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- PDB-7rx6: Structure of METTL3-METTL14(R298C) mutant methyltransferase complex -

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Basic information

Entry
Database: PDB / ID: 7rx6
TitleStructure of METTL3-METTL14(R298C) mutant methyltransferase complex
Components
  • N6-adenosine-methyltransferase 70 kDa subunit
  • N6-adenosine-methyltransferase non-catalytic subunit
KeywordsTRANSFERASE / RNA methyltransferase complex / mutant
Function / homology
Function and homology information


negative regulation of hematopoietic progenitor cell differentiation / positive regulation of cap-independent translational initiation / mRNA m6A methyltransferase / mRNA m(6)A methyltransferase activity / RNA N6-methyladenosine methyltransferase complex / RNA methylation / endothelial to hematopoietic transition / regulation of meiotic cell cycle / RNA methyltransferase activity / primary miRNA processing ...negative regulation of hematopoietic progenitor cell differentiation / positive regulation of cap-independent translational initiation / mRNA m6A methyltransferase / mRNA m(6)A methyltransferase activity / RNA N6-methyladenosine methyltransferase complex / RNA methylation / endothelial to hematopoietic transition / regulation of meiotic cell cycle / RNA methyltransferase activity / primary miRNA processing / forebrain radial glial cell differentiation / dosage compensation by inactivation of X chromosome / oxidoreductase complex / S-adenosyl-L-methionine binding / gliogenesis / mRNA stabilization / regulation of hematopoietic stem cell differentiation / mRNA modification / regulation of neuron differentiation / regulation of T cell differentiation / negative regulation of type I interferon-mediated signaling pathway / oogenesis / stem cell population maintenance / mRNA destabilization / Processing of Capped Intron-Containing Pre-mRNA / negative regulation of Notch signaling pathway / positive regulation of translation / response to nutrient levels / circadian rhythm / mRNA splicing, via spliceosome / mRNA processing / cellular response to UV / spermatogenesis / nuclear speck / nuclear body / protein heterodimerization activity / innate immune response / mRNA binding / DNA damage response / Golgi apparatus / nucleoplasm / nucleus / cytosol
Similarity search - Function
N6-adenosine-methyltransferase non-catalytic subunit METTL14-like / mRNA (2'-O-methyladenosine-N(6)-)-methyltransferase-like (MT-A70-like) family profile. / N6-adenosine-methyltransferase MT-A70-like / mRNA (2'-O-methyladenosine-N(6)-)-methyltransferase (EC 2.1.1.62) family profile. / MT-A70-like / MT-A70 / MT-A70-like family profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
N(6)-adenosine-methyltransferase catalytic subunit METTL3 / N(6)-adenosine-methyltransferase non-catalytic subunit METTL14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWang, P. / Nam, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
Cancer Prevention and Research Institute of Texas (CPRIT) United States
CitationJournal: To Be Published
Title: Structure of METTL3-METTL14(R298C) mutant methyltransferase complex
Authors: Zhang, C. / Nam, Y.
History
DepositionAug 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

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Assembly

Deposited unit
A: N6-adenosine-methyltransferase 70 kDa subunit
B: N6-adenosine-methyltransferase non-catalytic subunit


Theoretical massNumber of molelcules
Total (without water)65,2522
Polymers65,2522
Non-polymers00
Water6,648369
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-20 kcal/mol
Surface area20530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.743, 99.743, 118.378
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein N6-adenosine-methyltransferase 70 kDa subunit / MT-A70 / Methyltransferase-like protein 3


Mass: 25732.504 Da / Num. of mol.: 1 / Fragment: Catalytic domain residues 357-580
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METTL3, MTA70 / Production host: Escherichia coli (E. coli)
References: UniProt: Q86U44, mRNA (2'-O-methyladenosine-N6-)-methyltransferase
#2: Protein N6-adenosine-methyltransferase non-catalytic subunit / Methyltransferase-like protein 14 / hMETTL14


Mass: 39519.648 Da / Num. of mol.: 1 / Mutation: R298C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METTL14, KIAA1627 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HCE5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / Source method: isolated from a natural source / Formula: H2O

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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: 2.26 Å3/Da / Density % sol: 45.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris (pH 8.0) and 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97938 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97938 Å / Relative weight: 1
ReflectionResolution: 1.796→50 Å / Num. obs: 56123 / % possible obs: 100 % / Redundancy: 11.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 23.6
Reflection shellResolution: 1.796→1.86 Å / Rmerge(I) obs: 1.08 / Num. unique obs: 5499

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5k7m

5k7m


Resolution: 1.8→49.87 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2189 2747 4.95 %
Rwork0.1928 52735 -
obs0.1941 55482 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.31 Å2 / Biso mean: 25.0239 Å2 / Biso min: 6.11 Å2
Refinement stepCycle: final / Resolution: 1.8→49.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3891 0 0 369 4260
Biso mean---28.41 -
Num. residues----477
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.830.3323990.2742085218479
1.83-1.860.26681350.25942507264295
1.86-1.90.26261270.23692583271099
1.9-1.930.28261550.218226192774100
1.93-1.980.25521320.215526262758100
1.98-2.020.2171490.209926282777100
2.02-2.070.26841230.198726622785100
2.07-2.130.21681370.205226362773100
2.13-2.190.20521130.202326752788100
2.19-2.260.22291530.205126272780100
2.26-2.340.22751330.189526532786100
2.34-2.440.24041420.19526522794100
2.44-2.550.25971470.199526702817100
2.55-2.680.22191300.197626752805100
2.68-2.850.22641450.197926782823100
2.85-3.070.20291660.198826552821100
3.07-3.380.21941250.184927142839100
3.38-3.870.19571540.172427132867100
3.87-4.870.16341500.150527472897100
4.87-49.870.22651320.197629303062100

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