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- PDB-4ww5: Crystal structure of binary complex Bud32-Cgi121 in complex with AMPP -

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Basic information

Entry
Database: PDB / ID: 4ww5
TitleCrystal structure of binary complex Bud32-Cgi121 in complex with AMPP
Components(EKC/KEOPS complex subunit ...) x 2
KeywordsTRANSFERASE / 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 / chromosome, telomeric region ...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 / chromosome, telomeric region / non-specific serine/threonine protein kinase / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
PF0523-like / CGI121/TPRKB / Lipopolysaccharide kinase (Kdo/WaaP) family / 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. ...PF0523-like / CGI121/TPRKB / Lipopolysaccharide kinase (Kdo/WaaP) family / 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 / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / 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: 1.997 Å
AuthorsZhang, W.
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 8, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
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)51,92512
Polymers50,6692
Non-polymers1,25610
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
  • DIMERIC
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-69 kcal/mol
Surface area18720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.930, 112.930, 87.230
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


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: 20686.812 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

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Non-polymers , 5 types, 176 molecules

#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.74 Å3/Da / Density % sol: 55.18 %
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,10 mM Tris-HCl pH 7.5, 5 mM AMPPNP and 5 mM L-threonine.
PH range: 4.6-5.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.997→39.93 Å / Num. all: 283335 / Num. obs: 37119 / % possible obs: 99.79 % / Redundancy: 7.6 % / Rsym value: 0.049 / Net I/σ(I): 27.29
Reflection shellResolution: 1.997→2.069 Å / Mean I/σ(I) obs: 5.54 / % possible all: 98.1

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Processing

SoftwareName: PHENIX / Version: (phenix.refine) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.997→39.927 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 21.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2223 1855 5 %
Rwork0.1834 --
obs0.1853 37113 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.862 Å2 / ksol: 0.386 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.1618 Å2-0 Å20 Å2
2---4.1618 Å2-0 Å2
3---8.3236 Å2
Refinement stepCycle: LAST / Resolution: 1.997→39.927 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3221 0 65 166 3452
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073362
X-RAY DIFFRACTIONf_angle_d1.0834562
X-RAY DIFFRACTIONf_dihedral_angle_d16.3571195
X-RAY DIFFRACTIONf_chiral_restr0.069510
X-RAY DIFFRACTIONf_plane_restr0.008573
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9972-2.05120.27771380.20872629X-RAY DIFFRACTION98
2.0512-2.11150.23811430.19242726X-RAY DIFFRACTION100
2.1115-2.17970.23671410.18832677X-RAY DIFFRACTION100
2.1797-2.25760.23661440.17962731X-RAY DIFFRACTION100
2.2576-2.34790.23121420.18032700X-RAY DIFFRACTION100
2.3479-2.45480.22241440.1882722X-RAY DIFFRACTION100
2.4548-2.58420.23011410.19292686X-RAY DIFFRACTION100
2.5842-2.7460.26661430.19742726X-RAY DIFFRACTION100
2.746-2.9580.23811430.20642711X-RAY DIFFRACTION100
2.958-3.25560.25471440.19672729X-RAY DIFFRACTION100
3.2556-3.72640.221420.17572702X-RAY DIFFRACTION100
3.7264-4.69360.18521440.15372743X-RAY DIFFRACTION100
4.6936-39.93470.19661460.18052776X-RAY DIFFRACTION100

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