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- PDB-4wwa: Crystal structure of binary complex Bud32-Cgi121 -

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Basic information

Entry
Database: PDB / ID: 4wwa
TitleCrystal structure of binary complex Bud32-Cgi121
Components
  • EKC/KEOPS complex subunit BUD32
  • EKC/KEOPS complex subunit CGI121
KeywordsTRANSFERASE / KEOPS / binary complex / Bud32-Cgi121 / tRNA t6A / hydrolase
Function / homology
Function and homology information


tRNA threonylcarbamoyladenosine metabolic process / EKC/KEOPS complex / tRNA threonylcarbamoyladenosine modification / cellular bud site selection / Hydrolases; Acting on acid anhydrides / telomere maintenance via recombination / telomere maintenance / maintenance of translational fidelity / DNA recombination / tRNA binding ...tRNA threonylcarbamoyladenosine metabolic process / EKC/KEOPS complex / tRNA threonylcarbamoyladenosine modification / cellular bud site selection / Hydrolases; Acting on acid anhydrides / telomere maintenance via recombination / telomere maintenance / maintenance of translational fidelity / DNA recombination / tRNA binding / chromosome, telomeric region / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Lipopolysaccharide kinase (Kdo/WaaP) family / PF0523-like / CGI121/TPRKB / Serine/threonine-protein kinase Bud32 / CGI121/TPRKB / CGI121/TPRKB superfamily / Kinase binding protein CGI-121 / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein kinase domain profile. ...Lipopolysaccharide kinase (Kdo/WaaP) family / PF0523-like / CGI121/TPRKB / Serine/threonine-protein kinase Bud32 / CGI121/TPRKB / CGI121/TPRKB superfamily / Kinase binding protein CGI-121 / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
EKC/KEOPS complex subunit BUD32 / EKC/KEOPS complex subunit CGI121
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.953 Å
AuthorsZhang, W. / van Tilbeurgh, H.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Crystal structures of the Gon7/Pcc1 and Bud32/Cgi121 complexes provide a model for the complete yeast KEOPS complex.
Authors: Zhang, W. / Collinet, B. / Graille, M. / Daugeron, M.C. / Lazar, N. / Libri, D. / Durand, D. / van Tilbeurgh, H.
History
DepositionNov 10, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references
Revision 1.2Jan 17, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EKC/KEOPS complex subunit BUD32
B: EKC/KEOPS complex subunit CGI121
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9787
Polymers51,4982
Non-polymers4805
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-59 kcal/mol
Surface area17430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.540, 111.540, 86.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein EKC/KEOPS complex subunit BUD32 / Atypical serine/threonine protein kinase BUD32 / Bud site selection protein 32 / Low-dye-binding ...Atypical serine/threonine protein kinase BUD32 / Bud site selection protein 32 / Low-dye-binding protein 14 / piD261


Mass: 29982.377 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: BUD32, LDB14, YGR262C
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P53323, Hydrolases; Acting on acid anhydrides, non-specific serine/threonine protein kinase
#2: Protein EKC/KEOPS complex subunit CGI121 / CGI-121 homolog


Mass: 21515.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: CGI121, YML036W
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q03705
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M Sodium Acetate pH 4.6, 2.0 M Ammounium Sulfate, 0.1 M NaCl and 10 mM Tris-HCl pH 7.5
PH range: 4.6-5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97918 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.95→43.2 Å / Num. obs: 11205 / % possible obs: 99.8 % / Redundancy: 4.58 % / Rsym value: 0.124 / Net I/σ(I): 14.32
Reflection shellResolution: 2.953→3.059 Å

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
XDS2011data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.953→43.2 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 31.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2959 560 5 %
Rwork0.217 --
obs0.221 11197 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.467 Å2 / ksol: 0.349 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--11.1054 Å20 Å20 Å2
2---11.1054 Å2-0 Å2
3---22.2108 Å2
Refinement stepCycle: LAST / Resolution: 2.953→43.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2933 0 25 13 2971
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083012
X-RAY DIFFRACTIONf_angle_d1.0574104
X-RAY DIFFRACTIONf_dihedral_angle_d17.6851007
X-RAY DIFFRACTIONf_chiral_restr0.067478
X-RAY DIFFRACTIONf_plane_restr0.004523
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9532-3.25030.35811390.26182636X-RAY DIFFRACTION99
3.2503-3.72040.30031400.21882659X-RAY DIFFRACTION100
3.7204-4.68640.29861400.18672658X-RAY DIFFRACTION100
4.6864-43.20650.26221410.21822684X-RAY DIFFRACTION100

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