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- PDB-8brh: Co-crystal structure of She4 with Myo4 peptide -

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Basic information

Entry
Database: PDB / ID: 8brh
TitleCo-crystal structure of She4 with Myo4 peptide
Components
  • KLLA0E16699p
  • Myo4 peptide (LYS-PHE-ILE-VAL-SER-HIS-TYR)
KeywordsCHAPERONE / UNC-45 / UCS / myosin
Function / homologyUNC-45/Cro1/She4, central domain / Myosin-binding striated muscle assembly central / Hsp90 protein binding / Armadillo-like helical / Armadillo-type fold / cytoplasm / KLLA0E16699p
Function and homology information
Biological speciesKluyveromyces lactis (yeast)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsArnese, R. / Gudino, R. / Meinhart, A. / Clausen, T.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science Fund Austria
Citation
Journal: Nat Commun / Year: 2024
Title: UNC-45 assisted myosin folding depends on a conserved FX 3 HY motif implicated in Freeman Sheldon Syndrome.
Authors: Vogel, A. / Arnese, R. / Gudino Carrillo, R.M. / Sehr, D. / Deszcz, L. / Bylicki, A. / Meinhart, A. / Clausen, T.
#1: Journal: bioRxiv / Year: 2022
Title: UNC-45 assisted myosin folding depends on a conserved FX3HY motif implicated in Freeman Sheldon Syndrome
Authors: Vogel, A. / Arnese, R. / Gudino, R. / Sehr, D. / Bylicki, A. / Meinhart, A. / Clausen, T.
History
DepositionNov 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.id ..._citation.country / _citation.id / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KLLA0E16699p
B: Myo4 peptide (LYS-PHE-ILE-VAL-SER-HIS-TYR)


Theoretical massNumber of molelcules
Total (without water)76,7522
Polymers76,7522
Non-polymers00
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.480, 128.480, 77.540
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein KLLA0E16699p


Mass: 75856.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: She4 / Source: (gene. exp.) Kluyveromyces lactis (yeast) / Gene: KLLA0_E16699g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6CMY7
#2: Protein/peptide Myo4 peptide (LYS-PHE-ILE-VAL-SER-HIS-TYR)


Mass: 895.056 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.41 Å3/Da / Density % sol: 48.9 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100mM bicine/Trizma base pH 8.5 10% P20K, 20% PEG MME 550 20mM carboxylic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.1512 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1512 Å / Relative weight: 1
ReflectionResolution: 2.4→49.47 Å / Num. obs: 29225 / % possible obs: 99.9 % / Redundancy: 8.1 % / Biso Wilson estimate: 51.9 Å2 / Rmerge(I) obs: 0.1406 / Rrim(I) all: 0.1502 / Net I/σ(I): 10.05
Reflection shellResolution: 2.4→2.54 Å / Num. unique obs: 4655 / CC1/2: 0.465 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8BRG

8brg


Resolution: 2.4→49.47 Å / SU ML: 0.3596 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.7169
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2501 1483 5.09 %
Rwork0.2118 27668 -
obs0.2137 29151 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.15 Å2
Refinement stepCycle: LAST / Resolution: 2.4→49.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5083 0 0 132 5215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075158
X-RAY DIFFRACTIONf_angle_d0.92766983
X-RAY DIFFRACTIONf_chiral_restr0.0565839
X-RAY DIFFRACTIONf_plane_restr0.0052882
X-RAY DIFFRACTIONf_dihedral_angle_d13.941930
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.480.391210.38112496X-RAY DIFFRACTION99.85
2.48-2.570.33321310.2992494X-RAY DIFFRACTION99.96
2.57-2.670.31821360.26082488X-RAY DIFFRACTION99.96
2.67-2.790.32691240.27612507X-RAY DIFFRACTION100
2.79-2.940.2471450.2342466X-RAY DIFFRACTION99.96
2.94-3.120.30771370.23132508X-RAY DIFFRACTION99.96
3.12-3.360.26011480.22712487X-RAY DIFFRACTION99.96
3.36-3.70.26691440.21852507X-RAY DIFFRACTION100
3.7-4.240.22241270.18332522X-RAY DIFFRACTION99.92
4.24-5.340.20771340.1792564X-RAY DIFFRACTION99.96
5.34-49.470.21211360.1852629X-RAY DIFFRACTION99.68
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)
13.068316634530.520306447078-0.336234123181.56356497881-0.2839087197482.253023804940.2283903420810.259884233065-0.291434861154-0.355193779555-0.152215195888-0.2816716273970.182738817560.120256698779-0.07575228083690.4553913038690.1203934004050.05248718148210.5672530325230.004646578537260.539181849952-68.7727197377-6.6905047891510.8806182747
23.526680290351.55197489325-1.624368013571.68624590277-0.7484371197571.129869158590.0741592416007-0.1768421427130.04732058862940.204676980007-0.008353419323380.101954553521-0.02650601115350.0710932786522-0.04868356278120.3624466736670.0461457998346-0.01122325963270.392994887440.02263173005920.268104856098-19.574828951420.9731927759-3.46068052377
33.543782220642.31277240506-3.283887548822.53543088546-1.658978485513.324526516310.252989846446-0.6267008970820.08799613630920.0999882256696-0.05346368172030.352677390566-0.1189364976010.720459503473-0.1472636926440.4933116944280.0423656024605-0.090278476740.770167070095-0.009433687868060.474177233877-10.646093219226.4568069737-0.730648153153
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 246 )AA1 - 2461 - 241
22chain 'A' and (resid 247 through 665 )AA247 - 665242 - 632
33chain 'B' and (resid 74 through 80 )BB74 - 801 - 7

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