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- PDB-7rx8: Structure of METTL3-METTL14(R298H) mutant methyltransferase complex -

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Basic information

Entry
Database: PDB / ID: 7rx8
TitleStructure of METTL3-METTL14(R298H) 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: 1.85 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(R298H) 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)65,2872
Polymers65,2872
Non-polymers00
Water6,882382
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-19 kcal/mol
Surface area20760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.483, 101.483, 117.338
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: 39554.652 Da / Num. of mol.: 1 / Mutation: R298H
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.: 382 / 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: 2.31 Å3/Da / Density % sol: 46.84 %
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: 1.849→50 Å / Num. obs: 52967 / % possible obs: 100 % / Redundancy: 15.8 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 31.4
Reflection shellResolution: 1.849→50 Å / Rmerge(I) obs: 1.24 / Num. unique obs: 5223

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5k7m

5k7m


Resolution: 1.85→46.57 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.202 2514 4.86 %
Rwork0.1711 49219 -
obs0.1725 51733 97.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.42 Å2 / Biso mean: 28.3549 Å2 / Biso min: 6.42 Å2
Refinement stepCycle: final / Resolution: 1.85→46.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3957 0 0 382 4339
Biso mean---30.75 -
Num. residues----485
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.880.2988930.27271900199369
1.88-1.920.27651340.22622549268392
1.92-1.970.2491480.21422699284798
1.97-2.010.25251490.19412719286899
2.01-2.060.19711530.182327422895100
2.06-2.120.22031320.179827592891100
2.12-2.180.23091240.174227752899100
2.18-2.250.2011420.174427852927100
2.25-2.330.2061410.162227522893100
2.33-2.420.1941250.162228012926100
2.42-2.530.20211450.172727712916100
2.53-2.670.19221430.166428092952100
2.67-2.830.19761560.177127702926100
2.83-3.050.22221450.181128122957100
3.05-3.360.18621290.173828262955100
3.36-3.850.22151480.153728362984100
3.85-4.840.16051600.139128743034100
4.85-46.570.18061470.174330403187100
Refinement TLS params.Method: refined / Origin x: -21.5807 Å / Origin y: 8.4596 Å / Origin z: -12.2584 Å
111213212223313233
T0.0757 Å20.0274 Å2-0.0104 Å2-0.1112 Å20.0017 Å2--0.1075 Å2
L0.8945 °20.1021 °2-0.4307 °2-1.0476 °20.5282 °2--2.1095 °2
S0.0239 Å °-0.241 Å °-0.0218 Å °0.1011 Å °0.0625 Å °-0.1279 Å °0.017 Å °0.2343 Å °-0.0474 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA369 - 569
2X-RAY DIFFRACTION1allB116 - 399
3X-RAY DIFFRACTION1allS1 - 421

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