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- PDB-8owy: Crystal structure of METTL6 mutant 40-269 bound to SAH -

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Basic information

Entry
Database: PDB / ID: 8owy
TitleCrystal structure of METTL6 mutant 40-269 bound to SAH
ComponentstRNA N(3)-methylcytidine methyltransferase METTL6
KeywordsRNA BINDING PROTEIN / tRNA modification / m3C / methyltransferase
Function / homology
Function and homology information


tRNA (cytidine-3-)-methyltransferase activity / tRNA methylation / tRNA modification / Transferases; Transferring one-carbon groups; Methyltransferases / enzyme binding / nucleus / cytoplasm
Similarity search - Function
tRNA N(3)-methylcytidine methyltransferase METTL2/6/8-like / Methyltransferase type 12 / Methyltransferase domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / tRNA N(3)-methylcytidine methyltransferase METTL6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsThroll, P. / Basu, S. / Dolce, L.G. / Kowalinski, E.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Structural basis of the cooperation between the m3C RNA-methyltransferase METTL6 with SerRS amino-acyl-synthetase for tRNA recognition
Authors: Throll, P. / Dolce, L.G. / Lastres, P.R. / Arnold, K. / Tengo, L. / Basu, S. / Kaiser, S. / Schneider, R. / Kowalinski, E.
History
DepositionApr 28, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2024Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Refinement description / Category: pdbx_initial_refinement_model / Item: _pdbx_initial_refinement_model.accession_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA N(3)-methylcytidine methyltransferase METTL6
B: tRNA N(3)-methylcytidine methyltransferase METTL6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0844
Polymers55,3152
Non-polymers7692
Water0
1
A: tRNA N(3)-methylcytidine methyltransferase METTL6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0422
Polymers27,6581
Non-polymers3841
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: tRNA N(3)-methylcytidine methyltransferase METTL6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0422
Polymers27,6581
Non-polymers3841
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.971, 138.129, 39.660
Angle α, β, γ (deg.)90.00, 115.26, 90.00
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein tRNA N(3)-methylcytidine methyltransferase METTL6 / Methyltransferase-like protein 6 / hMETTL6


Mass: 27657.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METTL6 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8TCB7, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / 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

Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M BisTRIS, 0.2 M ammonium sulfate and 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.008 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 3.2→39.11 Å / Num. obs: 6561 / % possible obs: 85.31 % / Redundancy: 6.5 % / Biso Wilson estimate: 65.28 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.2055 / Net I/σ(I): 6.97
Reflection shellResolution: 3.2→3.315 Å / Rmerge(I) obs: 2.196 / Num. unique obs: 318 / CC1/2: 0.861

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
Coot0.8.9.2model building
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→39.11 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2996 243 4.31 %
Rwork0.2602 --
obs0.2619 5635 85.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→39.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2673 0 0 0 2673
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132736
X-RAY DIFFRACTIONf_angle_d2.0413721
X-RAY DIFFRACTIONf_dihedral_angle_d15.521953
X-RAY DIFFRACTIONf_chiral_restr0.127427
X-RAY DIFFRACTIONf_plane_restr0.011463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2002-4.03190.33821160.26492255X-RAY DIFFRACTION72
4.0319-39.110.27991270.25823137X-RAY DIFFRACTION98

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