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- PDB-7u20: Crystal structure of human METTL1 and WDR4 complex -

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Basic information

Entry
Database: PDB / ID: 7u20
TitleCrystal structure of human METTL1 and WDR4 complex
Components
  • tRNA (guanine-N(7)-)-methyltransferase
  • tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4
KeywordsTRANSFERASE / METTL1 WDR4 tRNA methyltransferase
Function / homology
Function and homology information


internal mRNA (guanine-N7-)-methyltransferase activity / tRNA (m7G46) methyltransferase complex / tRNA (guanine-N7)-methylation / tRNA stabilization / RNA (guanine-N7)-methylation / tRNA (guanine46-N7)-methyltransferase / tRNA (guanine(46)-N7)-methyltransferase activity / tRNA methyltransferase activator activity / tRNA methyltransferase complex / tRNA modification in the nucleus and cytosol ...internal mRNA (guanine-N7-)-methyltransferase activity / tRNA (m7G46) methyltransferase complex / tRNA (guanine-N7)-methylation / tRNA stabilization / RNA (guanine-N7)-methylation / tRNA (guanine46-N7)-methyltransferase / tRNA (guanine(46)-N7)-methyltransferase activity / tRNA methyltransferase activator activity / tRNA methyltransferase complex / tRNA modification in the nucleus and cytosol / tRNA modification / tRNA methylation / cellular response to stress / Transferases; Transferring one-carbon groups; Methyltransferases / enzyme activator activity / chromosome / tRNA binding / DNA damage response / nucleolus / nucleoplasm / nucleus / cytosol
Similarity search - Function
tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit / tRNA (guanine-N-7) methyltransferase catalytic subunit Trm8, eukaryote / SAM-dependent methyltransferase TRMB-type domain profile. / tRNA (guanine-N-7) methyltransferase, Trmb type / Putative methyltransferase / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. ...tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit / tRNA (guanine-N-7) methyltransferase catalytic subunit Trm8, eukaryote / SAM-dependent methyltransferase TRMB-type domain profile. / tRNA (guanine-N-7) methyltransferase, Trmb type / Putative methyltransferase / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 / tRNA (guanine-N(7)-)-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsLi, J. / Nowak, R.P. / Fischer, E.S. / Gregory, R.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)5R35CA232115 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA218278 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA214608 United States
CitationJournal: Nature / Year: 2023
Title: Structural basis of regulated mG tRNA modification by METTL1-WDR4.
Authors: Jiazhi Li / Longfei Wang / Quentin Hahn / Radosław P Nowak / Thibault Viennet / Esteban A Orellana / Shourya S Roy Burman / Hong Yue / Moritz Hunkeler / Pietro Fontana / Hao Wu / Haribabu ...Authors: Jiazhi Li / Longfei Wang / Quentin Hahn / Radosław P Nowak / Thibault Viennet / Esteban A Orellana / Shourya S Roy Burman / Hong Yue / Moritz Hunkeler / Pietro Fontana / Hao Wu / Haribabu Arthanari / Eric S Fischer / Richard I Gregory /
Abstract: Chemical modifications of RNA have key roles in many biological processes. N-methylguanosine (mG) is required for integrity and stability of a large subset of tRNAs. The methyltransferase 1-WD repeat- ...Chemical modifications of RNA have key roles in many biological processes. N-methylguanosine (mG) is required for integrity and stability of a large subset of tRNAs. The methyltransferase 1-WD repeat-containing protein 4 (METTL1-WDR4) complex is the methyltransferase that modifies G46 in the variable loop of certain tRNAs, and its dysregulation drives tumorigenesis in numerous cancer types. Mutations in WDR4 cause human developmental phenotypes including microcephaly. How METTL1-WDR4 modifies tRNA substrates and is regulated remains elusive. Here we show,  through structural, biochemical and cellular studies of human METTL1-WDR4, that WDR4 serves as a scaffold for METTL1 and the tRNA T-arm. Upon tRNA binding, the αC region of METTL1 transforms into a helix, which together with the α6 helix secures both ends of the tRNA variable loop. Unexpectedly, we find that the predicted disordered N-terminal region of METTL1 is part of the catalytic pocket and essential for methyltransferase activity. Furthermore, we reveal that S27 phosphorylation in the METTL1 N-terminal region inhibits methyltransferase activity by locally disrupting the catalytic centre. Our results provide a molecular understanding of tRNA substrate recognition and phosphorylation-mediated regulation of METTL1-WDR4, and reveal the presumed disordered N-terminal region of METTL1 as a nexus of methyltransferase activity.
History
DepositionFeb 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 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: tRNA (guanine-N(7)-)-methyltransferase
B: tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,1685
Polymers78,8802
Non-polymers2883
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Elutes from the size exclusion Superdex 200 Increase 10/300 (GE Healthcare) column as a heterodimer at expected elution volume of 0.55 column volume.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-53 kcal/mol
Surface area24770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.407, 194.574, 86.346
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein tRNA (guanine-N(7)-)-methyltransferase / Methyltransferase-like protein 1 / mRNA (guanine-N(7)-)-methyltransferase / miRNA (guanine-N(7)-)- ...Methyltransferase-like protein 1 / mRNA (guanine-N(7)-)-methyltransferase / miRNA (guanine-N(7)-)-methyltransferase / tRNA (guanine(46)-N(7))-methyltransferase / tRNA(m7G46)-methyltransferase


Mass: 31516.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residues not visible in the structure have not been modeled. Recombinant protein did not have any affinity tags.
Source: (gene. exp.) Homo sapiens (human) / Gene: METTL1, C12orf1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UBP6, tRNA (guanine46-N7)-methyltransferase, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Protein tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 / Protein Wuho homolog / hWH / WD repeat-containing protein 4


Mass: 47363.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: MGSSHHHHHHSQDPNS is part of the expression tag and a linker. Residues not visible in the structure have not been modeled.
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR4 / Production host: Escherichia coli (E. coli) / References: UniProt: P57081
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 3.39 Å3/Da / Density % sol: 63.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2M (NH4)2SO4, 0.2M K Na Tartrate, 0.1 M Na3 citrate pH 6.5
Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 2, 2020 / Details: monochromatros
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.09→47.87 Å / Num. obs: 19262 / % possible obs: 99 % / Redundancy: 4.6 % / Biso Wilson estimate: 85.6 Å2 / Rmerge(I) obs: 0.308 / Rpim(I) all: 0.214 / Rrim(I) all: 0.377 / Net I/σ(I): 5.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) all% possible all
8.75-47.874.50.03920.88920.0280.04896.4
3.09-3.314.72.6490.933811.8313.23697.5

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
PHENIX1.20.1_4487refinement
XDSVERSION Jan 31, 2020 BUILT=20200131data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CKK for METTL1, chain D of 2VDU for WDR4

3ckk

2vdu


Resolution: 3.1→47.87 Å / SU ML: 0.4274 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.9413
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2708 966 5.09 %
Rwork0.2215 18006 -
obs0.224 18972 97.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.05 Å2
Refinement stepCycle: LAST / Resolution: 3.1→47.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4327 0 15 12 4354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00194444
X-RAY DIFFRACTIONf_angle_d0.43466033
X-RAY DIFFRACTIONf_chiral_restr0.0425668
X-RAY DIFFRACTIONf_plane_restr0.0024773
X-RAY DIFFRACTIONf_dihedral_angle_d3.6801593
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.260.40751300.33742350X-RAY DIFFRACTION91.04
3.26-3.470.34671380.3062586X-RAY DIFFRACTION99.23
3.47-3.740.31221430.25682586X-RAY DIFFRACTION99.67
3.74-4.110.23731370.23292607X-RAY DIFFRACTION99.42
4.11-4.710.26721400.18482580X-RAY DIFFRACTION98.91
4.71-5.920.25351450.18482621X-RAY DIFFRACTION99.14
5.93-47.870.22551330.19722676X-RAY DIFFRACTION96.26

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