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- PDB-4i2w: Crystal structure of the myosin chaperone UNC-45 from C.elegans i... -

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Basic information

Entry
Database: PDB / ID: 4i2w
TitleCrystal structure of the myosin chaperone UNC-45 from C.elegans in complex with a Hsp70 peptide
Components
  • Heat shock 70 kDa protein A
  • Protein UNC-45
KeywordsChaperone/protein binding / chaperone / myosin folding / protein filaments / myofilament formation / TPR-peptide interaction / UCS domain containing protein / Hsp70 and Hsp90 co-chaperone / Chaperone-protein binding complex
Function / homology
Function and homology information


GABA synthesis, release, reuptake and degradation / Regulation of HSF1-mediated heat shock response / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / mRNA Splicing - Major Pathway / HSF1-dependent transactivation / Clathrin-mediated endocytosis / Neutrophil degranulation / egg-laying behavior / locomotion / retrograde transport, endosome to Golgi ...GABA synthesis, release, reuptake and degradation / Regulation of HSF1-mediated heat shock response / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / mRNA Splicing - Major Pathway / HSF1-dependent transactivation / Clathrin-mediated endocytosis / Neutrophil degranulation / egg-laying behavior / locomotion / retrograde transport, endosome to Golgi / embryo development ending in birth or egg hatching / muscle organ development / sarcomere organization / cleavage furrow / chaperone cofactor-dependent protein refolding / chaperone-mediated protein folding / heat shock protein binding / protein folding chaperone / determination of adult lifespan / ATP-dependent protein folding chaperone / Hsp90 protein binding / cell cortex / response to heat / protein refolding / ubiquitin protein ligase binding / perinuclear region of cytoplasm / ATP hydrolysis activity / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
UNC-45/Cro1/She4, central domain / Myosin-binding striated muscle assembly central / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily ...UNC-45/Cro1/She4, central domain / Myosin-binding striated muscle assembly central / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily / Tetratricopeptide repeat domain / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / ATPase, nucleotide binding domain / Armadillo-like helical / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
UNC-45 / Heat shock protein hsp-1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsClausen, T. / Gazda, L. / Hellerschmied, D.
CitationJournal: Cell(Cambridge,Mass.) / 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. / Lowe, T. / Forne, I. / Mueller-Planitz, F. / Hoppe, T. / Clausen, T.
History
DepositionNov 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein UNC-45
B: Heat shock 70 kDa protein A


Theoretical massNumber of molelcules
Total (without water)109,9152
Polymers109,9152
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-2 kcal/mol
Surface area41440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.276, 86.276, 808.978
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 Protein UNC-45 / UNC-45


Mass: 108928.070 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 (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: G5EG62
#2: Protein/peptide Heat shock 70 kDa protein A


Mass: 987.019 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Caenorhabditis elegans (invertebrata) / References: UniProt: P09446

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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: 3.95 Å3/Da / Density % sol: 68.89 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M HEPES, 10% PEG 8000, 12% ethylene glycol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 22485 / % possible obs: 99.9 % / Redundancy: 6.1 % / Rsym value: 0.139 / Net I/σ(I): 8.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3.6-3.7960.6971.11894231320.697100
3.79-4.026.40.4211.81905829860.421100
4.02-4.36.60.2682.91884528580.268100
4.3-4.656.40.2033.81703526420.203100
4.65-5.096.20.1774.31539524870.177100
5.09-5.695.70.1784.31279622480.17899.9
5.69-6.576.20.1425.31256220380.142100
6.57-8.055.90.0917.51028917520.091100
8.05-11.3850.05711.7720214320.05799.4
11.38-47.8174.70.05311.642809100.05398.3

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
CNSrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.6→47.817 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7941 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2845 1945 5 %
Rwork0.2345 --
obs-22485 99.7 %
Solvent computationBsol: 90.5247 Å2
Displacement parametersBiso max: 200 Å2 / Biso mean: 125.948 Å2 / Biso min: 41.26 Å2
Baniso -1Baniso -2Baniso -3
1--13.734 Å20 Å20 Å2
2---13.734 Å20 Å2
3---27.469 Å2
Refinement stepCycle: LAST / Resolution: 3.6→47.817 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7052 0 0 0 7052
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it2.7621.5
X-RAY DIFFRACTIONc_scbond_it3.8052
X-RAY DIFFRACTIONc_mcangle_it4.7342
X-RAY DIFFRACTIONc_scangle_it6.0522.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4water_rep.param

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