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- PDB-7o2h: Crystal structure of the human METTL3-METTL14 complex bound to Co... -

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Basic information

Entry
Database: PDB / ID: 7o2h
TitleCrystal structure of the human METTL3-METTL14 complex bound to Compound 13 (ADO_AD_091)
Components
  • N6-adenosine-methyltransferase catalytic subunit
  • N6-adenosine-methyltransferase non-catalytic subunit
KeywordsTRANSFERASE / METTL3 / Inhibitor / complex
Function / homology
Function and homology information


mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity / mRNA (N6-adenosine)-methyltransferase activity / RNA N6-methyladenosine methyltransferase complex / negative regulation of hematopoietic progenitor cell differentiation / mRNA m6A methyltransferase / positive regulation of cap-independent translational initiation / adenosine to inosine editing / endothelial to hematopoietic transition / RNA methyltransferase activity / regulation of meiotic cell cycle ...mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity / mRNA (N6-adenosine)-methyltransferase activity / RNA N6-methyladenosine methyltransferase complex / negative regulation of hematopoietic progenitor cell differentiation / mRNA m6A methyltransferase / positive regulation of cap-independent translational initiation / adenosine to inosine editing / endothelial to hematopoietic transition / RNA methyltransferase activity / regulation of meiotic cell cycle / : / primary miRNA processing / RNA methylation / forebrain radial glial cell differentiation / gliogenesis / S-adenosyl-L-methionine binding / dosage compensation by inactivation of X chromosome / regulation of hematopoietic stem cell differentiation / regulation of T cell differentiation / regulation of neuron differentiation / negative regulation of type I interferon-mediated signaling pathway / oogenesis / stem cell population maintenance / mRNA destabilization / negative regulation of Notch signaling pathway / mRNA catabolic process / Processing of Capped Intron-Containing Pre-mRNA / mRNA splicing, via spliceosome / positive regulation of translation / mRNA processing / circadian rhythm / cellular response to UV / spermatogenesis / nuclear body / nuclear speck / 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-UZ2 / N6-adenosine-methyltransferase catalytic subunit / N6-adenosine-methyltransferase non-catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBedi, R.K. / Dolbois, A. / Caflisch, A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030B_189363 Switzerland
CitationJournal: To Be Published
Title: Crystal structure of the human METTL3-METTL14 complex bound to Compound 13 (ADO_AD_091)
Authors: Bedi, R.K. / Dolbois, A. / Caflisch, A.
History
DepositionMar 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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 catalytic subunit
B: N6-adenosine-methyltransferase non-catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3164
Polymers61,7652
Non-polymers5512
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-25 kcal/mol
Surface area18430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.060, 64.060, 225.100
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
Components on special symmetry positions
IDModelComponents
11A-714-

HOH

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Components

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


Mass: 28144.080 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 / hMETTL14


Mass: 33621.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METTL14, KIAA1627 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9HCE5
#3: Chemical ChemComp-UZ2 / 4-[4-[(4,4-dimethylpiperidin-1-yl)methyl]phenyl]-1-methyl-9-[6-(methylamino)pyrimidin-4-yl]-1,4,9-triazaspiro[5.5]undecan-2-one


Mass: 491.671 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H41N7O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.16 Å3/Da / Density % sol: 43.02 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 400mM Mg 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: Dec 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→45.02 Å / Num. obs: 19567 / % possible obs: 99.9 % / Redundancy: 8.2 % / Biso Wilson estimate: 61.64 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.7
Reflection shellResolution: 2.5→2.65 Å / Num. unique obs: 3089 / CC1/2: 0.43

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.19.1_4122refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ACD
Resolution: 2.5→44.61 Å / SU ML: 0.403 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.4186
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2746 976 5.01 %
Rwork0.2106 18505 -
obs0.2137 19481 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.7 Å2
Refinement stepCycle: LAST / Resolution: 2.5→44.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3344 0 40 53 3437
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00873473
X-RAY DIFFRACTIONf_angle_d1.05144738
X-RAY DIFFRACTIONf_chiral_restr0.0548516
X-RAY DIFFRACTIONf_plane_restr0.0092609
X-RAY DIFFRACTIONf_dihedral_angle_d12.1947483
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.630.41711350.33712562X-RAY DIFFRACTION99.74
2.63-2.790.32611370.29532614X-RAY DIFFRACTION99.75
2.79-3.010.35491360.27992574X-RAY DIFFRACTION99.82
3.01-3.310.31761380.22882619X-RAY DIFFRACTION99.82
3.31-3.790.26931390.19762636X-RAY DIFFRACTION100
3.79-4.770.21231400.16592671X-RAY DIFFRACTION99.93
4.77-44.610.27471510.20552829X-RAY DIFFRACTION99.97

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