[English] 日本語
Yorodumi
- PDB-8gu3: Crystal structure of Caenorhabditis elegans METT-10 methyltransfe... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8gu3
TitleCrystal structure of Caenorhabditis elegans METT-10 methyltransferase domain
ComponentsU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase
KeywordsTRANSFERASE / SAM homeostasis / U6 snRNA
Function / homology
Function and homology information


U6 snRNA m6A methyltransferase / U6 snRNA (adenine-(43)-N(6))-methyltransferase activity / vulval development / 23S rRNA (adenine(1618)-N(6))-methyltransferase activity / mRNA m6A methyltransferase / mRNA m(6)A methyltransferase activity / rRNA base methylation / centrosome cycle / embryo development ending in birth or egg hatching / post-transcriptional regulation of gene expression ...U6 snRNA m6A methyltransferase / U6 snRNA (adenine-(43)-N(6))-methyltransferase activity / vulval development / 23S rRNA (adenine(1618)-N(6))-methyltransferase activity / mRNA m6A methyltransferase / mRNA m(6)A methyltransferase activity / rRNA base methylation / centrosome cycle / embryo development ending in birth or egg hatching / post-transcriptional regulation of gene expression / negative regulation of mRNA splicing, via spliceosome / meiotic cell cycle / cell division / nucleus
Similarity search - Function
Methyltransferase METTL16/PsiM / RNA methyltransferase / METTL16/RlmF family / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsJu, J. / Tomita, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H03980 Japan
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Structure of the Caenorhabditis elegans m6A methyltransferase METT10 that regulates SAM homeostasis.
Authors: Ju, J. / Aoyama, T. / Yashiro, Y. / Yamashita, S. / Kuroyanagi, H. / Tomita, K.
History
DepositionSep 9, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase


Theoretical massNumber of molelcules
Total (without water)36,5051
Polymers36,5051
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12690 Å2
Unit cell
Length a, b, c (Å)43.210, 70.080, 94.230
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / N6-adenosine-methyltransferase mett-10


Mass: 36504.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: mett-10 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q09357, U6 snRNA m6A methyltransferase

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 37.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: ammonium acetate, Tris-HCl pH8.5, PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.01→47.12 Å / Num. obs: 6086 / % possible obs: 99.9 % / Redundancy: 12.545 % / Biso Wilson estimate: 83.35 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Rrim(I) all: 0.117 / Χ2: 0.899 / Net I/σ(I): 17.92 / Num. measured all: 76348
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.01-3.0812.3771.3411.5955454524480.6911.39899.1
3.08-3.1713.8051.0772.2658674254250.8141.119100
3.17-3.2613.4670.7633.3155624134130.9120.793100
3.26-3.3613.3580.6933.8455574164160.9210.72100
3.36-3.4713.1840.4676.1150763853850.9660.486100
3.47-3.5913.0470.4036.8249973833830.9770.42100
3.59-3.7312.6230.3039.4946583693690.9870.316100
3.73-3.8812.4970.21113.1343743503500.9910.221100
3.88-4.0511.2190.15717.0738373433420.9930.16599.7
4.05-4.2510.6680.12421.1734353223220.9940.13100
4.25-4.4810.9810.09624.4635253213210.9970.101100
4.48-4.7512.3670.0863237103003000.9980.09100
4.75-5.0813.370.07934.5636502732730.9970.082100
5.08-5.4913.130.08529.4736242762760.9990.088100
5.49-6.0113.2270.07332.5831482382380.9980.076100
6.01-6.7212.8020.0735.5528422222220.9980.073100
6.72-7.7612.4980.05242.6825372032030.9990.054100
7.76-9.511.8910.0448.6120691741740.9990.042100
9.5-13.4411.1250.03550.6216021441440.9990.036100
13.44-47.128.9390.03444.1773385820.9990.03696.5

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6B91

6b91


Resolution: 3.01→47.12 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2975 305 5.01 %
Rwork0.2414 5780 -
obs0.2438 6085 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 256.44 Å2 / Biso mean: 103.7401 Å2 / Biso min: 47.1 Å2
Refinement stepCycle: final / Resolution: 3.01→47.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2039 0 0 0 2039
Num. residues----256
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.01-3.790.34051490.268828312980
3.79-47.120.28561560.233229493105
Refinement TLS params.Method: refined / Origin x: -23.7015 Å / Origin y: -0.421 Å / Origin z: -9.7799 Å
111213212223313233
T0.5512 Å20.172 Å20.1763 Å2-0.6411 Å2-0.0107 Å2--0.7041 Å2
L2.3797 °2-1.4799 °21.9121 °2-8.7535 °2-4.9607 °2--5.3709 °2
S-0.3086 Å °-0.5257 Å °0.0505 Å °0.8014 Å °0.8218 Å °0.1623 Å °-1.1309 Å °-0.6587 Å °-0.3372 Å °
Refinement TLS groupSelection details: all

+
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://pdbjlvh1.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