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- PDB-9m86: Crystal structure of SpMETTL16 kinase associated 1 domain in comp... -

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Basic information

Entry
Database: PDB / ID: 9m86
TitleCrystal structure of SpMETTL16 kinase associated 1 domain in complex with U6 snRNA internal stem loop
Components
  • RNA (31-MER)
  • U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase
KeywordsTRANSFERASE/RNA / m6A methyltransferase / U6 snRNA / protein-RNA complex / splicing / TRANSFERASE / TRANSFERASE-RNA complex
Function / homology
Function and homology information


snRNA (adenine-N6)-methylation / U6 snRNA m6A methyltransferase / U6 snRNA (adenine-(43)-N(6))-methyltransferase activity / rRNA base methylation / mRNA splicing, via spliceosome / nucleus / cytosol
Similarity search - Function
Methyltransferase METTL16/PsiM / RNA methyltransferase / METTL16/RlmF family / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.795 Å
AuthorsJu, J. / Tomita, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23H00368 Japan
CitationJournal: Nat Commun / Year: 2025
Title: Structures and mechanisms of U6 snRNA mA modification by METTL16.
Authors: Jue Ju / Kozo Tomita /
Abstract: The N-methyladenosine (mA) modification in U6 snRNA, catalyzed by METTL16 using S-adenosylmethionine (SAM) as the methyl donor, is required for efficient and accurate pre-mRNA splicing. However, the ...The N-methyladenosine (mA) modification in U6 snRNA, catalyzed by METTL16 using S-adenosylmethionine (SAM) as the methyl donor, is required for efficient and accurate pre-mRNA splicing. However, the mechanism by which METTL16 modifies U6 snRNA with mA remains elusive. Here, we present cryo-EM structures of METTL16 in complex with U6 snRNA, providing insights into the METTL16-mediated modification of U6 snRNA with mA. The structures reveal that U6 snRNA is recruited to METTL16 through specific interactions between the C-terminal kinase-associated 1 (KA-1) domain of METTL16 and the internal stem-loop (ISL) of U6 snRNA. Upon SAM binding to the catalytic pocket within the N-terminal methyltransferase domain (MTD), U6 snRNA undergoes a structural rearrangement that positions the target adenine-containing motif at the catalytic site. This conformational change is followed by an additional structural adjustment of U6 snRNA into a productive conformation, bringing the target adenosine closer to SAM within the catalytic pocket and thereby ensuring efficient mA modification. The KA-1 domain functions as a scaffold for initial substrate recognition and facilitates the subsequent dynamic methylation process within the MTD, highlighting the cooperative roles of METTL16 domains for U6 snRNA modification.
History
DepositionMar 11, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2025Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase
B: RNA (31-MER)
C: U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase
D: RNA (31-MER)


Theoretical massNumber of molelcules
Total (without water)50,1404
Polymers50,1404
Non-polymers00
Water00
1
A: U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase
B: RNA (31-MER)


Theoretical massNumber of molelcules
Total (without water)25,0702
Polymers25,0702
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-15 kcal/mol
Surface area12180 Å2
MethodPISA
2
C: U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase
D: RNA (31-MER)


Theoretical massNumber of molelcules
Total (without water)25,0702
Polymers25,0702
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-14 kcal/mol
Surface area12340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.135, 47.136, 61.831
Angle α, β, γ (deg.)87.53, 88.35, 62.87
Int Tables number1
Space group name H-MP1

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Components

#1: Protein U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase


Mass: 15097.939 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: SPAC27D7.08c / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta2 / References: UniProt: O42662, U6 snRNA m6A methyltransferase
#2: RNA chain RNA (31-MER)


Mass: 9972.022 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: U6 small nuclear RNA / Source: (synth.) Schizosaccharomyces pombe (fission yeast)
Has ligand of interestN
Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: sodium acetate, sodium cacodylate pH 7.0, Tris-HCl pH 8.5, PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.978 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 11, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.79→50 Å / Num. obs: 10820 / % possible obs: 98.7 % / Redundancy: 8.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.168 / Rrim(I) all: 0.179 / Net I/σ(I): 12.94
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.79-2.870.7127720.8190.7561
2.87-2.940.6538090.8990.6911
2.94-3.030.5017240.9650.5311
3.03-3.120.337590.9910.351
3.12-3.230.2976830.9910.3161
3.23-3.340.2827040.9830.3011
3.34-3.460.266660.9840.2781
3.46-3.610.2396560.9890.2551
3.61-3.770.195970.9950.2021
3.77-3.950.196130.9920.2011
3.95-4.160.1735330.9940.1831
4.16-4.420.1625580.9940.1721
4.42-4.720.1295000.9930.1371
4.72-5.10.1124510.9930.121
5.1-5.590.1114420.9950.1181
5.59-6.250.1123780.9950.1191
6.25-7.210.1023420.9950.1091
7.21-8.830.0792930.9960.0841
8.83-12.490.062190.9980.0651
12.49-500.0621210.9940.0671

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACT4.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.795→33.49 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 2.05 / Phase error: 28.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.26 542 5.02 %
Rwork0.2059 --
obs0.2086 10788 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.795→33.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1918 1320 0 0 3238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063430
X-RAY DIFFRACTIONf_angle_d0.8244932
X-RAY DIFFRACTIONf_dihedral_angle_d18.3681478
X-RAY DIFFRACTIONf_chiral_restr0.046598
X-RAY DIFFRACTIONf_plane_restr0.005392
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.795-3.07570.32641340.26592514X-RAY DIFFRACTION98
3.0757-3.52030.27561360.22712567X-RAY DIFFRACTION98
3.5203-4.43360.251360.19732589X-RAY DIFFRACTION99
4.4336-33.490.23941360.18442576X-RAY DIFFRACTION99

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