[English] 日本語
Yorodumi
- PDB-4ww5: Crystal structure of binary complex Bud32-Cgi121 in complex with AMPP -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more