[English] 日本語
Yorodumi
- PDB-2vdu: Structure of trm8-trm82, THE YEAST TRNA m7G methylation complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2vdu
TitleStructure of trm8-trm82, THE YEAST TRNA m7G methylation complex
Components
  • TRNA (GUANINE-N(7)-)-METHYLTRANSFERASE
  • TRNA (GUANINE-N(7)-)-METHYLTRANSFERASE-ASSOCIATED WD REPEAT PROTEIN TRM82
KeywordsTRANSFERASE / S-ADENOSYL-L-METHIONINE / TRNA PROCESSING / PHOSPHORYLATION / METHYLTRANSFERASE / M7G / TRNA / SPOUT MT / WD REPEAT
Function / homology
Function and homology information


tRNA (m7G46) methyltransferase complex / tRNA (guanine-N7)-methylation / RNA (guanine-N7)-methylation / tRNA (guanine46-N7)-methyltransferase / tRNA (guanine(46)-N7)-methyltransferase activity / tRNA methyltransferase complex / tRNA methylation / tRNA modification / tRNA binding / nucleoplasm ...tRNA (m7G46) methyltransferase complex / tRNA (guanine-N7)-methylation / RNA (guanine-N7)-methylation / tRNA (guanine46-N7)-methyltransferase / tRNA (guanine(46)-N7)-methyltransferase activity / tRNA methyltransferase complex / tRNA methylation / tRNA modification / tRNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit / tRNA (guanine-N-7) methyltransferase catalytic subunit Trm8, eukaryote / SAM-dependent methyltransferase TRMB-type domain profile. / tRNA (guanine-N-7) methyltransferase, Trmb type / Putative methyltransferase / : / Vaccinia Virus protein VP39 / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats ...tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit / tRNA (guanine-N-7) methyltransferase catalytic subunit Trm8, eukaryote / SAM-dependent methyltransferase TRMB-type domain profile. / tRNA (guanine-N-7) methyltransferase, Trmb type / Putative methyltransferase / : / Vaccinia Virus protein VP39 / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit TRM82 / tRNA (guanine-N(7)-)-methyltransferase
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsLeulliot, N. / Chaillet, M. / Durand, D. / Ulryck, N. / Blondeau, K. / Van Tilbeurgh, H.
CitationJournal: Structure / Year: 2008
Title: Structure of the Yeast tRNA M7G Methylation Complex.
Authors: Leulliot, N. / Chaillet, M. / Durand, D. / Ulryck, N. / Blondeau, K. / Van Tilbeurgh, H.
History
DepositionOct 11, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: TRNA (GUANINE-N(7)-)-METHYLTRANSFERASE-ASSOCIATED WD REPEAT PROTEIN TRM82
D: TRNA (GUANINE-N(7)-)-METHYLTRANSFERASE-ASSOCIATED WD REPEAT PROTEIN TRM82
E: TRNA (GUANINE-N(7)-)-METHYLTRANSFERASE
F: TRNA (GUANINE-N(7)-)-METHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,5506
Polymers162,3604
Non-polymers1902
Water4,666259
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6430 Å2
ΔGint-49.4 kcal/mol
Surface area59830 Å2
MethodPQS
2
B: TRNA (GUANINE-N(7)-)-METHYLTRANSFERASE-ASSOCIATED WD REPEAT PROTEIN TRM82
E: TRNA (GUANINE-N(7)-)-METHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2753
Polymers81,1802
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-15.2 kcal/mol
Surface area30960 Å2
MethodPQS
3
D: TRNA (GUANINE-N(7)-)-METHYLTRANSFERASE-ASSOCIATED WD REPEAT PROTEIN TRM82
F: TRNA (GUANINE-N(7)-)-METHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2753
Polymers81,1802
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-15.6 kcal/mol
Surface area30930 Å2
MethodPQS
Unit cell
Length a, b, c (Å)53.376, 107.676, 127.749
Angle α, β, γ (deg.)90.00, 91.53, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein TRNA (GUANINE-N(7)-)-METHYLTRANSFERASE-ASSOCIATED WD REPEAT PROTEIN TRM82


Mass: 51383.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): GOLD (DE3) / References: UniProt: Q03774
#2: Protein TRNA (GUANINE-N(7)-)-METHYLTRANSFERASE / TRM8 / TRNA(M7G46)-METHYLTRANSFERASE


Mass: 29796.221 Da / Num. of mol.: 2 / Fragment: 46-END, RESIDUES 39-286
Source method: isolated from a genetically manipulated source
Details: 46 N-TERMNIAL TRUNCATION
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): GOLD (DE3)
References: UniProt: Q12009, tRNA (guanine46-N7)-methyltransferase
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL 46 RESIDUE TRUNCATION CTERM HIS TAG

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 45.56 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97953
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97953 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 26954 / % possible obs: 98.2 % / Observed criterion σ(I): 1.5 / Redundancy: 3.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.2
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.5 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.4→20 Å / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2764 --
Rwork0.228 --
obs-26954 99.1 %
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9302 0 10 259 9571

+
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