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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: To Be Published
Title: Structures and mechanisms of U6 snRNA m6A modification by METTL16
Authors: Ju, J. / Tomita, K.
History
DepositionMar 11, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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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