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- PDB-5k7w: Crystal structure of the catalytic domain of Mettl3/Mettl14 compl... -

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Basic information

Entry
Database: PDB / ID: 5k7w
TitleCrystal structure of the catalytic domain of Mettl3/Mettl14 complex with SAH
Components
  • N6-adenosine-methyltransferase 70 kDa subunit
  • N6-adenosine-methyltransferase subunit METTL14
KeywordsTRANSFERASE / methyltransferase / methyladenosine / m6A
Function / homology
Function and homology information


negative regulation of hematopoietic progenitor cell differentiation / mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity / mRNA m6A methyltransferase / mRNA m(6)A methyltransferase activity / RNA N6-methyladenosine methyltransferase complex / positive regulation of cap-independent translational initiation / adenosine to inosine editing / RNA methyltransferase activity / endothelial to hematopoietic transition / RNA methylation ...negative regulation of hematopoietic progenitor cell differentiation / mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity / mRNA m6A methyltransferase / mRNA m(6)A methyltransferase activity / RNA N6-methyladenosine methyltransferase complex / positive regulation of cap-independent translational initiation / adenosine to inosine editing / RNA methyltransferase activity / endothelial to hematopoietic transition / RNA methylation / regulation of meiotic cell cycle / primary miRNA processing / dosage compensation by inactivation of X chromosome / : / forebrain radial glial cell differentiation / S-adenosyl-L-methionine binding / gliogenesis / mRNA stabilization / regulation of hematopoietic stem cell differentiation / regulation of T cell differentiation / regulation of neuron differentiation / negative regulation of type I interferon-mediated signaling pathway / stem cell population maintenance / oogenesis / mRNA destabilization / negative regulation of Notch signaling pathway / mRNA catabolic process / Processing of Capped Intron-Containing Pre-mRNA / positive regulation of translation / mRNA processing / mRNA splicing, via spliceosome / 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
S-ADENOSYL-L-HOMOCYSTEINE / N6-adenosine-methyltransferase catalytic subunit / N6-adenosine-methyltransferase non-catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsWang, P. / Doxtader, K.A. / Nam, Y.
Funding support United States, 4items
OrganizationGrant numberCountry
Pew Scholar United States
Packard Fellow United States
Welch FoundationI-1851 United States
Cancer Prevention and Research Institute of Texas (CPRIT)R1221 United States
CitationJournal: Mol.Cell / Year: 2016
Title: Structural Basis for Cooperative Function of Mettl3 and Mettl14 Methyltransferases.
Authors: Wang, P. / Doxtader, K.A. / Nam, Y.
History
DepositionMay 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Aug 10, 2016Group: Database references
Revision 1.3Apr 24, 2019Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N6-adenosine-methyltransferase 70 kDa subunit
B: N6-adenosine-methyltransferase subunit METTL14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6913
Polymers65,3062
Non-polymers3841
Water9,980554
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-18 kcal/mol
Surface area21030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.942, 101.942, 118.009
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 BL21(DE3) (bacteria)
References: UniProt: Q86U44, mRNA (2'-O-methyladenosine-N6-)-methyltransferase
#2: Protein N6-adenosine-methyltransferase subunit METTL14 / Methyltransferase-like protein 14


Mass: 39573.699 Da / Num. of mol.: 1 / Fragment: Catalytic domain residues 111-456
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METTL14, KIAA1627 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9HCE5, mRNA (2'-O-methyladenosine-N6-)-methyltransferase
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 554 / 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: 2.33 Å3/Da / Density % sol: 47.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Tris pH 8.0, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 75134 / % possible obs: 100 % / Redundancy: 16.2 % / Net I/σ(I): 32.8

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155)refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.65→46.793 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.98
RfactorNum. reflection% reflection
Rfree0.1794 3774 5.03 %
Rwork0.1598 --
obs0.1608 75006 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.65→46.793 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4011 0 0 554 4565
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064143
X-RAY DIFFRACTIONf_angle_d0.9245629
X-RAY DIFFRACTIONf_dihedral_angle_d15.9892477
X-RAY DIFFRACTIONf_chiral_restr0.058603
X-RAY DIFFRACTIONf_plane_restr0.006729
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6504-1.67120.21871150.19782605X-RAY DIFFRACTION99
1.6712-1.69320.21171400.18982588X-RAY DIFFRACTION100
1.6932-1.71640.22091250.18292601X-RAY DIFFRACTION100
1.7164-1.7410.18691510.17562576X-RAY DIFFRACTION100
1.741-1.76690.20271210.172615X-RAY DIFFRACTION100
1.7669-1.79460.18441600.16382590X-RAY DIFFRACTION100
1.7946-1.8240.20661350.16522619X-RAY DIFFRACTION100
1.824-1.85540.18971160.16142636X-RAY DIFFRACTION100
1.8554-1.88920.1541450.15722573X-RAY DIFFRACTION100
1.8892-1.92550.2071380.16552615X-RAY DIFFRACTION100
1.9255-1.96480.18251240.1672631X-RAY DIFFRACTION100
1.9648-2.00750.18661480.15682608X-RAY DIFFRACTION100
2.0075-2.05420.17461230.14932639X-RAY DIFFRACTION100
2.0542-2.10560.15981500.15462613X-RAY DIFFRACTION100
2.1056-2.16250.18281460.15022619X-RAY DIFFRACTION100
2.1625-2.22620.17521430.15682620X-RAY DIFFRACTION100
2.2262-2.2980.18631550.15692604X-RAY DIFFRACTION100
2.298-2.38020.18941470.15552634X-RAY DIFFRACTION100
2.3802-2.47540.18251370.16392642X-RAY DIFFRACTION100
2.4754-2.58810.17231280.16342650X-RAY DIFFRACTION100
2.5881-2.72450.17981390.16112637X-RAY DIFFRACTION100
2.7245-2.89520.18321330.16322671X-RAY DIFFRACTION100
2.8952-3.11870.17191150.16582716X-RAY DIFFRACTION100
3.1187-3.43250.18571590.16032644X-RAY DIFFRACTION100
3.4325-3.92890.171400.14252721X-RAY DIFFRACTION100
3.9289-4.94920.14021780.13982699X-RAY DIFFRACTION100
4.9492-46.81150.20951630.17972866X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -21.5231 Å / Origin y: 8.9624 Å / Origin z: -11.8504 Å
111213212223313233
T0.04 Å20.0244 Å2-0.0114 Å2-0.0695 Å20.0054 Å2--0.0503 Å2
L0.7814 °20.0008 °2-0.2575 °2-0.6137 °20.4188 °2--1.0858 °2
S-0.0325 Å °-0.1753 Å °-0.0327 Å °0.0309 Å °0.0629 Å °-0.0707 Å °0.0145 Å °0.1325 Å °-0.0033 Å °
Refinement TLS groupSelection details: all

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