[English] 日本語
Yorodumi
- PDB-6h2u: Crystal structure of human METTL5-TRMT112 complex, the 18S rRNA m... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6h2u
TitleCrystal structure of human METTL5-TRMT112 complex, the 18S rRNA m6A1832 methyltransferase at 1.6A resolution
Components
  • Methyltransferase-like protein 5
  • Multifunctional methyltransferase subunit TRM112-like protein
KeywordsTRANSFERASE / rRNA maturation / methyltransferase / translation / ribosome synthesis
Function / homology
Function and homology information


rRNA (adenine-N6-)-methyltransferase activity / peptidyl-glutamine methylation / rRNA (guanine-N7)-methylation / tRNA methyltransferase activator activity / tRNA modification in the nucleus and cytosol / Methylation / protein methyltransferase activity / tRNA methylation / positive regulation of rRNA processing / S-adenosyl-L-methionine binding ...rRNA (adenine-N6-)-methyltransferase activity / peptidyl-glutamine methylation / rRNA (guanine-N7)-methylation / tRNA methyltransferase activator activity / tRNA modification in the nucleus and cytosol / Methylation / protein methyltransferase activity / tRNA methylation / positive regulation of rRNA processing / S-adenosyl-L-methionine binding / rRNA modification in the nucleus and cytosol / rRNA methylation / Eukaryotic Translation Termination / transcription initiation-coupled chromatin remodeling / Transferases; Transferring one-carbon groups; Methyltransferases / positive regulation of translation / cell projection / stem cell differentiation / presynapse / transferase activity / postsynapse / nucleic acid binding / protein heterodimerization activity / perinuclear region of cytoplasm / protein-containing complex / nucleoplasm / nucleus / cytosol
Similarity search - Function
Multifunctional methyltransferase subunit Trm112 / Trm112-like / Trm112p-like protein / Methyltransferase small domain / Methyltransferase small domain / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / rRNA N6-adenosine-methyltransferase METTL5 / Multifunctional methyltransferase subunit TRM112-like protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
Authorsvan Tran, N. / Graille, M.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-14-CE09-0016 France
French National Research AgencyANR-16-CE11-0003 France
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: The human 18S rRNA m6A methyltransferase METTL5 is stabilized by TRMT112.
Authors: van Tran, N. / Ernst, F.G.M. / Hawley, B.R. / Zorbas, C. / Ulryck, N. / Hackert, P. / Bohnsack, K.E. / Bohnsack, M.T. / Jaffrey, S.R. / Graille, M. / Lafontaine, D.L.J.
History
DepositionJul 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Methyltransferase-like protein 5
B: Multifunctional methyltransferase subunit TRM112-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,93810
Polymers38,0372
Non-polymers9018
Water5,765320
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, SEC-MALLS experiments
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-18 kcal/mol
Surface area15020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.887, 70.634, 84.776
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein Methyltransferase-like protein 5


Mass: 24597.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METTL5, DC3, HSPC133 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NRN9, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Protein Multifunctional methyltransferase subunit TRM112-like protein / tRNA methyltransferase 112 homolog


Mass: 13439.646 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRMT112, AD-001, HSPC152, HSPC170 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UI30

-
Non-polymers , 4 types, 328 molecules

#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 25% PEG 4,000; 0.2 M ammonium sulfate; 100 mM Na citrate pH 5.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.6→47.24 Å / Num. obs: 45777 / % possible obs: 99.9 % / Redundancy: 6.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.03 / Rrim(I) all: 0.075 / Net I/σ(I): 14 / Num. measured all: 279014
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.887 / Num. unique obs: 2230 / CC1/2: 0.623 / Rpim(I) all: 0.406 / Rrim(I) all: 0.978 / % possible all: 99.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.1data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→35.317 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.36
RfactorNum. reflection% reflection
Rfree0.2148 2285 5 %
Rwork0.1857 --
obs0.1872 45704 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 71.32 Å2 / Biso mean: 25.8144 Å2 / Biso min: 9.38 Å2
Refinement stepCycle: final / Resolution: 1.6→35.317 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2549 0 57 320 2926
Biso mean--32.12 37.26 -
Num. residues----320
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9707-0.2496-0.21961.7234-0.06532.04380.03340.04650.1211-0.0401-0.0279-0.0287-0.2087-0.02130.00870.1193-0.01220.00480.09870.01780.092810.80299.49228.5138
22.4376-0.6790.20432.0874-0.37572.55290.0189-0.0883-0.12170.01420.02060.04980.08120.0027-0.00960.0972-0.02030.02310.0847-0.02040.151410.242-14.5685.5361
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 3 through 211)A3 - 211
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 118)B1 - 118

+
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