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- PDB-8ipm: The structure of human mitochondrial methyltransferase METTL15 wi... -

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Basic information

Entry
Database: PDB / ID: 8ipm
TitleThe structure of human mitochondrial methyltransferase METTL15 with h44_RNA, RBFA and SAM
Components
  • 12S rRNA N4-methylcytidine (m4C) methyltransferase
  • Putative ribosome-binding factor A, mitochondrial
  • RNA (5'-R(*CP*GP*AP*CP*CP*GP*CP*CP*CP*GP*UP*AP*AP*CP*GP*GP*UP*CP*G)-3')
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 / rRNA processing / 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 / Putative ribosome-binding factor A, mitochondrial / Ribosome-binding factor A, conserved site / Ribosome-binding factor A signature. / Ribosome-binding factor A / Ribosome-binding factor A domain superfamily / Ribosome-binding factor A / K homology domain-like, alpha/beta / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
SINEFUNGIN / RNA / RNA (> 10) / 12S rRNA N(4)-cytidine methyltransferase METTL15 / Putative ribosome-binding factor A, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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
C: Putative ribosome-binding factor A, mitochondrial
D: 12S rRNA N4-methylcytidine (m4C) methyltransferase
A: RNA (5'-R(*CP*GP*AP*CP*CP*GP*CP*CP*CP*GP*UP*AP*AP*CP*GP*GP*UP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0334
Polymers47,6523
Non-polymers3811
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-20 kcal/mol
Surface area16870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.220, 134.111, 93.026
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein/peptide Putative ribosome-binding factor A, mitochondrial


Mass: 3815.315 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBFA, C18orf22 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N0V3
#2: 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
#3: RNA chain RNA (5'-R(*CP*GP*AP*CP*CP*GP*CP*CP*CP*GP*UP*AP*AP*CP*GP*GP*UP*CP*G)-3')


Mass: 6067.681 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N7O5 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.33 Å3/Da / Density % sol: 47.23 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 4000, 0.2 M ADA (pH 6.4)

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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: Dec 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.1→33.53 Å / Num. obs: 8176 / % possible obs: 97.42 % / Redundancy: 9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.105 / Net I/σ(I): 14.7
Reflection shellResolution: 3.1→3.21 Å / Rmerge(I) obs: 0.616 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 888

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
SCALAdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→33.528 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2878 888 10.86 %
Rwork0.2525 --
obs0.2564 8176 97.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→33.528 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2264 296 27 0 2587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022659
X-RAY DIFFRACTIONf_angle_d0.5373666
X-RAY DIFFRACTIONf_dihedral_angle_d8.9321574
X-RAY DIFFRACTIONf_chiral_restr0.035442
X-RAY DIFFRACTIONf_plane_restr0.003416
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1001-3.29410.40581540.381201X-RAY DIFFRACTION99
3.2941-3.54820.41221420.33841227X-RAY DIFFRACTION100
3.5482-3.90480.3261400.28471048X-RAY DIFFRACTION87
3.9048-4.46870.30441380.2351261X-RAY DIFFRACTION100
4.4687-5.62580.28881520.22991238X-RAY DIFFRACTION100
5.6258-33.5280.22361620.22141313X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.5889-2.4859-1.15796.44920.65755.9745-0.3745-0.5818-0.50051.25290.735-0.2292-0.34130.5375-0.08230.90990.001-0.0370.84260.03350.640630.90327.2935-0.825
22.3754-0.1925-0.38542.63430.99991.191-0.0683-0.273-0.1011-0.39170.2027-0.00060.00480.2239-0.18080.5601-0.0153-0.01740.5276-0.03740.402220.848125.8799-5.3322
32.58320.19911.75750.0542-0.16213.22510.1814-0.9406-1.08760.62520.33390.54681.7111-0.2527-0.46281.4282-0.15040.03241.3091-0.23951.8970.99251.5595-13.2596
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'C' and resid 2 through 22)
2X-RAY DIFFRACTION2(chain 'D' and resid 7 through 338)
3X-RAY DIFFRACTION3(chain 'A' and resid 2 through 15)

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