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- PDB-4ww9: Crystal structure of binary complex Bud32-Cgi121 in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 4ww9
TitleCrystal structure of binary complex Bud32-Cgi121 in complex with ADP
Components(EKC/KEOPS complex subunit ...) x 2
KeywordsTRANSCRIPTION / KEOPS / binary complex / Bud32-Cgi121 / tRNA t6A
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
ACETATE ION / ADENOSINE-5'-DIPHOSPHATE / 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: 1.951 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 1.2May 1, 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

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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)52,45210
Polymers51,4982
Non-polymers9548
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-74 kcal/mol
Surface area18910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.010, 113.010, 86.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

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EKC/KEOPS complex subunit ... , 2 types, 2 molecules AB

#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 / Bud32


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(DE3) (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 / Cgi121


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(DE3) (bacteria) / References: UniProt: Q03705

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Non-polymers , 5 types, 288 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.68 Å3/Da / Density % sol: 54.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M Sodium Acetate pH 4.8, 2.0 M Ammonium Sulfate, 0.1 M NaCl, 10 mM Tris-HcL pH 7.5 and 5 mM ATP
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: 0.97911 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 1.951→35.74 Å / Num. all: 289733 / Num. obs: 39488 / % possible obs: 99.9 % / Redundancy: 7.34 % / Rsym value: 0.055 / Net I/σ(I): 25.08
Reflection shellResolution: 1.951→2.021 Å / % possible all: 98.96

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
XDS2012data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Methanocaldococcus jannaschii Bud32/Cgi121

Resolution: 1.951→35.737 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 20.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2092 1973 5 %
Rwork0.179 --
obs0.1805 39480 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.295 Å2 / ksol: 0.383 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.0786 Å2-0 Å20 Å2
2---4.0786 Å2-0 Å2
3---8.1571 Å2
Refinement stepCycle: LAST / Resolution: 1.951→35.737 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3206 0 56 280 3542
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053328
X-RAY DIFFRACTIONf_angle_d0.9914523
X-RAY DIFFRACTIONf_dihedral_angle_d15.8541185
X-RAY DIFFRACTIONf_chiral_restr0.072516
X-RAY DIFFRACTIONf_plane_restr0.004565
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9508-1.99960.19841380.17542628X-RAY DIFFRACTION99
1.9996-2.05370.25311410.17362665X-RAY DIFFRACTION100
2.0537-2.11410.21991410.17852676X-RAY DIFFRACTION100
2.1141-2.18230.23311390.17722645X-RAY DIFFRACTION100
2.1823-2.26030.19481420.16732703X-RAY DIFFRACTION100
2.2603-2.35080.22121400.17272661X-RAY DIFFRACTION100
2.3508-2.45770.23661420.17832691X-RAY DIFFRACTION100
2.4577-2.58730.19251400.18282665X-RAY DIFFRACTION100
2.5873-2.74930.23551410.18622686X-RAY DIFFRACTION100
2.7493-2.96150.22431400.19592662X-RAY DIFFRACTION100
2.9615-3.25940.19991420.18722685X-RAY DIFFRACTION100
3.2594-3.73060.22321420.17382692X-RAY DIFFRACTION100
3.7306-4.69840.18971420.15792709X-RAY DIFFRACTION100
4.6984-35.74290.18641430.18442739X-RAY DIFFRACTION100

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