.26071460.19142777X-RAY DIFFRACTION99
2.4036-2.46860.24491480.19112815X-RAY DIFFRACTION99
2.4686-2.54130.23381470.18612778X-RAY DIFFRACTION99
2.5413-2.62330.23291460.18472776X-RAY DIFFRACTION98
2.6233-2.71710.19721470.16972803X-RAY DIFFRACTION98
2.7171-2.82590.19681470.18012781X-RAY DIFFRACTION98
2.8259-2.95450.21261470.1772800X-RAY DIFFRACTION99
2.9545-3.11020.20341480.17392810X-RAY DIFFRACTION98
3.1102-3.30510.23481450.17582760X-RAY DIFFRACTION98
3.3051-3.56030.20571490.18072823X-RAY DIFFRACTION98
3.5603-3.91860.19361470.16682804X-RAY DIFFRACTION98
3.9186-4.48560.17581490.16912822X-RAY DIFFRACTION99
4.4856-5.65120.20741470.18952797X-RAY DIFFRACTION98
5.6512-84.10990.18341500.18472838X-RAY DIFFRACTION98

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