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- PDB-5il1: Crystal structure of SAM-bound METTL3-METTL14 complex -

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Basic information

Entry
Database: PDB / ID: 5il1
TitleCrystal structure of SAM-bound METTL3-METTL14 complex
Components
  • METTL14
  • METTL3
KeywordsRNA BINDING PROTEIN / 6-adenosine methylation / METTL3-METTL14 complex
Function / homology
Function and homology information


primary miRNA processing => GO:0031053 / regulation of meiotic cell cycle / RNA N6-methyladenosine methyltransferase complex / mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity / mRNA m6A methyltransferase / mRNA (N6-adenosine)-methyltransferase activity / negative regulation of hematopoietic progenitor cell differentiation / endothelial to hematopoietic transition / positive regulation of cap-independent translational initiation / adenosine to inosine editing ...primary miRNA processing => GO:0031053 / regulation of meiotic cell cycle / RNA N6-methyladenosine methyltransferase complex / mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity / mRNA m6A methyltransferase / mRNA (N6-adenosine)-methyltransferase activity / negative regulation of hematopoietic progenitor cell differentiation / endothelial to hematopoietic transition / positive regulation of cap-independent translational initiation / adenosine to inosine editing / forebrain radial glial cell differentiation / gliogenesis / RNA methylation / RNA methyltransferase activity / primary miRNA processing / S-adenosyl-L-methionine binding / regulation of T cell differentiation / dosage compensation by inactivation of X chromosome / regulation of hematopoietic stem cell differentiation / negative regulation of type I interferon-mediated signaling pathway / Processing of Capped Intron-Containing Pre-mRNA / stem cell population maintenance / mRNA destabilization / negative regulation of Notch signaling pathway / oogenesis / mRNA catabolic process / methyltransferase activity / positive regulation of translation / mRNA splicing, via spliceosome / circadian rhythm / mRNA methylation / cellular response to UV / mRNA processing / spermatogenesis / nuclear speck / protein heterodimerization activity / mRNA binding / cellular response to DNA damage stimulus / innate immune response / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
N6-adenosine-methyltransferase non-catalytic subunit METTL14-like / N6-adenosine-methyltransferase MT-A70-like / MT-A70 / MT-A70-like / MT-A70-like family profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / N6-adenosine-methyltransferase catalytic subunit / N6-adenosine-methyltransferase non-catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.71 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: METTL3
B: METTL14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8066
Polymers59,2222
Non-polymers5854
Water6,071337
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-9 kcal/mol
Surface area20850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.344, 102.344, 116.720
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-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 2.58 Å3/Da / Density % sol: 52.33 %
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: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.71→45 Å / Num. obs: 67836 / % possible obs: 100 % / Redundancy: 13.2 % / Net I/σ(I): 17.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata processing
Aimlessdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.71→45 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.47
RfactorNum. reflection% reflection
Rfree0.2069 3369 4.97 %
Rwork0.1798 --
obs0.1811 67756 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.71→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3960 0 39 337 4336
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074102
X-RAY DIFFRACTIONf_angle_d0.9045568
X-RAY DIFFRACTIONf_dihedral_angle_d17.1012442
X-RAY DIFFRACTIONf_chiral_restr0.059594
X-RAY DIFFRACTIONf_plane_restr0.006721
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7067-1.73110.34131360.31372595X-RAY DIFFRACTION99
1.7311-1.75690.31311500.27022636X-RAY DIFFRACTION100
1.7569-1.78440.28071160.25092679X-RAY DIFFRACTION100
1.7844-1.81360.31181370.24212625X-RAY DIFFRACTION100
1.8136-1.84490.27281540.23882634X-RAY DIFFRACTION100
1.8449-1.87850.26341510.22242632X-RAY DIFFRACTION100
1.8785-1.91460.25571350.22612665X-RAY DIFFRACTION100
1.9146-1.95370.23181390.20422634X-RAY DIFFRACTION100
1.9537-1.99610.23031260.19872678X-RAY DIFFRACTION100
1.9961-2.04260.21481330.18612689X-RAY DIFFRACTION100
2.0426-2.09370.21481250.18332658X-RAY DIFFRACTION100
2.0937-2.15030.20631290.18592659X-RAY DIFFRACTION100
2.1503-2.21350.21571540.1822659X-RAY DIFFRACTION100
2.2135-2.2850.24281280.18422687X-RAY DIFFRACTION100
2.285-2.36660.20681440.17892663X-RAY DIFFRACTION100
2.3666-2.46140.21591320.18122684X-RAY DIFFRACTION100
2.4614-2.57340.22631450.18642680X-RAY DIFFRACTION100
2.5734-2.70910.231210.18262709X-RAY DIFFRACTION100
2.7091-2.87880.21791510.19672674X-RAY DIFFRACTION100
2.8788-3.1010.22421510.1882718X-RAY DIFFRACTION100
3.101-3.4130.21481560.18122700X-RAY DIFFRACTION100
3.413-3.90660.16731440.16192743X-RAY DIFFRACTION100
3.9066-4.9210.16671520.13872770X-RAY DIFFRACTION100
4.921-45.78610.19251600.17652916X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 9.4879 Å / Origin y: 21.197 Å / Origin z: 17.7794 Å
111213212223313233
T0.2857 Å2-0.0495 Å20.0006 Å2-0.1725 Å20.0199 Å2--0.2343 Å2
L1.0938 °2-0.0344 °20.6482 °2-1.0263 °20.3807 °2--1.6749 °2
S0.1054 Å °-0.1138 Å °-0.1576 Å °0.3371 Å °-0.0519 Å °0.0131 Å °0.2844 Å °-0.0806 Å °-0.0447 Å °
Refinement TLS groupSelection details: all

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