[English] 日本語
Yorodumi
- PDB-4qtu: Structure of S. cerevisiae Bud23-Trm112 complex involved in forma... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4qtu
TitleStructure of S. cerevisiae Bud23-Trm112 complex involved in formation of m7G1575 on 18S rRNA (SAM bound form)
Components
  • Multifunctional methyltransferase subunit TRM112
  • Putative methyltransferase BUD23
KeywordsTRANSFERASE / Class I / Methyltransferase
Function / homology
Function and homology information


Methylation / positive regulation of termination of DNA-templated transcription / 18S rRNA (guanine1575-N7)-methyltransferase / Eukaryotic Translation Termination / eRF1 methyltransferase complex / tRNA (m2G10) methyltransferase complex / rRNA (guanine-N7)-methylation / tRNA methyltransferase activator activity / tRNA methyltransferase complex / rRNA (guanine) methyltransferase activity ...Methylation / positive regulation of termination of DNA-templated transcription / 18S rRNA (guanine1575-N7)-methyltransferase / Eukaryotic Translation Termination / eRF1 methyltransferase complex / tRNA (m2G10) methyltransferase complex / rRNA (guanine-N7)-methylation / tRNA methyltransferase activator activity / tRNA methyltransferase complex / rRNA (guanine) methyltransferase activity / tRNA wobble uridine modification / tRNA methylation / positive regulation of rRNA processing / maturation of LSU-rRNA / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal small subunit export from nucleus / ribosomal large subunit biogenesis / maturation of SSU-rRNA / ribosomal small subunit biogenesis / ribosome / protein heterodimerization activity / nucleolus / nucleus / cytosol / cytoplasm
Similarity search - Function
18S rRNA (guanine(1575)-N(7))-methyltransferase Bud23, C-terminal / 18S rRNA (guanine(1575)-N(7))-methyltransferase Bud23-like / Methyltransferase involved in Williams-Beuren syndrome / Multifunctional methyltransferase subunit Trm112 / Trm112-like / Trm112p-like protein / Methyltransferase type 11 / Methyltransferase domain / N-terminal domain of TfIIb - #10 / N-terminal domain of TfIIb ...18S rRNA (guanine(1575)-N(7))-methyltransferase Bud23, C-terminal / 18S rRNA (guanine(1575)-N(7))-methyltransferase Bud23-like / Methyltransferase involved in Williams-Beuren syndrome / Multifunctional methyltransferase subunit Trm112 / Trm112-like / Trm112p-like protein / Methyltransferase type 11 / Methyltransferase domain / N-terminal domain of TfIIb - #10 / N-terminal domain of TfIIb / Single Sheet / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / 18S rRNA (guanine(1575)-N(7))-methyltransferase / Multifunctional methyltransferase subunit TRM112
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.124 Å
AuthorsLetoquart, J. / Huvelle, E. / Wacheul, L. / Bourgeois, G. / Zorbas, C. / Graille, M. / Heurgue-Hamard, V. / Lafontaine, D.L.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural and functional studies of Bud23-Trm112 reveal 18S rRNA N7-G1575 methylation occurs on late 40S precursor ribosomes.
Authors: Letoquart, J. / Huvelle, E. / Wacheul, L. / Bourgeois, G. / Zorbas, C. / Graille, M. / Heurgue-Hamard, V. / Lafontaine, D.L.
History
DepositionJul 9, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Aug 24, 2022Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Multifunctional methyltransferase subunit TRM112
B: Putative methyltransferase BUD23
C: Multifunctional methyltransferase subunit TRM112
D: Putative methyltransferase BUD23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,36027
Polymers76,2534
Non-polymers2,10723
Water3,117173
1
A: Multifunctional methyltransferase subunit TRM112
B: Putative methyltransferase BUD23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,58320
Polymers38,1262
Non-polymers1,45718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-13 kcal/mol
Surface area15270 Å2
MethodPISA
2
C: Multifunctional methyltransferase subunit TRM112
D: Putative methyltransferase BUD23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7767
Polymers38,1262
Non-polymers6505
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-13 kcal/mol
Surface area14480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.472, 53.733, 85.205
Angle α, β, γ (deg.)90.00, 94.55, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 2 types, 4 molecules ACBD

#1: Protein Multifunctional methyltransferase subunit TRM112 / rRNA MTase activator subunit / eRF1 methyltransferase subunit TRM112 / eRF1 MTase subunit TRM112 / ...rRNA MTase activator subunit / eRF1 methyltransferase subunit TRM112 / eRF1 MTase subunit TRM112 / tRNA methyltransferase 112


Mass: 15078.209 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Gene: N3445, TRM112, YNR046W / Production host: Escherichia coli (E. coli) / References: UniProt: P53738
#2: Protein Putative methyltransferase BUD23 / rRNA MTase catalytic subunit / Bud site selection protein 23


Mass: 23048.053 Da / Num. of mol.: 2 / Fragment: fragment residues 1-202
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Gene: BUD23, YCR047C, YCR47C / Production host: Escherichia coli (E. coli)
References: UniProt: P25627, Transferases; Transferring one-carbon groups; Methyltransferases

-
Non-polymers , 4 types, 196 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2012
RadiationMonochromator: Channel cut cryogenically cooled monochromator crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.124→50 Å / Num. obs: 38373 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 37.1 Å2
Reflection shellResolution: 2.2→2.33 Å / % possible all: 94.7

-
Processing

Software
NameVersionClassification
XDSdata scaling
SHARPphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QTT

4qtt


Resolution: 2.124→38.307 Å / FOM work R set: 0.8226 / SU ML: 0.27 / σ(F): 1.99 / Phase error: 24.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2286 1917 5 %
Rwork0.178 --
obs0.1806 38373 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.94 Å2 / Biso mean: 44.88 Å2 / Biso min: 19.75 Å2
Refinement stepCycle: LAST / Resolution: 2.124→38.307 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4946 0 132 173 5251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085165
X-RAY DIFFRACTIONf_angle_d1.116963
X-RAY DIFFRACTIONf_chiral_restr0.046783
X-RAY DIFFRACTIONf_plane_restr0.005893
X-RAY DIFFRACTIONf_dihedral_angle_d15.531913
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1235-2.17660.33341230.26062338246190
2.1766-2.23550.33021390.251826352774100
2.2355-2.30120.31251310.26132526265798
2.3012-2.37550.27641390.212326372776100
2.3755-2.46040.29151370.197725972734100
2.4604-2.55890.26231380.198626242762100
2.5589-2.67530.231360.193525942730100
2.6753-2.81630.27141400.193826462786100
2.8163-2.99270.29061370.190726122749100
2.9927-3.22370.22251380.195426132751100
3.2237-3.54790.19541380.18182640277899
3.5479-4.06080.20191390.15772624276399
4.0608-5.11420.1991400.141526582798100
5.1142-38.31360.19711420.15782712285499

+
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