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- PDB-7rx7: Structure of METTL3-METTL14(R298P) mutant methyltransferase complex -

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Basic information

Entry
Database: PDB / ID: 7rx7
TitleStructure of METTL3-METTL14(R298P) 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 / mRNA m6A methyltransferase / mRNA m(6)A methyltransferase activity / RNA N6-methyladenosine methyltransferase complex / positive regulation of cap-independent translational initiation / endothelial to hematopoietic transition / RNA methylation / regulation of meiotic cell cycle / RNA methyltransferase activity / primary miRNA processing ...negative regulation of hematopoietic progenitor cell differentiation / mRNA m6A methyltransferase / mRNA m(6)A methyltransferase activity / RNA N6-methyladenosine methyltransferase complex / positive regulation of cap-independent translational initiation / endothelial to hematopoietic transition / RNA methylation / regulation of meiotic cell cycle / RNA methyltransferase activity / primary miRNA processing / forebrain radial glial cell differentiation / oxidoreductase complex / dosage compensation by inactivation of X chromosome / S-adenosyl-L-methionine binding / gliogenesis / mRNA stabilization / mRNA modification / regulation of hematopoietic stem cell differentiation / 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 / mRNA splicing, via spliceosome / circadian rhythm / 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: 1.645 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(R298P) 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)65,2462
Polymers65,2462
Non-polymers00
Water8,359464
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-22 kcal/mol
Surface area21000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.391, 101.391, 117.758
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: 39513.621 Da / Num. of mol.: 1 / Mutation: R298P
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.: 464 / 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: 2.32 Å3/Da / Density % sol: 46.97 %
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: 1.645→50 Å / Num. obs: 74404 / % possible obs: 99.6 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 23.9
Reflection shellResolution: 1.645→1.71 Å / Rmerge(I) obs: 0.892 / Num. unique obs: 7285

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5k7m

5k7m


Resolution: 1.645→46.564 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1877 3595 5.05 %
Rwork0.1666 67617 -
obs0.1677 71212 95.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.47 Å2 / Biso mean: 24.6641 Å2 / Biso min: 3.02 Å2
Refinement stepCycle: final / Resolution: 1.645→46.564 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3973 0 0 464 4437
Biso mean---32.8 -
Num. residues----488
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6451-1.66670.2973610.2582142752
1.6667-1.68960.2965990.2607194972
1.6896-1.71370.2611170.229227785
1.7137-1.73930.25311430.2148243391
1.7393-1.76650.2241160.1925251193
1.7665-1.79540.20361550.1846249894
1.7954-1.82640.19751320.1807262797
1.8264-1.85960.21561240.1758266199
1.8596-1.89540.18611490.1734268699
1.8954-1.93410.19431310.16382714100
1.9341-1.97610.19921480.1722677100
1.9761-2.02210.19761430.1682264497
2.0221-2.07270.18681330.1656270499
2.0727-2.12870.17191480.16322703100
2.1287-2.19130.17291520.162714100
2.1913-2.26210.19161570.16692720100
2.2621-2.34290.16531580.15912682100
2.3429-2.43670.19181420.16022748100
2.4367-2.54760.20461420.16612742100
2.5476-2.68190.16441280.1631269698
2.6819-2.84990.20391400.16872739100
2.8499-3.06990.1841250.17072787100
3.0699-3.37880.17041590.16272784100
3.3788-3.86750.18851450.1469274299
3.8675-4.87180.14811820.13622806100
4.8718-46.5640.20891660.18294699
Refinement TLS params.Method: refined / Origin x: -21.4395 Å / Origin y: 8.8101 Å / Origin z: -12.0696 Å
111213212223313233
T0.0357 Å20.0303 Å2-0.0086 Å2-0.0469 Å2-0.0138 Å2--0.0697 Å2
L0.9611 °20.126 °2-0.5645 °2-0.9202 °20.3651 °2--2.2461 °2
S0.0295 Å °-0.271 Å °-0.0072 Å °0.0846 Å °0.0539 Å °-0.1167 Å °-0.0268 Å °0.2574 Å °-0.036 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA369 - 572
2X-RAY DIFFRACTION1allB116 - 399
3X-RAY DIFFRACTION1allS1 - 499

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