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- PDB-7f1e: Structure of METTL6 bound with SAM -

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Basic information

Entry
Database: PDB / ID: 7f1e
TitleStructure of METTL6 bound with SAM
ComponentstRNA N(3)-methylcytidine methyltransferase METTL6
KeywordsTRANSFERASE / RNA methyltransferase / RNA
Function / homology
Function and homology information


tRNA (cytidine-3-)-methyltransferase activity / tRNA modification / tRNA methylation / 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-ADENOSYLMETHIONINE / tRNA N(3)-cytidine methyltransferase METTL6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.589 Å
AuthorsLi, S. / Liao, S. / Xu, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770806 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Structural basis for METTL6-mediated m3C RNA methylation.
Authors: Li, S. / Zhou, H. / Liao, S. / Wang, X. / Zhu, Z. / Zhang, J. / Xu, C.
History
DepositionJun 9, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)67,7794
Polymers66,9832
Non-polymers7972
Water90150
1
A: tRNA N(3)-methylcytidine methyltransferase METTL6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8902
Polymers33,4911
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: tRNA N(3)-methylcytidine methyltransferase METTL6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8902
Polymers33,4911
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.457, 83.457, 129.686
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

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


Mass: 33491.250 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 BL21(DE3) (bacteria)
References: UniProt: Q8TCB7, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 3.37 Å3/Da / Density % sol: 63.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M Sodium acetate pH5.2, 2.0M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.589→26.857 Å / Num. obs: 41739 / % possible obs: 99.9 % / Redundancy: 12.5 % / CC1/2: 0.992 / Rmerge(I) obs: 0.094 / Net I/σ(I): 20.8
Reflection shellResolution: 2.589→2.63 Å / Rmerge(I) obs: 1.056 / Num. unique obs: 870 / CC1/2: 0.699

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4nec

4nec


Resolution: 2.589→26.857 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2265 3061 7.33 %
Rwork0.1908 38678 -
obs0.1934 41739 76.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 149.64 Å2 / Biso mean: 51.4533 Å2 / Biso min: 14.04 Å2
Refinement stepCycle: final / Resolution: 2.589→26.857 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3842 0 54 45 3941
Biso mean--38.75 42.09 -
Num. residues----485
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5895-2.62990.34670.376187038
2.6299-2.6730.3552860.3365107446
2.673-2.7190.3196840.3024113150
2.719-2.76840.2911940.2892115850
2.7684-2.82160.3272940.2924115551
2.8216-2.87920.3022900.277118951
2.8792-2.94170.2973920.2761113050
2.9417-3.010.3334960.2744121053
3.01-3.08520.28331110.2451130557
3.0852-3.16850.2711270.2274160069
3.1685-3.26160.25931590.218191584
3.2616-3.36670.23021790.2166222496
3.3667-3.48670.21161750.1993225299
3.4867-3.6260.23651840.1847227399
3.626-3.79060.21721880.1779225999
3.7906-3.98990.2331860.1677226698
3.9899-4.23890.19361750.1772223699
4.2389-4.56480.19041800.1513229199
4.5648-5.02140.19561760.14712256100
5.0214-5.74190.2071800.17192308100
5.7419-7.21090.25411740.19182292100
7.2109-26.8570.17251640.1631228498
Refinement TLS params.Method: refined / Origin x: 25.5556 Å / Origin y: -27.9604 Å / Origin z: 25.2045 Å
111213212223313233
T0.1343 Å2-0.0375 Å2-0.0147 Å2-0.233 Å2-0.0267 Å2--0.1937 Å2
L0.4475 °20.0155 °2-0.2152 °2-0.6865 °20.0235 °2--1.0079 °2
S0.0716 Å °-0.2144 Å °0.0654 Å °-0.2251 Å °-0.0213 Å °0.0788 Å °-0.0769 Å °-0.1745 Å °0.0025 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA15 - 270
2X-RAY DIFFRACTION1allB28 - 270
3X-RAY DIFFRACTION1allC301
4X-RAY DIFFRACTION1allD301
5X-RAY DIFFRACTION1allS1 - 46

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