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

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Basic information

Entry
Database: PDB / ID: 6qdk
TitleMolecular features of the UNC-45 chaperone critical for binding and folding muscle myosin
ComponentsUNC-45,UNC-45
KeywordsCHAPERONE / MYOSIN FOLDING / PROTEIN FILAMENTS / MYOFILAMENT FORMATION
Function / homology
Function and homology information


egg-laying behavior / locomotion / embryo development ending in birth or egg hatching / muscle organ development / sarcomere organization / cleavage furrow / chaperone-mediated protein folding / protein folding chaperone / Hsp90 protein binding / cell cortex ...egg-laying behavior / locomotion / embryo development ending in birth or egg hatching / muscle organ development / sarcomere organization / cleavage furrow / chaperone-mediated protein folding / protein folding chaperone / Hsp90 protein binding / cell cortex / ubiquitin protein ligase binding / perinuclear region of cytoplasm / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
UNC-45/Cro1/She4, central domain / Myosin-binding striated muscle assembly central / Tetratricopeptide repeats / Tetratricopeptide repeat / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold
Similarity search - Domain/homology
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.4 Å
AuthorsMeinhart, A. / Clausen, T. / Hellerschmied, D.
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UNC-45,UNC-45


Theoretical massNumber of molelcules
Total (without water)107,8471
Polymers107,8471
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area42310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.910, 86.910, 718.540
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein UNC-45,UNC-45


Mass: 107847.391 Da / Num. of mol.: 1 / Mutation: G427E,G427E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: unc-45, CELE_F30H5.1, F30H5.1 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / References: UniProt: G5EG62

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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: 3.64 Å3/Da / Density % sol: 66.2 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 77 mM HEPES pH 8.0 3.8 % Tacsimate 7.7% PEG MME 600 231 mM (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.4→30 Å / Num. obs: 41611 / % possible obs: 99.6 % / Redundancy: 18.2 % / Rrim(I) all: 0.176 / Net I/σ(I): 12
Reflection shellResolution: 3.4→3.49 Å / Redundancy: 8.8 % / Mean I/σ(I) obs: 1.9 / Rrim(I) all: 0.848 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
CNSrefinement
Omodel building
SHARPphasing
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.4→29.962 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.78 / Phase error: 32.56
RfactorNum. reflection% reflectionSelection details
Rfree0.3189 2057 4.94 %random
Rwork0.2872 ---
obs0.2887 41611 99.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.4→29.962 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6851 0 0 0 6851
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086945
X-RAY DIFFRACTIONf_angle_d1.0679374
X-RAY DIFFRACTIONf_dihedral_angle_d16.6164372
X-RAY DIFFRACTIONf_chiral_restr0.0541096
X-RAY DIFFRACTIONf_plane_restr0.0061206
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3998-3.47880.36131540.33652591X-RAY DIFFRACTION96
3.4788-3.56570.42921350.34822561X-RAY DIFFRACTION100
3.5657-3.66190.4081600.33542639X-RAY DIFFRACTION100
3.6619-3.76950.38871430.33852704X-RAY DIFFRACTION100
3.7695-3.89090.30171290.31172565X-RAY DIFFRACTION100
3.8909-4.02970.34251290.30612659X-RAY DIFFRACTION100
4.0297-4.19060.34611310.32052658X-RAY DIFFRACTION100
4.1906-4.38080.34871510.30272622X-RAY DIFFRACTION100
4.3808-4.61090.32681260.29282671X-RAY DIFFRACTION100
4.6109-4.89870.34651440.29012632X-RAY DIFFRACTION100
4.8987-5.2750.30841220.30842629X-RAY DIFFRACTION100
5.275-5.80240.35771500.31772690X-RAY DIFFRACTION100
5.8024-6.6340.32011280.31392629X-RAY DIFFRACTION100
6.634-8.32830.28241440.25712616X-RAY DIFFRACTION100
8.3283-29.96270.22141110.21312688X-RAY DIFFRACTION100

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