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- PDB-5il0: Crystal structural of the METTL3-METTL14 complex for N6-adenosine... -

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Basic information

Entry
Database: PDB / ID: 5il0
TitleCrystal structural of the METTL3-METTL14 complex for N6-adenosine methylation
Components
  • METTL14
  • METTL3
KeywordsRNA BINDING PROTEIN / methyltransferase
Function / homology
Function and homology information


negative regulation of hematopoietic progenitor cell differentiation / mRNA m6A methyltransferase / mRNA m(6)A methyltransferase activity / RNA N6-methyladenosine methyltransferase complex / positive regulation of cap-independent translational initiation / endothelial to hematopoietic transition / RNA methyltransferase activity / regulation of meiotic cell cycle / RNA methylation / dosage compensation by inactivation of X chromosome ...negative regulation of hematopoietic progenitor cell differentiation / mRNA m6A methyltransferase / mRNA m(6)A methyltransferase activity / RNA N6-methyladenosine methyltransferase complex / positive regulation of cap-independent translational initiation / endothelial to hematopoietic transition / RNA methyltransferase activity / regulation of meiotic cell cycle / RNA methylation / dosage compensation by inactivation of X chromosome / primary miRNA processing / forebrain radial glial cell differentiation / oxidoreductase complex / S-adenosyl-L-methionine binding / mRNA stabilization / gliogenesis / mRNA modification / regulation of hematopoietic stem cell differentiation / regulation of neuron differentiation / regulation of T cell 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 splicing, via spliceosome / 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
BROMIDE ION / N6-adenosine-methyltransferase catalytic subunit / N6-adenosine-methyltransferase non-catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.882 Å
AuthorsWang, X. / Guan, Z. / Zou, T. / Yin, P.
CitationJournal: Nature / Year: 2016
Title: Structural basis of N6-adenosine methylation by the METTL3-METTL14 complex
Authors: Wang, X. / Feng, J. / Xue, Y. / Guan, Z. / Zhang, D. / Liu, Z. / Gong, Z. / Wang, Q. / Huang, J. / Tang, C. / Zou, T. / Yin, P.
History
DepositionMar 4, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: METTL3
B: METTL14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4265
Polymers59,2222
Non-polymers2043
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5520 Å2
ΔGint-15 kcal/mol
Surface area21720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.695, 101.695, 116.478
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 METTL3 / MT-A70 / Methyltransferase-like protein 3


Mass: 24427.109 Da / Num. of mol.: 1 / Fragment: UNP residues 369-580
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METTL3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q86U44, mRNA (2'-O-methyladenosine-N6-)-methyltransferase
#2: Protein METTL14 / Methyltransferase-like protein 14


Mass: 34794.402 Da / Num. of mol.: 1 / Fragment: UNP residues 109-408
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METTL14 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9HCE5, mRNA (2'-O-methyladenosine-N6-)-methyltransferase
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#4: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Br
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / Source method: isolated from a natural source / Formula: H2O
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: 2.55 Å3/Da / Density % sol: 51.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.7 / Details: PEG 8000, sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.92 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 50152 / % possible obs: 99.9 % / Redundancy: 14.6 % / Net I/σ(I): 37.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data scaling
SHELXDEphasing
BUCCANEERmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.882→36.272 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.52
RfactorNum. reflection% reflection
Rfree0.205 2511 5.01 %
Rwork0.1747 --
obs0.1763 50070 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.882→36.272 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4016 0 0 331 4347
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074117
X-RAY DIFFRACTIONf_angle_d0.8795584
X-RAY DIFFRACTIONf_dihedral_angle_d16.7722459
X-RAY DIFFRACTIONf_chiral_restr0.055596
X-RAY DIFFRACTIONf_plane_restr0.006725
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8817-1.91790.27961170.23562588X-RAY DIFFRACTION99
1.9179-1.9570.25821140.22422637X-RAY DIFFRACTION100
1.957-1.99960.24511300.21332589X-RAY DIFFRACTION100
1.9996-2.04610.24251290.20682600X-RAY DIFFRACTION100
2.0461-2.09730.2521350.19432609X-RAY DIFFRACTION100
2.0973-2.1540.22771500.18272611X-RAY DIFFRACTION100
2.154-2.21730.2041440.17072599X-RAY DIFFRACTION100
2.2173-2.28890.19371300.17682612X-RAY DIFFRACTION100
2.2889-2.37070.22171590.17162623X-RAY DIFFRACTION100
2.3707-2.46560.21261390.1772615X-RAY DIFFRACTION100
2.4656-2.57780.1811360.17662636X-RAY DIFFRACTION100
2.5778-2.71360.24541460.18042640X-RAY DIFFRACTION100
2.7136-2.88360.23051340.18552641X-RAY DIFFRACTION100
2.8836-3.10610.20391350.18662655X-RAY DIFFRACTION100
3.1061-3.41850.20051470.18082658X-RAY DIFFRACTION100
3.4185-3.91260.19581490.15552681X-RAY DIFFRACTION100
3.9126-4.92760.17071440.14182714X-RAY DIFFRACTION100
4.9276-36.2790.19791730.18232851X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 9.5129 Å / Origin y: 21.5197 Å / Origin z: 133.6862 Å
111213212223313233
T0.2302 Å2-0.0395 Å2-0.0092 Å2-0.1612 Å20.019 Å2--0.1952 Å2
L1.1611 °2-0.0578 °20.5277 °2-1.0202 °20.3359 °2--1.5488 °2
S0.0851 Å °-0.1434 Å °-0.1284 Å °0.2861 Å °0.01 Å °-0.0546 Å °0.2412 Å °-0.0659 Å °-0.0689 Å °
Refinement TLS groupSelection details: all

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