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- PDB-4ww7: Crystal structure of binary complex Bud32-Cgi121 in complex with AMP -

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Basic information

Entry
Database: PDB / ID: 4ww7
TitleCrystal structure of binary complex Bud32-Cgi121 in complex with AMP
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 / 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 MONOPHOSPHATE / 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: 1.669 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)52,37010
Polymers51,4982
Non-polymers8728
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-40 kcal/mol
Surface area18570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.890, 113.890, 87.410
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(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


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 , 4 types, 222 molecules

#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.75 Å3/Da / Density % sol: 55.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
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, 5 mM AMP and MgCl2
PH range: 4.6-4.8

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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: 1.669→36.02 Å / Num. all: 236981 / Num. obs: 64292 / % possible obs: 99.4 % / Redundancy: 3.69 % / Rsym value: 0.045 / Net I/σ(I): 18.48
Reflection shellResolution: 1.669→1.729 Å / % possible all: 98.46

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Processing

SoftwareName: PHENIX / Version: (phenix.refine) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Methanocaldococcus jannaschii Bud32/Cgi121

Resolution: 1.669→36.015 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 20.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2133 3214 5 %
Rwork0.1933 --
obs0.1943 64286 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.191 Å2 / ksol: 0.385 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.2628 Å2-0 Å20 Å2
2---2.2628 Å2-0 Å2
3---4.5255 Å2
Refinement stepCycle: LAST / Resolution: 1.669→36.015 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3149 0 54 214 3417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083268
X-RAY DIFFRACTIONf_angle_d1.0934437
X-RAY DIFFRACTIONf_dihedral_angle_d15.6221140
X-RAY DIFFRACTIONf_chiral_restr0.074508
X-RAY DIFFRACTIONf_plane_restr0.005555
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6694-1.69440.28041340.24472551X-RAY DIFFRACTION97
1.6944-1.72080.24351380.22862618X-RAY DIFFRACTION100
1.7208-1.7490.24291420.21872698X-RAY DIFFRACTION100
1.749-1.77920.23961380.1972630X-RAY DIFFRACTION100
1.7792-1.81160.23461400.19742653X-RAY DIFFRACTION100
1.8116-1.84640.21431390.1922634X-RAY DIFFRACTION100
1.8464-1.88410.22681390.19382652X-RAY DIFFRACTION100
1.8841-1.9250.22651400.19142655X-RAY DIFFRACTION100
1.925-1.96980.20941400.20512658X-RAY DIFFRACTION100
1.9698-2.01910.2511400.19042667X-RAY DIFFRACTION100
2.0191-2.07370.2361400.19082654X-RAY DIFFRACTION100
2.0737-2.13470.20821410.18922685X-RAY DIFFRACTION100
2.1347-2.20360.20521380.19282622X-RAY DIFFRACTION100
2.2036-2.28230.23911410.18762669X-RAY DIFFRACTION99
2.2823-2.37370.19711410.19542673X-RAY DIFFRACTION100
2.3737-2.48170.23181400.19362671X-RAY DIFFRACTION100
2.4817-2.61250.21681400.20352664X-RAY DIFFRACTION100
2.6125-2.77610.23511400.20362662X-RAY DIFFRACTION99
2.7761-2.99040.2191400.20532642X-RAY DIFFRACTION100
2.9904-3.29110.21281400.2042677X-RAY DIFFRACTION99
3.2911-3.76690.18421400.18482659X-RAY DIFFRACTION99
3.7669-4.74420.16011410.15892671X-RAY DIFFRACTION99
4.7442-36.02350.22391420.18632707X-RAY DIFFRACTION99

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