[English] 日本語
Yorodumi
- PDB-8ipk: The structure of human mitochondrial methyltransferase METTL15 wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ipk
TitleThe structure of human mitochondrial methyltransferase METTL15 with SAM
Components12S rRNA N4-methylcytidine (m4C) methyltransferase
KeywordsRIBOSOMAL PROTEIN / human mitochondrial methyltransferase METTL15
Function / homology
Function and homology information


rRNA (cytosine-N4-)-methyltransferase activity / rRNA base methylation / Transferases; Transferring one-carbon groups; Methyltransferases / mitochondrial matrix / mitochondrion
Similarity search - Function
Ribosomal RNA small subunit methyltransferase H / S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily / MraW methylase family / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / 12S rRNA N(4)-cytidine methyltransferase METTL15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLv, M.Q. / Zhou, W.W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32293213, 32100958, 32090042 and 31870760 China
CitationJournal: Cell Discov / Year: 2024
Title: Structural insights into the specific recognition of mitochondrial ribosome-binding factor hsRBFA and 12 S rRNA by methyltransferase METTL15.
Authors: Lv, M. / Zhou, W. / Hao, Y. / Li, F. / Zhang, H. / Yao, X. / Shi, Y. / Zhang, L.
History
DepositionMar 14, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 3, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 12S rRNA N4-methylcytidine (m4C) methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5356
Polymers37,7691
Non-polymers7675
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.506, 70.506, 134.674
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein 12S rRNA N4-methylcytidine (m4C) methyltransferase / 12S rRNA m4C methyltransferase / Methyltransferase 5 domain-containing protein 1 / ...12S rRNA m4C methyltransferase / Methyltransferase 5 domain-containing protein 1 / Methyltransferase-like protein 15


Mass: 37768.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METTL15, METT5D1 / Production host: Escherichia coli (E. coli)
References: UniProt: A6NJ78, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.92 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 42% PEG 600, 0.2 M imidazole malate, pH 5.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→25.25 Å / Num. obs: 31270 / % possible obs: 99.9 % / Redundancy: 15 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 23.2
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 1.003 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1647

-
Processing

Software
NameVersionClassification
SCALAdata scaling
PHENIX3.3.22refinement
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→25.245 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2207 1647 5.27 %
Rwork0.1823 --
obs0.1842 31223 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→25.245 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2384 0 51 99 2534
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062474
X-RAY DIFFRACTIONf_angle_d0.7843337
X-RAY DIFFRACTIONf_dihedral_angle_d8.5581507
X-RAY DIFFRACTIONf_chiral_restr0.047385
X-RAY DIFFRACTIONf_plane_restr0.004421
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9003-1.95620.30781560.25082405X-RAY DIFFRACTION100
1.9562-2.01930.26051420.20282407X-RAY DIFFRACTION100
2.0193-2.09150.22571370.20432422X-RAY DIFFRACTION100
2.0915-2.17520.24951400.1992426X-RAY DIFFRACTION100
2.1752-2.27410.23081240.1912474X-RAY DIFFRACTION100
2.2741-2.39390.22371470.18642402X-RAY DIFFRACTION100
2.3939-2.54380.24341390.18912450X-RAY DIFFRACTION100
2.5438-2.740.21921340.19382471X-RAY DIFFRACTION100
2.74-3.01530.21371460.1992433X-RAY DIFFRACTION100
3.0153-3.45070.23411210.1892520X-RAY DIFFRACTION100
3.4507-4.34390.19011270.15552535X-RAY DIFFRACTION100
4.3439-25.2450.20611340.16912631X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -34.5896 Å / Origin y: 10.3295 Å / Origin z: 14.9396 Å
111213212223313233
T0.1904 Å20.0256 Å20.0088 Å2-0.1095 Å2-0.0093 Å2--0.1686 Å2
L1.3005 °2-0.0327 °2-0.4775 °2-1.8618 °2-0.3918 °2--1.5102 °2
S-0.0517 Å °0.0014 Å °-0.0057 Å °0.0668 Å °0.0447 Å °0.0567 Å °-0.076 Å °0.0051 Å °0.0069 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 5 through 338)

+
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