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- PDB-5mzu: Crystal structure of the myosin chaperone UNC-45 from C. elegans ... -

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Basic information

Entry
Database: PDB / ID: 5mzu
TitleCrystal structure of the myosin chaperone UNC-45 from C. elegans (alternative conformation)
ComponentsUNC-45
KeywordsCHAPERONE / myosin folding / protein filament / UCS domain / ARM repeats
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.8 Å
Model detailsAlternative conformation, with rearranged UCS domain
AuthorsHellerschmied, D. / Gazda, L. / Clausen, T.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP22750 Austria
Citation
Journal: Nat Commun / Year: 2018
Title: UFD-2 is an adaptor-assisted E3 ligase targeting unfolded proteins.
Authors: Hellerschmied, D. / Roessler, M. / Lehner, A. / Gazda, L. / Stejskal, K. / Imre, R. / Mechtler, K. / Dammermann, A. / Clausen, T.
#1: Journal: Cell / Year: 2013
Title: The myosin chaperone UNC-45 is organized in tandem modules to support myofilament formation in C. elegans.
Authors: Gazda, L. / Pokrzywa, W. / Hellerschmied, D. / Loewe, T. / Forne, I. / Mueller-Planitz, F. / Hoppe, T. / Clausen, T.
History
DepositionFeb 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2018Provider: 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


Theoretical massNumber of molelcules
Total (without water)108,5531
Polymers108,5531
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area43590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.149, 86.149, 716.465
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein UNC-45


Mass: 108552.898 Da / Num. of mol.: 1
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 BL21(DE3) (bacteria) / 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: 4.43 Å3/Da / Density % sol: 72.24 % / Mosaicity: 0.213 °
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Hepes pH 7.0, 10% PEG8000, 12% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 2, 2010 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.8→50 Å / Num. obs: 16050 / % possible obs: 93.5 % / Redundancy: 4.4 % / Biso Wilson estimate: 160.67 Å2 / Rmerge(I) obs: 0.085 / Χ2: 0.987 / Net I/σ(I): 7.4 / Num. measured all: 70085
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsΧ2Diffraction-ID% possible all
3.8-3.874.70.3670.846197.9
3.87-3.944.60.260.915198.3
3.94-4.014.60.2420.929198.1
4.01-4.094.70.230.982197.8
4.09-4.184.60.2171.002197.8
4.18-4.284.60.1691.017197.9
4.28-4.394.50.171.087197.7
4.39-4.54.70.1421.035198.1
4.5-4.644.60.1471.07197.3
4.64-4.794.50.121.071198
4.79-4.964.50.1311.014197.5
4.96-5.164.50.1210.991197.7
5.16-5.394.40.1120.97197.6
5.39-5.674.40.111.022197.5
5.67-6.034.30.0941.021197.6
6.03-6.494.20.080.994197.2
6.49-7.154.20.0670.994196.3
7.15-8.183.80.0520.99188.9
8.18-10.293.20.0420.921174.4
10.29-503.20.0340.668159

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXdev_2645refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
HKLdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.8→29.4 Å / SU ML: 0.67 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3189 731 4.81 %
Rwork0.2976 14482 -
obs0.2986 15213 90.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 334.86 Å2 / Biso mean: 183.7562 Å2 / Biso min: 108.09 Å2
Refinement stepCycle: final / Resolution: 3.8→29.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5994 0 0 0 5994
Num. residues----869
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066073
X-RAY DIFFRACTIONf_angle_d0.8378287
X-RAY DIFFRACTIONf_chiral_restr0.0441009
X-RAY DIFFRACTIONf_plane_restr0.0061098
X-RAY DIFFRACTIONf_dihedral_angle_d16.0443698
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.8001-4.09280.38691410.36382462260380
4.0928-4.50330.38891540.3542927308194
4.5033-5.15190.38761530.35883087324098
5.1519-6.47940.39481340.36173195332998
6.4794-29.40070.24531490.23012811296081
Refinement TLS params.Method: refined / Origin x: 12.7028 Å / Origin y: -34.2048 Å / Origin z: 27.4897 Å
111213212223313233
T0.3054 Å2-0.3632 Å20.3574 Å2-2.2822 Å2-0.3885 Å2--1.0145 Å2
L0.0319 °2-0.0478 °2-0.0523 °2-0.2664 °20.0504 °2--0.2677 °2
S0.3686 Å °0.4397 Å °-0.0853 Å °0.0993 Å °-0.2051 Å °0.102 Å °0.3632 Å °-0.107 Å °0.1638 Å °
Refinement TLS groupSelection details: all

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