[English] 日本語
Yorodumi
- PDB-7cva: RNA methyltransferase METTL4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7cva
TitleRNA methyltransferase METTL4
ComponentsMethyltransferase-like protein 2
KeywordsNUCLEAR PROTEIN / RNA methyltransferase
Function / homology
Function and homology information


nucleic acid metabolic process / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation / nucleic acid binding
Similarity search - Function
MT-A70-like / MT-A70 / MT-A70-like family profile. / 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
Methyltransferase-like protein 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsLuo, Q. / Ma, J.
CitationJournal: Nat Commun / Year: 2022
Title: Structural insights into molecular mechanism for N6-adenosine methylation by MT-A70 family methyltransferase METTL4
Authors: Luo, Q. / Mo, J. / Chen, H. / Hu, Z. / Wang, B. / Wu, J. / Liang, Z. / Xie, W. / Du, K. / Peng, M. / Li, Y. / Li, T. / Zhang, Y. / Shi, X. / Shen, W.H. / Shi, Y. / Dong, A. / Wang, H. / Ma, J.
History
DepositionAug 25, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Methyltransferase-like protein 2
B: Methyltransferase-like protein 2


Theoretical massNumber of molelcules
Total (without water)96,4732
Polymers96,4732
Non-polymers00
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-7 kcal/mol
Surface area31420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.812, 94.323, 95.769
Angle α, β, γ (deg.)90.000, 101.750, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 2 through 3 and (name N...
21(chain B and (resid 2 through 91 or (resid 92...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and ((resid 2 through 3 and (name N...A2 - 3
121(chain A and ((resid 2 through 3 and (name N...A2 - 413
131(chain A and ((resid 2 through 3 and (name N...A2 - 413
141(chain A and ((resid 2 through 3 and (name N...A2 - 413
151(chain A and ((resid 2 through 3 and (name N...A2 - 413
211(chain B and (resid 2 through 91 or (resid 92...B2 - 91
221(chain B and (resid 2 through 91 or (resid 92...B92
231(chain B and (resid 2 through 91 or (resid 92...B2 - 414
241(chain B and (resid 2 through 91 or (resid 92...B2 - 414
251(chain B and (resid 2 through 91 or (resid 92...B2 - 414
261(chain B and (resid 2 through 91 or (resid 92...B2 - 414

-
Components

#1: Protein Methyltransferase-like protein 2


Mass: 48236.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g19340, F18O14.6 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q8LFA9, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M tacsimate pH 5.5 and 8% PEG3350

-
Data collection

DiffractionMean temperature: 291 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 65279 / % possible obs: 98.2 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.065 / Rrim(I) all: 0.148 / Χ2: 5.404 / Net I/σ(I): 12.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.593.30.41334210.6980.2580.4913.51393.7
2.59-2.693.90.31235650.7690.1720.3591.31797.2
2.69-2.824.10.30135710.7020.1620.3442.05697.6
2.82-2.964.50.22836000.9360.1130.2552.11398.7
2.96-3.154.90.19536420.9640.0940.2172.5999.5
3.15-3.3950.19336350.9290.0960.2164.26598.6
3.39-3.735.60.13936500.9830.0640.1534.65199.4
3.73-4.275.50.11636540.9860.0540.1297.01199.4
4.27-5.385.50.10336780.9880.0490.1149.16599.2
5.38-305.40.10137110.9870.0480.11212.44598.8

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC7.0.076refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
REFMACphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→29.668 Å / SU ML: 0.57 / Cross valid method: THROUGHOUT / σ(F): 1.52 / Phase error: 31.7 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.265 2541 3.89 %
Rwork0.2264 --
obs0.2279 65279 90.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 156.49 Å2 / Biso mean: 50.1888 Å2 / Biso min: 10.38 Å2
Refinement stepCycle: final / Resolution: 2.5→29.668 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5326 0 0 11 5337
Biso mean---29.51 -
Num. residues----674
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2646X-RAY DIFFRACTION13.468TORSIONAL
12B2646X-RAY DIFFRACTION13.468TORSIONAL
Refinement TLS params.Method: refined / Origin x: -16.4904 Å / Origin y: 0.64 Å / Origin z: -17.2147 Å
111213212223313233
T0.0256 Å20.0117 Å20.0319 Å2-0.0976 Å2-0.006 Å2--0.1009 Å2
L0.1515 °20.0311 °20.1488 °2-0.8611 °2-0.2751 °2--0.7707 °2
S0.0515 Å °0.0219 Å °-0.0174 Å °0.023 Å °-0.0437 Å °-0.0004 Å °-0.0469 Å °0.0555 Å °-0.0008 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 413
2X-RAY DIFFRACTION1allB2 - 414
3X-RAY DIFFRACTION1allC1 - 11

+
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