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- PDB-9ohl: TRMT112-METTL5 bound to SAM and FWG-33B -

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Basic information

Entry
Database: PDB / ID: 9ohl
TitleTRMT112-METTL5 bound to SAM and FWG-33B
Components
  • Multifunctional methyltransferase subunit TRM112-like protein
  • rRNA N(6)-adenosine-methyltransferase METTL5
KeywordsTRANSFERASE / tRNA methyltransferase 112 homolog / Methyltransferase-like protein 5 / stereoselective probe
Function / homology
Function and homology information


rRNA (adenine-N6-)-methyltransferase activity / peptidyl-glutamine methylation / tRNA (m2G10) methyltransferase complex / rRNA (guanine-N7)-methylation / tRNA methyltransferase activator activity / tRNA modification in the nucleus and cytosol / Methylation / protein methyltransferase activity / tRNA methylation / positive regulation of rRNA processing ...rRNA (adenine-N6-)-methyltransferase activity / peptidyl-glutamine methylation / tRNA (m2G10) methyltransferase complex / rRNA (guanine-N7)-methylation / tRNA methyltransferase activator activity / tRNA modification in the nucleus and cytosol / Methylation / protein methyltransferase activity / tRNA methylation / positive regulation of rRNA processing / S-adenosyl-L-methionine binding / rRNA methylation / rRNA modification in the nucleus and cytosol / Eukaryotic Translation Termination / maturation of LSU-rRNA / transcription initiation-coupled chromatin remodeling / Transferases; Transferring one-carbon groups; Methyltransferases / positive regulation of translation / cell projection / maturation of SSU-rRNA / stem cell differentiation / fibrillar center / rRNA processing / presynapse / nucleic acid binding / postsynapse / protein heterodimerization activity / nucleolus / perinuclear region of cytoplasm / protein-containing complex / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Multifunctional methyltransferase subunit Trm112 / Trm112-like / Trm112p-like protein / Methyltransferase small domain / Methyltransferase small domain / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
: / S-ADENOSYLMETHIONINE / rRNA N(6)-adenosine-methyltransferase METTL5 / Multifunctional methyltransferase subunit TRM112-like protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.286 Å
AuthorsGoetzke, F.W. / Bernard, S.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R35 CA231991 United States
Other private
CitationJournal: Biorxiv / Year: 2025
Title: Complexoform-restricted covalent TRMT112 ligands that allosterically agonize METTL5.
Authors: Goetzke, F.W. / Bernard, S.M. / Ju, C.W. / Pollock, J. / DeMeester, K.E. / Gross, J. / Simon, G.M. / He, C. / Melillo, B. / Cravatt, B.F.
History
DepositionMay 5, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2025Group: Database references / Category: citation / Item: _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: rRNA N(6)-adenosine-methyltransferase METTL5
D: Multifunctional methyltransferase subunit TRM112-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8855
Polymers37,9682
Non-polymers9173
Water8,143452
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-12 kcal/mol
Surface area15380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.684, 70.640, 84.553
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules CD

#1: Protein rRNA N(6)-adenosine-methyltransferase METTL5 / Methyltransferase-like protein 5


Mass: 23752.543 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METTL5, DC3, HSPC133 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NRN9, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Protein Multifunctional methyltransferase subunit TRM112-like protein / tRNA methyltransferase 112 homolog


Mass: 14215.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRMT112, AD-001, HSPC152, HSPC170 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UI30

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Non-polymers , 4 types, 455 molecules

#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical ChemComp-A1CBE / N-(4-{[(3aS,4R,6S,6aR)-6-(3-chlorophenyl)-2-propanoyloctahydrocyclopenta[c]pyrrol-4-yl]oxy}phenyl)acetamide


Mass: 426.936 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H27ClN2O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 452 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.23 Å3/Da / Density % sol: 44.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 21% PEG3350, 0.36 M ammonium sulfate, 0.1 M Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00005 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00005 Å / Relative weight: 1
ReflectionResolution: 1.286→47.127 Å / Num. obs: 80248 / % possible obs: 93.2 % / Redundancy: 5.8 % / CC1/2: 0.996 / Net I/σ(I): 9.6
Reflection shellResolution: 1.29→1.336 Å / Num. unique obs: 5110 / CC1/2: 0.333

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.286→47.127 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 0.994 / SU ML: 0.041 / Cross valid method: FREE R-VALUE / ESU R: 0.055 / ESU R Free: 0.059
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2174 4112 5.124 %
Rwork0.1864 76136 -
all0.188 --
obs-80248 92.409 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 13.347 Å2
Baniso -1Baniso -2Baniso -3
1--0.178 Å2-0 Å20 Å2
2--0.041 Å2-0 Å2
3---0.138 Å2
Refinement stepCycle: LAST / Resolution: 1.286→47.127 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2589 0 63 452 3104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122716
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162629
X-RAY DIFFRACTIONr_angle_refined_deg1.7491.6513669
X-RAY DIFFRACTIONr_angle_other_deg0.5661.5736066
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.495326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.264522
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.29551
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.24410491
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg5.72101
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.83510120
X-RAY DIFFRACTIONr_chiral_restr0.0920.2415
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023109
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02600
X-RAY DIFFRACTIONr_nbd_refined0.2340.2490
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.22405
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21335
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21453
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2266
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2160.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1990.216
X-RAY DIFFRACTIONr_nbd_other0.2310.258
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.5640.243
X-RAY DIFFRACTIONr_mcbond_it1.3371.1671310
X-RAY DIFFRACTIONr_mcbond_other1.3361.1671310
X-RAY DIFFRACTIONr_mcangle_it2.0282.0981634
X-RAY DIFFRACTIONr_mcangle_other2.0282.0991635
X-RAY DIFFRACTIONr_scbond_it2.7161.5371406
X-RAY DIFFRACTIONr_scbond_other2.7151.5381407
X-RAY DIFFRACTIONr_scangle_it4.192.6512035
X-RAY DIFFRACTIONr_scangle_other4.1892.6522036
X-RAY DIFFRACTIONr_lrange_it6.29820.1943152
X-RAY DIFFRACTIONr_lrange_other6.01715.592988
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.286-1.3190.3521550.34330000.34463320.9120.91949.82630.334
1.319-1.3550.3122250.32341810.32361730.930.93471.37530.308
1.355-1.3950.3142530.28348000.28560340.9470.9583.74210.264
1.395-1.4370.2612730.24752840.24858620.9560.9694.7970.222
1.437-1.4850.253130.20953330.21156590.9580.96999.77030.18
1.485-1.5370.2012940.19352020.19355220.9710.97499.52920.165
1.537-1.5950.222650.18249810.18452830.9670.97799.29960.158
1.595-1.660.2262600.17548150.17850980.9660.97999.54880.156
1.66-1.7330.2152410.17446580.17649200.9710.97999.57320.156
1.733-1.8180.1992330.1744690.17147200.9730.98199.61860.155
1.818-1.9160.1962230.16842160.16944690.9760.98299.32870.157
1.916-2.0320.2052210.17140190.17342640.9750.98399.43710.165
2.032-2.1720.2122050.18437750.18540110.9750.9899.22710.18
2.172-2.3460.2242100.17634960.17837290.9660.98199.38320.177
2.346-2.5690.2041980.1732280.17234470.970.98199.39080.175
2.569-2.8710.2031510.17229630.17431290.9730.9899.52060.183
2.871-3.3130.2171370.17626370.17827980.9690.9899.14230.193
3.313-4.0530.1941100.16522600.16623950.9770.98398.95620.188
4.053-5.710.195890.17717780.17818730.9840.98699.67970.21
5.71-47.1270.255560.23110410.23211210.9720.97597.85910.267

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