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

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Basic information

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


egg-laying behavior / embryo development ending in birth or egg hatching / locomotion / sarcomere organization / muscle organ development / cleavage furrow / protein folding chaperone / Hsp90 protein binding / protein folding / cell cortex ...egg-laying behavior / embryo development ending in birth or egg hatching / locomotion / sarcomere organization / muscle organ development / cleavage furrow / protein folding chaperone / Hsp90 protein binding / protein folding / 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 repeat domain / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Armadillo-like helical / Alpha Horseshoe ...UNC-45/Cro1/She4, central domain / Myosin-binding striated muscle assembly central / Tetratricopeptide repeat domain / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Armadillo-like helical / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.929 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
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: UNC-45


Theoretical massNumber of molelcules
Total (without water)107,6021
Polymers107,6021
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 area38130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.124, 114.323, 85.006
Angle α, β, γ (deg.)90.00, 107.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein UNC-45


Mass: 107602.109 Da / Num. of mol.: 1 / Mutation: I822F
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: 2.32 Å3/Da / Density % sol: 47.09 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM MES/NaOH pH 6.5 200 mM ammonium acetate 30 % glycerol ethoxylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.9→47 Å / Num. obs: 20543 / % possible obs: 97 % / Redundancy: 3.1 % / Rrim(I) all: 0.119 / Net I/σ(I): 8.5
Reflection shellResolution: 2.9→3.09 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1.4 / Rrim(I) all: 0.675 / % possible all: 82.3

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
Cootmodel building
Omodel building
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4i2z

4i2z


Resolution: 2.929→46.704 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.8
RfactorNum. reflection% reflectionSelection details
Rfree0.2676 1063 5.17 %RANDOM
Rwork0.2213 ---
obs0.2237 20543 96.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.929→46.704 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6931 0 0 0 6931
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077028
X-RAY DIFFRACTIONf_angle_d0.9939473
X-RAY DIFFRACTIONf_dihedral_angle_d11.5942668
X-RAY DIFFRACTIONf_chiral_restr0.0581101
X-RAY DIFFRACTIONf_plane_restr0.0061214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9292-3.06250.35391100.31651972X-RAY DIFFRACTION79
3.0625-3.22390.36931440.29512449X-RAY DIFFRACTION99
3.2239-3.42580.28791200.25582528X-RAY DIFFRACTION99
3.4258-3.69020.28721220.23952496X-RAY DIFFRACTION99
3.6902-4.06140.27541510.21782493X-RAY DIFFRACTION100
4.0614-4.64860.27081360.192482X-RAY DIFFRACTION99
4.6486-5.8550.26071300.21842526X-RAY DIFFRACTION100
5.855-46.710.21051500.19042534X-RAY DIFFRACTION99

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