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- PDB-5k7m: Crystal structure of the catalytic domains of Mettl3/Mettl14 complex -

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Basic information

Entry
Database: PDB / ID: 5k7m
TitleCrystal structure of the catalytic domains of Mettl3/Mettl14 complex
Components
  • N6-adenosine-methyltransferase 70 kDa subunit
  • N6-adenosine-methyltransferase subunit METTL14
KeywordsTRANSFERASE / methyltransferase / methyladenosine / m6A
Function / homology
Function and homology information


mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity / mRNA m6A methyltransferase / RNA N6-methyladenosine methyltransferase complex / negative regulation of hematopoietic progenitor cell differentiation / mRNA m(6)A methyltransferase activity / 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 m6A methyltransferase / RNA N6-methyladenosine methyltransferase complex / negative regulation of hematopoietic progenitor cell differentiation / mRNA m(6)A methyltransferase activity / positive regulation of cap-independent translational initiation / adenosine to inosine editing / endothelial to hematopoietic transition / RNA methyltransferase activity / regulation of meiotic cell cycle / RNA methylation / primary miRNA processing / : / forebrain radial glial cell differentiation / gliogenesis / dosage compensation by inactivation of X chromosome / S-adenosyl-L-methionine binding / 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 / positive regulation of translation / mRNA splicing, via spliceosome / mRNA processing / circadian rhythm / cellular response to UV / spermatogenesis / nuclear body / nuclear speck / protein heterodimerization activity / mRNA binding / innate immune response / 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
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 1.5Mar 6, 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


Theoretical massNumber of molelcules
Total (without water)65,3062
Polymers65,3062
Non-polymers00
Water8,791488
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-18 kcal/mol
Surface area21040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.864, 101.864, 117.661
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 488 / 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: 2.34 Å3/Da / Density % sol: 47.36 %
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 PILATUS 12M / Detector: PIXEL / Date: Feb 18, 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: 74698 / % possible obs: 100 % / Redundancy: 20 % / Net I/σ(I): 47.3

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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→38.506 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1838 3758 5.04 %
Rwork0.16 --
obs0.1612 74606 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→38.506 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3965 0 0 488 4453
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074108
X-RAY DIFFRACTIONf_angle_d0.9325585
X-RAY DIFFRACTIONf_dihedral_angle_d15.2292467
X-RAY DIFFRACTIONf_chiral_restr0.057600
X-RAY DIFFRACTIONf_plane_restr0.006726
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6498-1.67070.21251090.19542392X-RAY DIFFRACTION91
1.6707-1.69270.22671380.18782591X-RAY DIFFRACTION100
1.6927-1.71580.17981270.17942590X-RAY DIFFRACTION100
1.7158-1.74040.21111500.16972575X-RAY DIFFRACTION100
1.7404-1.76630.18371250.1692628X-RAY DIFFRACTION100
1.7663-1.79390.18641600.16492558X-RAY DIFFRACTION100
1.7939-1.82330.19051330.16482629X-RAY DIFFRACTION100
1.8233-1.85480.18551090.16342613X-RAY DIFFRACTION100
1.8548-1.88850.17571530.15332579X-RAY DIFFRACTION100
1.8885-1.92480.18071320.15762616X-RAY DIFFRACTION100
1.9248-1.96410.17461260.15542638X-RAY DIFFRACTION100
1.9641-2.00680.18071440.15892569X-RAY DIFFRACTION100
2.0068-2.05350.20481260.15412635X-RAY DIFFRACTION100
2.0535-2.10490.15831520.1592582X-RAY DIFFRACTION100
2.1049-2.16180.19661430.15462642X-RAY DIFFRACTION100
2.1618-2.22540.17991410.15592618X-RAY DIFFRACTION100
2.2254-2.29720.18521530.15912593X-RAY DIFFRACTION100
2.2972-2.37930.18991500.15622604X-RAY DIFFRACTION100
2.3793-2.47450.1781330.16532646X-RAY DIFFRACTION100
2.4745-2.58710.1831340.15942644X-RAY DIFFRACTION100
2.5871-2.72350.17871350.16042640X-RAY DIFFRACTION100
2.7235-2.89410.17521330.16522660X-RAY DIFFRACTION100
2.8941-3.11740.19331130.1672694X-RAY DIFFRACTION100
3.1174-3.4310.18371590.16322647X-RAY DIFFRACTION100
3.431-3.9270.17831400.1432710X-RAY DIFFRACTION100
3.927-4.9460.15231770.13492688X-RAY DIFFRACTION100
4.946-38.51690.22571630.18592867X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -21.7672 Å / Origin y: 8.4815 Å / Origin z: -12.3176 Å
111213212223313233
T0.0651 Å20.0261 Å2-0.0141 Å2-0.0854 Å20.0036 Å2--0.0751 Å2
L0.9834 °20.1468 °2-0.4688 °2-0.8288 °20.3361 °2--1.8027 °2
S0.0231 Å °-0.2495 Å °-0.0124 Å °0.1075 Å °0.0307 Å °-0.0756 Å °-0.0429 Å °0.2399 Å °-0.0365 Å °
Refinement TLS groupSelection details: all

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