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- PDB-4i2z: Crystal structure of the myosin chaperone UNC-45 from C.elegans i... -

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Basic information

Entry
Database: PDB / ID: 4i2z
TitleCrystal structure of the myosin chaperone UNC-45 from C.elegans in complex with a Hsp90 peptide
Components
  • Heat shock protein 90
  • 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


protein phosphatase 5 binding / eNOS activation / HSF1 activation / : / Drug-mediated inhibition of ERBB2 signaling / Signaling by ERBB2 / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Attenuation phase / Downregulation of ERBB2 signaling / Aryl hydrocarbon receptor signalling ...protein phosphatase 5 binding / eNOS activation / HSF1 activation / : / Drug-mediated inhibition of ERBB2 signaling / Signaling by ERBB2 / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Attenuation phase / Downregulation of ERBB2 signaling / Aryl hydrocarbon receptor signalling / ESR-mediated signaling / Extra-nuclear estrogen signaling / dauer larval development / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / VEGFR2 mediated vascular permeability / HSF1-dependent transactivation / Neutrophil degranulation / nematode larval development / protein serine/threonine phosphatase complex / egg-laying behavior / HSP90-CDC37 chaperone complex / regulation of chemotaxis / nuclear glucocorticoid receptor binding / locomotion / protein folding chaperone complex / embryo development ending in birth or egg hatching / muscle organ development / protein maturation by protein folding / sarcomere organization / cleavage furrow / positive regulation of phosphoprotein phosphatase activity / chaperone-mediated protein folding / protein folding chaperone / protein export from nucleus / protein dephosphorylation / determination of adult lifespan / ATP-dependent protein folding chaperone / Hsp90 protein binding / chemotaxis / disordered domain specific binding / unfolded protein binding / protein folding / cellular response to heat / cell cortex / response to heat / defense response to Gram-negative bacterium / protein stabilization / membrane raft / cell cycle / ubiquitin protein ligase binding / perinuclear region of cytoplasm / ATP hydrolysis activity / protein-containing complex / ATP binding / identical protein binding / plasma membrane / cytoplasm / cytosol
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 / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase ...UNC-45/Cro1/She4, central domain / Myosin-binding striated muscle assembly central / Tetratricopeptide repeat domain / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Tetratricopeptide repeats / Tetratricopeptide repeat / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Armadillo-like helical / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / Ribosomal protein S5 domain 2-type fold / Mainly Alpha
Similarity search - Domain/homology
UNC-45 / Heat shock protein 90
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 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 protein 90


Theoretical massNumber of molelcules
Total (without water)110,1092
Polymers110,1092
Non-polymers00
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-1 kcal/mol
Surface area41440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.633, 86.633, 815.015
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 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 protein 90 / Abnormal dauer formation protein 21


Mass: 1181.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Caenorhabditis elegans (invertebrata) / References: UniProt: Q18688
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 4.01 Å3/Da / Density % sol: 69.32 %
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: ESRF / Beamline: ID23-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 2, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 41180 / Rsym value: 0.102

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Processing

Software
NameVersionClassification
SHARPphasing
PHENIX(phenix.refine: 1.6_289)refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.9→19.931 Å / SU ML: 0.4 / σ(F): 0.05 / Phase error: 25.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2559 2009 5.07 %
Rwork0.2375 --
obs0.2384 39598 93.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.213 Å2 / ksol: 0.213 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.9598 Å2-0 Å20 Å2
2---9.9598 Å20 Å2
3---19.9196 Å2
Refinement stepCycle: LAST / Resolution: 2.9→19.931 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7015 0 0 43 7058
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087117
X-RAY DIFFRACTIONf_angle_d1.449611
X-RAY DIFFRACTIONf_dihedral_angle_d20.4972660
X-RAY DIFFRACTIONf_chiral_restr0.0971121
X-RAY DIFFRACTIONf_plane_restr0.0061241
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.97240.46341260.40492400X-RAY DIFFRACTION87
2.9724-3.05250.38451390.38292487X-RAY DIFFRACTION90
3.0525-3.1420.40131450.36012528X-RAY DIFFRACTION91
3.142-3.2430.35871200.34292599X-RAY DIFFRACTION93
3.243-3.35830.29111420.31622621X-RAY DIFFRACTION93
3.3583-3.49210.29651480.28812652X-RAY DIFFRACTION95
3.4921-3.65010.27771430.25382718X-RAY DIFFRACTION96
3.6501-3.84130.27031260.24362729X-RAY DIFFRACTION97
3.8413-4.080.20641550.22212775X-RAY DIFFRACTION98
4.08-4.39190.22831330.18872827X-RAY DIFFRACTION98
4.3919-4.82820.22191540.17572836X-RAY DIFFRACTION98
4.8282-5.51390.20621750.19482813X-RAY DIFFRACTION98
5.5139-6.89870.21931540.20622910X-RAY DIFFRACTION97
6.8987-19.93190.18941490.16422694X-RAY DIFFRACTION84
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.34950.38140.09880.6174-0.11510.53810.22121.2559-0.13130.0405-0.4017-0.0209-0.10380.3120.00240.0554-0.0567-0.0231.2023-0.20560.45162.129415.200633.613
22.3524-0.15660.19460.7590.11221.32440.14880.59540.12960.01890.05150.0244-0.0806-0.07820.0345-0.1397-0.1889-0.05530.52910.01030.049134.802125.186349.6446
30.34990.1544-0.5910.719-0.06711.05670.45570.20260.54720.191-0.12510.3087-0.3133-0.30780.02950.18140.02620.10870.99160.20240.609711.33441.582434.5778
40.37080.0311-0.06151.1461-0.230.41070.38210.2440.6065-0.3737-0.43070.38950.3373-0.12760.03360.1571-0.00270.12181.1160.11630.36330.445746.98328.0078
50.41890.06540.44350.3540.14950.4869-0.56630.2986-0.5039-0.19770.1514-0.6339-0.33390.2802-0.00550.4278-0.1630.28771.82970.3960.79161.162550.32514.8171
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 7:115)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 116:468)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 469:620)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 621:719)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 720:911)

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