[English] 日本語
Yorodumi
- PDB-5erg: Crystal structure of the two-subunit tRNA m1A58 methyltransferase... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5erg
TitleCrystal structure of the two-subunit tRNA m1A58 methyltransferase TRM6-TRM61 in complex with SAM
Components
  • tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRM61
  • tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6
KeywordsTRANSFERASE / tRNA / complex / SAM / methylation
Function / homology
Function and homology information


tRNA (adenine58-N1)-methyltransferase / tRNA (m1A) methyltransferase complex / tRNA (adenine(58)-N1)-methyltransferase activity / tRNA methylation / RNA binding / nucleus
Similarity search - Function
tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6 / Gcd10p family / Vcp-like ATPase; Chain A, domain 2 - #20 / tRNA (1-methyladenosine) methyltransferase catalytic subunit Gcd14 / : / tRNA methyltransferase complex GCD14 subunit / tRNA (adenine(57)-N(1)/adenine(58)-N(1) or adenine(58)-N(1)) (EC 2.1.1.219 or EC 2.1.1.220) family profile. / Vcp-like ATPase; Chain A, domain 2 / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily ...tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6 / Gcd10p family / Vcp-like ATPase; Chain A, domain 2 - #20 / tRNA (1-methyladenosine) methyltransferase catalytic subunit Gcd14 / : / tRNA methyltransferase complex GCD14 subunit / tRNA (adenine(57)-N(1)/adenine(58)-N(1) or adenine(58)-N(1)) (EC 2.1.1.219 or EC 2.1.1.220) family profile. / Vcp-like ATPase; Chain A, domain 2 / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6 / tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRM61
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.202 Å
AuthorsZhu, Y. / Wang, M. / Wang, C. / Fan, X. / Jiang, X. / Teng, M. / Li, X.
CitationJournal: Sci Rep / Year: 2016
Title: Crystal structure of the two-subunit tRNA m(1)A58 methyltransferase TRM6-TRM61 from Saccharomyces cerevisiae.
Authors: Wang, M. / Zhu, Y. / Wang, C. / Fan, X. / Jiang, X. / Ebrahimi, M. / Qiao, Z. / Niu, L. / Teng, M. / Li, X.
History
DepositionNov 14, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6
B: tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRM61
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,1073
Polymers99,7082
Non-polymers3981
Water3,585199
1
A: tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6
B: tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRM61
hetero molecules

A: tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6
B: tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRM61
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,2136
Polymers199,4164
Non-polymers7972
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-2/31
Buried area19010 Å2
ΔGint-71 kcal/mol
Surface area56070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.916, 139.916, 103.472
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6 / General control non-derepressible protein 10 / Protein GCD10 / tRNA(m1A58)-methyltransferase ...General control non-derepressible protein 10 / Protein GCD10 / tRNA(m1A58)-methyltransferase subunit TRM6 / tRNA(m1A58)MTase subunit TRM6


Mass: 55720.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: GCD10, TIF33, TRM6, YNL062C, N2422 / Production host: Escherichia coli (E. coli) / References: UniProt: P41814
#2: Protein tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRM61 / General control non-derepressible protein 14 / Protein GCD14 / tRNA(m1A58)-methyltransferase ...General control non-derepressible protein 14 / Protein GCD14 / tRNA(m1A58)-methyltransferase subunit TRM61 / tRNA(m1A58)MTase subunit TRM61


Mass: 43987.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: GCD14, TRM61, YJL125C, J0710 / Production host: Escherichia coli (E. coli)
References: UniProt: P46959, tRNA (adenine58-N1)-methyltransferase
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES, PH 7.5, 2% v/v(+/-)-2-Methyl-2,4-pentanediol, 10% w/v Polyethylene glycol 6000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.9785 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 59358 / % possible obs: 99.9 % / Redundancy: 7.7 % / Net I/σ(I): 21.6
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 7.9 % / Mean I/σ(I) obs: 2.4 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
SCALAdata scaling
AutoSolphasing
RefinementResolution: 2.202→47.58 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2136 2912 4.91 %
Rwork0.1842 --
obs0.1856 59326 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.202→47.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5266 0 27 199 5492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095483
X-RAY DIFFRACTIONf_angle_d1.127416
X-RAY DIFFRACTIONf_dihedral_angle_d15.3092025
X-RAY DIFFRACTIONf_chiral_restr0.053815
X-RAY DIFFRACTIONf_plane_restr0.005942
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2017-2.23770.25511090.28012679X-RAY DIFFRACTION100
2.2377-2.27630.38121510.30252631X-RAY DIFFRACTION100
2.2763-2.31770.29941490.25092660X-RAY DIFFRACTION100
2.3177-2.36230.26361540.22512646X-RAY DIFFRACTION100
2.3623-2.41050.28091670.22192638X-RAY DIFFRACTION100
2.4105-2.46290.22291160.21342663X-RAY DIFFRACTION100
2.4629-2.52020.26671210.20752685X-RAY DIFFRACTION100
2.5202-2.58320.23431580.20452658X-RAY DIFFRACTION100
2.5832-2.65310.2331430.20222657X-RAY DIFFRACTION100
2.6531-2.73110.2591560.20292646X-RAY DIFFRACTION100
2.7311-2.81930.22791240.20462682X-RAY DIFFRACTION100
2.8193-2.920.2421380.19932677X-RAY DIFFRACTION100
2.92-3.03690.26551270.20522707X-RAY DIFFRACTION100
3.0369-3.17510.23681230.19272697X-RAY DIFFRACTION100
3.1751-3.34250.24971610.19822677X-RAY DIFFRACTION100
3.3425-3.55180.21421190.18142704X-RAY DIFFRACTION100
3.5518-3.8260.20241560.17732671X-RAY DIFFRACTION100
3.826-4.21080.18311450.1572695X-RAY DIFFRACTION100
4.2108-4.81960.16861430.13952735X-RAY DIFFRACTION100
4.8196-6.07020.18781270.16972758X-RAY DIFFRACTION100
6.0702-47.59160.17251250.17662848X-RAY DIFFRACTION99

+
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