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- PDB-7ezg: The structure of the human METTL6 enzyme in complex with SAH -

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Basic information

Entry
Database: PDB / ID: 7ezg
TitleThe structure of the human METTL6 enzyme in complex with SAH
ComponentstRNA N(3)-methylcytidine methyltransferase METTL6
KeywordsMethyltransferase / M3C / tRNA modifications / cocrystal / METTL6 / TOXIN
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: 1.9 Å
AuthorsXie, W. / Chen, R. / Zhou, J. / Liu, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870782 China
CitationJournal: Commun Biol / Year: 2021
Title: Crystal structure of human METTL6, the m 3 C methyltransferase.
Authors: Chen, R. / Zhou, J. / Liu, L. / Mao, X.L. / Zhou, X. / Xie, W.
History
DepositionJun 1, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1702
Polymers35,7861
Non-polymers3841
Water3,063170
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.264, 110.264, 110.264
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number195
Space group name H-MP23
Space group name HallP223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z

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Components

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


Mass: 35785.793 Da / Num. of mol.: 1
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.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 3.12 Å3/Da / Density % sol: 60.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: PEGRX F7?25% PEG1500?0.1M BIS-Tris pH9.0?0.1M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.899→50 Å / Num. obs: 35491 / % possible obs: 100 % / Redundancy: 38.5 % / Biso Wilson estimate: 29.02 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.19 / Net I/σ(I): 28
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 1.76 / Mean I/σ(I) obs: 2 / Num. unique obs: 3525 / CC1/2: 0.75

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6C5B

6c5b


Resolution: 1.9→25.3 Å / SU ML: 0.2014 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.5623 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2005 1767 5 %
Rwork0.1791 33567 -
obs0.1802 35334 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→25.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2209 0 26 174 2409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00822290
X-RAY DIFFRACTIONf_angle_d1.1293100
X-RAY DIFFRACTIONf_chiral_restr0.0592336
X-RAY DIFFRACTIONf_plane_restr0.0059401
X-RAY DIFFRACTIONf_dihedral_angle_d12.2711372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.33491380.27962539X-RAY DIFFRACTION100
1.95-2.010.23421130.21622583X-RAY DIFFRACTION100
2.01-2.070.21861360.19942576X-RAY DIFFRACTION100
2.07-2.150.21571310.19242579X-RAY DIFFRACTION100
2.15-2.230.20171370.1832565X-RAY DIFFRACTION100
2.23-2.330.25681350.20892549X-RAY DIFFRACTION100
2.33-2.460.22591160.18862616X-RAY DIFFRACTION100
2.46-2.610.21641340.17712563X-RAY DIFFRACTION99.96
2.61-2.810.19311390.18162613X-RAY DIFFRACTION100
2.81-3.10.22371560.18162558X-RAY DIFFRACTION99.85
3.1-3.540.18431410.16942608X-RAY DIFFRACTION99.82
3.54-4.460.16971290.14752606X-RAY DIFFRACTION99.02
4.46-25.30.18291620.18112612X-RAY DIFFRACTION96.69

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