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- PDB-8ipi: The apo structure of human mitochondrial methyltransferase METTL15 -

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Basic information

Entry
Database: PDB / ID: 8ipi
TitleThe apo structure of human mitochondrial methyltransferase METTL15
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
12S rRNA N4-methylcytidine (m4C) methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,7691
Polymers37,7691
Non-polymers00
Water1,982110
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)70.607, 70.607, 136.063
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.55 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 10% PEG MME 2000, 0.2M Ammonium sulfate, 0.1 M sodium acetate (pH 5.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / 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: 2.1→31.34 Å / Num. obs: 23694 / % possible obs: 100 % / Redundancy: 17.9 % / Rmerge(I) obs: 0.148 / Net I/σ(I): 15.8
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1134

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHENIX3.3.22refinement
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→31.336 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2291 1134 4.8 %
Rwork0.1932 --
obs0.1949 23633 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→31.336 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2307 0 0 110 2417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072346
X-RAY DIFFRACTIONf_angle_d0.7933177
X-RAY DIFFRACTIONf_dihedral_angle_d2.9291424
X-RAY DIFFRACTIONf_chiral_restr0.045374
X-RAY DIFFRACTIONf_plane_restr0.005408
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.19380.25111080.2082789X-RAY DIFFRACTION100
2.1938-2.30940.29341350.24412758X-RAY DIFFRACTION100
2.3094-2.45410.25321380.19682779X-RAY DIFFRACTION100
2.4541-2.64350.20851530.19932769X-RAY DIFFRACTION100
2.6435-2.90930.2741530.20532778X-RAY DIFFRACTION100
2.9093-3.32990.25071480.20672817X-RAY DIFFRACTION100
3.3299-4.19370.23151230.1762862X-RAY DIFFRACTION100
4.1937-31.3360.18181760.17462947X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 26.4696 Å / Origin y: -26.3576 Å / Origin z: -7.8066 Å
111213212223313233
T0.1215 Å2-0.0392 Å20.0354 Å2-0.0908 Å2-0.0207 Å2--0.1046 Å2
L0.3882 °20.1679 °20.1162 °2-0.3029 °20.0378 °2--0.1765 °2
S0.0396 Å °0.0268 Å °0.0025 Å °0.0644 Å °-0.0748 Å °0.0434 Å °0.0085 Å °0.0391 Å °-0.0292 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 8 through 338)

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