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

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Basic information

Entry
Database: PDB / ID: 8ipl
TitleThe structure of human mitochondrial methyltransferase METTL15 with RBFA and SAM
Components
  • 12S rRNA N4-methylcytidine (m4C) methyltransferase
  • Putative ribosome-binding factor A, mitochondrial
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
S-ADENOSYLMETHIONINE / 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: 2.2 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
B: Putative ribosome-binding factor A, mitochondrial
A: 12S rRNA N4-methylcytidine (m4C) methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9823
Polymers41,5842
Non-polymers3981
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-12 kcal/mol
Surface area14000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.167, 70.978, 75.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
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: 2.05 Å3/Da / Density % sol: 39.9 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 17% w/v PEG 4000, 0.05M Potassium chloride, 0.1M Lithium chloride, 0.012M Spermine tetrahydrochloride, 0.05M MES PH6.5

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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: Oct 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→33.48 Å / Num. obs: 16587 / % possible obs: 92.61 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 16.5
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 6.2 / Num. unique obs: 789

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX3.3.22refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→33.477 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2346 789 4.76 %
Rwork0.1799 --
obs0.1825 16580 92.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→33.477 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2342 0 27 32 2401
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082409
X-RAY DIFFRACTIONf_angle_d0.9793258
X-RAY DIFFRACTIONf_dihedral_angle_d9.6391465
X-RAY DIFFRACTIONf_chiral_restr0.064379
X-RAY DIFFRACTIONf_plane_restr0.005415
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.33790.25411440.18952721X-RAY DIFFRACTION98
2.3379-2.51830.2781360.19192730X-RAY DIFFRACTION98
2.5183-2.77160.26351030.1972082X-RAY DIFFRACTION74
2.7716-3.17240.2361390.19962787X-RAY DIFFRACTION99
3.1724-3.99590.29021080.17532521X-RAY DIFFRACTION88
3.9959-33.4770.18341590.16382950X-RAY DIFFRACTION99
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)
12.6691-0.2742-0.17424.54521.12333.2608-0.14420.1104-0.251-0.16070.18160.26840.2061-0.342-0.03560.2394-0.0309-0.0720.2897-0.00830.3427-12.7319-5.5212-2.7049
20.81110.24760.0981.09110.29450.8298-0.04570.0825-0.007-0.04440.05120.0258-0.02910.078-0.00310.1688-0.0069-0.00070.1881-0.00890.20570.89234.581810.0533
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'B' and resid 1 through 22)
2X-RAY DIFFRACTION2(chain 'A' and resid 6 through 338)

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