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- PDB-8pw9: Crystal structure of the human METTL3-METTL14 in complex with a b... -

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Basic information

Entry
Database: PDB / ID: 8pw9
TitleCrystal structure of the human METTL3-METTL14 in complex with a bisubstrate analogue (BA1)
Components(N6-adenosine-methyltransferase ...) x 2
KeywordsTRANSFERASE / METTL3 / bisubstrate / complex / m6A
Function / homology
Function and homology information


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 ...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 / regulation of hematopoietic stem cell differentiation / mRNA modification / 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 / 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
ACETATE ION / Chem-H9D / N(6)-adenosine-methyltransferase non-catalytic subunit METTL14 / N(6)-adenosine-methyltransferase catalytic subunit METTL3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBedi, R.K. / Etheve-Quelquejeu, M. / Caflisch, A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030B_189363 Switzerland
Citation
Journal: Elife / Year: 2024
Title: The catalytic mechanism of the RNA methyltransferase METTL3.
Authors: Corbeski, I. / Vargas-Rosales, P.A. / Bedi, R.K. / Deng, J. / Coelho, D. / Braud, E. / Iannazzo, L. / Li, Y. / Huang, D. / Etheve-Quelquejeu, M. / Cui, Q. / Caflisch, A.
#1: Journal: Elife / Year: 2023
Title: The catalytic mechanism of the RNA methyltransferase METTL3
Authors: Corbeski, I. / Vargas-Rosales, P.A. / Bedi, R.K. / Deng, J. / Coelho, D. / Braud, E. / Iannazzo, L. / Li, Y. / Huang, D. / Etheve-Quelquejeu, M. / Cui, Q. / Caflisch, A.
#2: Journal: Biorxiv / Year: 2023
Title: The catalytic mechanism of the RNA methyltransferase METTL3.
Authors: Corbeski, I. / Vargas-Rosales, P.A. / Bedi, R.K. / Deng, J. / Coelho, D. / Braud, E. / Iannazzo, L. / Li, Y. / Huang, D. / Etheve-Quelquejeu, M. / Cui, Q. / Caflisch, A.
History
DepositionJul 19, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Database references / Category: citation / citation_author
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N6-adenosine-methyltransferase catalytic subunit
B: N6-adenosine-methyltransferase non-catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2085
Polymers59,5652
Non-polymers6433
Water2,342130
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-27 kcal/mol
Surface area19100 Å2
Unit cell
Length a, b, c (Å)63.940, 63.940, 225.140
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

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N6-adenosine-methyltransferase ... , 2 types, 2 molecules AB

#1: Protein N6-adenosine-methyltransferase catalytic subunit / Methyltransferase-like protein 3 / hMETTL3 / N6-adenosine-methyltransferase 70 kDa subunit / MT-A70


Mass: 26017.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METTL3, MTA70 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q86U44, mRNA m6A methyltransferase
#2: Protein N6-adenosine-methyltransferase non-catalytic subunit / Methyltransferase-like protein 14


Mass: 33547.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METTL14 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A4IFD8

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Non-polymers , 4 types, 133 molecules

#3: Chemical ChemComp-H9D / (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[[2-[[9-[(2~{R},3~{R},4~{S},5~{S})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]purin-6-yl]amino]ethylamino]methyl]oxolane-3,4-diol


Mass: 559.535 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H29N11O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.23 Å3/Da / Density % sol: 44.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 0.4M Magnesium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→49.7 Å / Num. obs: 24705 / % possible obs: 99.9 % / Redundancy: 9.6 % / Biso Wilson estimate: 45.64 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.35
Reflection shellResolution: 2.3→2.44 Å / Num. unique obs: 3897 / CC1/2: 0.687

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.19.1_4122refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→49.69 Å / SU ML: 0.283 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.6796
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2354 1230 5 %
Rwork0.1935 23386 -
obs0.1956 24616 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.52 Å2
Refinement stepCycle: LAST / Resolution: 2.3→49.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3470 0 45 130 3645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00823611
X-RAY DIFFRACTIONf_angle_d0.99714919
X-RAY DIFFRACTIONf_chiral_restr0.0549537
X-RAY DIFFRACTIONf_plane_restr0.0089631
X-RAY DIFFRACTIONf_dihedral_angle_d6.2815478
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.390.31511330.2612523X-RAY DIFFRACTION99.36
2.39-2.50.31821330.25392534X-RAY DIFFRACTION99.85
2.5-2.630.2911360.23692581X-RAY DIFFRACTION99.85
2.63-2.80.26461340.22982545X-RAY DIFFRACTION99.85
2.8-3.010.27881350.2322565X-RAY DIFFRACTION99.85
3.02-3.320.23831370.20382596X-RAY DIFFRACTION99.89
3.32-3.80.23581380.1722613X-RAY DIFFRACTION99.96
3.8-4.790.16681390.15012630X-RAY DIFFRACTION99.93
4.79-49.690.23851450.19642799X-RAY DIFFRACTION99.76

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