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

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Basic information

Entry
Database: PDB / ID: 6qdm
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 / sarcomere organization / muscle organ development / 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 / sarcomere organization / muscle organ development / 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 / Resolution: 3.8 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

Downloads & links

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Assembly

Deposited unit
A: UNC-45,UNC-45
B: UNC-45,UNC-45


Theoretical massNumber of molelcules
Total (without water)212,9312
Polymers212,9312
Non-polymers00
Water00
1
A: UNC-45,UNC-45


Theoretical massNumber of molelcules
Total (without water)106,4651
Polymers106,4651
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UNC-45,UNC-45


Theoretical massNumber of molelcules
Total (without water)106,4651
Polymers106,4651
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)157.392, 97.610, 148.882
Angle α, β, γ (deg.)90.00, 93.41, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein UNC-45,UNC-45


Mass: 106465.273 Da / Num. of mol.: 2 / Mutation: deltaTPR,deltaTPR
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: 2.65 Å3/Da / Density % sol: 53.64 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 100 mM Tris HCl pH 8.5 32 % glycerol ethoxylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97917 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 3.8→49 Å / Num. obs: 22138 / % possible obs: 98.9 % / Redundancy: 3.3 % / Rrim(I) all: 0.062 / Net I/σ(I): 9.1
Reflection shellResolution: 3.8→4.01 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.1 / Rrim(I) all: 1.275 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
Cootmodel building
Omodel building
CNSrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4i2z

4i2z


Resolution: 3.8→48.805 Å / SU ML: 0.86 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 45.51
RfactorNum. reflection% reflectionSelection details
Rfree0.3098 1137 5.14 %random
Rwork0.2796 ---
obs0.2812 22138 98.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.8→48.805 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11815 0 0 0 11815
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01311990
X-RAY DIFFRACTIONf_angle_d1.48116185
X-RAY DIFFRACTIONf_dihedral_angle_d10.9774516
X-RAY DIFFRACTIONf_chiral_restr0.0681905
X-RAY DIFFRACTIONf_plane_restr0.0112055
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8001-3.9730.51771230.4482517X-RAY DIFFRACTION94
3.973-4.18230.39061390.40762618X-RAY DIFFRACTION100
4.1823-4.44420.4211470.36892615X-RAY DIFFRACTION99
4.4442-4.78710.36751320.3462610X-RAY DIFFRACTION99
4.7871-5.26830.36861530.33712632X-RAY DIFFRACTION100
5.2683-6.02950.34551450.33762636X-RAY DIFFRACTION100
6.0295-7.59190.38111440.3192678X-RAY DIFFRACTION100
7.5919-48.8090.2361540.20422695X-RAY DIFFRACTION99

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