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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7dpe
TitleRNA methyltransferase METTL4
Components
  • DNA (5'-D(*GP*CP*CP*GP*CP*GP*TP*GP*AP*TP*CP*AP*CP*GP*CP*GP*GP*C)-3')
  • Methyltransferase-like protein 2
KeywordsTRANSFERASE/DNA / Methyltransferase / TRANSFERASE-DNA complex
Function / homology
Function and homology information


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
S-ADENOSYL-L-HOMOCYSTEINE / DNA / DNA (> 10) / Methyltransferase-like protein 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.751 Å
AuthorsLuo, Q. / Ma, J.B.
CitationJournal: To Be Published
Title: Structure of RNA m6A methyltransferase METTL4 in complex with DNA at 2.75 Angstroms resolutioon
Authors: Luo, Q. / Ma, J.B.
History
DepositionDec 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: DNA (5'-D(*GP*CP*CP*GP*CP*GP*TP*GP*AP*TP*CP*AP*CP*GP*CP*GP*GP*C)-3')
A: Methyltransferase-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2267
Polymers53,4742
Non-polymers7535
Water75742
1
A: Methyltransferase-like protein 2
hetero molecules

A: Methyltransferase-like protein 2
hetero molecules

B: DNA (5'-D(*GP*CP*CP*GP*CP*GP*TP*GP*AP*TP*CP*AP*CP*GP*CP*GP*GP*C)-3')

B: DNA (5'-D(*GP*CP*CP*GP*CP*GP*TP*GP*AP*TP*CP*AP*CP*GP*CP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)108,45314
Polymers106,9474
Non-polymers1,50610
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation2_557-x,y,-z+21
Buried area5640 Å2
ΔGint-15 kcal/mol
Surface area38610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.655, 93.494, 70.885
Angle α, β, γ (deg.)90.000, 107.190, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: DNA chain DNA (5'-D(*GP*CP*CP*GP*CP*GP*TP*GP*AP*TP*CP*AP*CP*GP*CP*GP*GP*C)-3')


Mass: 5518.555 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)
#2: Protein Methyltransferase-like protein 2


Mass: 47955.102 Da / Num. of mol.: 1
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)
References: UniProt: Q8LFA9, Transferases; Transferring one-carbon groups; Methyltransferases
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.68 Å3/Da / Density % sol: 54.16 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M sodium malonate pH5.0 and 12% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97776 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 2.75→30 Å / Num. obs: 14645 / % possible obs: 99.4 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.032 / Rrim(I) all: 0.081 / Χ2: 0.492 / Net I/σ(I): 5 / Num. measured all: 81664
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.75-2.853.80.31714380.7970.1730.3630.30397.2
2.85-2.964.50.28114340.9190.1410.3160.34398.4
2.96-3.150.22114640.9610.1050.2450.37399.5
3.1-3.265.30.14214590.9930.0640.1560.4399.9
3.26-3.465.60.11114580.9930.0490.1220.46499.8
3.46-3.735.60.09814690.9910.0440.1080.49499.4
3.73-4.116.30.08114630.9940.0340.0880.53499.7
4.11-4.76.60.06714740.9960.0270.0720.56499.9
4.7-5.916.20.06314850.9960.0270.0680.54799.8
5.91-306.60.05815010.9980.0240.0630.66100

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMACv1.0refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
REFMACphasing
RefinementMethod to determine structure: SAD / Resolution: 2.751→29.324 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.45 / Phase error: 26.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2616 757 5.17 %
Rwork0.2103 --
obs0.213 14631 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 216.66 Å2 / Biso mean: 95.1262 Å2 / Biso min: 29.17 Å2
Refinement stepCycle: final / Resolution: 2.751→29.324 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2778 365 50 42 3235
Biso mean--69.19 79.26 -
Num. residues----354
Refinement TLS params.Method: refined / Origin x: -2.775 Å / Origin y: 12.299 Å / Origin z: 83.38 Å
111213212223313233
T0.6174 Å2-0.0351 Å2-0.1624 Å2-0.5701 Å20.0818 Å2--0.5021 Å2
L2.4606 °2-0.5137 °2-0.7657 °2-1.9308 °2-0.2368 °2--2.7843 °2
S0.0009 Å °-0.6409 Å °-0.3038 Å °0.7407 Å °-0.068 Å °-0.8289 Å °0.0282 Å °0.1429 Å °0.1035 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1 - 18
2X-RAY DIFFRACTION1A3 - 411
3X-RAY DIFFRACTION1A501
4X-RAY DIFFRACTION1A502
5X-RAY DIFFRACTION1A503
6X-RAY DIFFRACTION1A504
7X-RAY DIFFRACTION1A505
8X-RAY DIFFRACTION1A601 - 632
9X-RAY DIFFRACTION1B101 - 110

+
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