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- PDB-6m1u: Crystal structure of the vertebrate conserved region (VCR) of hum... -

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Basic information

Entry
Database: PDB / ID: 6m1u
TitleCrystal structure of the vertebrate conserved region (VCR) of human METTL16
ComponentsRNA N6-adenosine-methyltransferase METTL16,RNA N6-adenosine-methyltransferase METTL16
KeywordsRNA BINDING PROTEIN / Methyltransferase
Function / homology
Function and homology information


snRNA (adenine-N6)-methylation / negative regulation of 3'-UTR-mediated mRNA stabilization / U6 snRNA m6A methyltransferase / U6 snRNA (adenine-(43)-N(6))-methyltransferase activity / 23S rRNA (adenine(1618)-N(6))-methyltransferase activity / U6 snRNA 3'-end binding / mRNA m6A methyltransferase / mRNA m(6)A methyltransferase activity / S-adenosylmethionine biosynthetic process / : ...snRNA (adenine-N6)-methylation / negative regulation of 3'-UTR-mediated mRNA stabilization / U6 snRNA m6A methyltransferase / U6 snRNA (adenine-(43)-N(6))-methyltransferase activity / 23S rRNA (adenine(1618)-N(6))-methyltransferase activity / U6 snRNA 3'-end binding / mRNA m6A methyltransferase / mRNA m(6)A methyltransferase activity / S-adenosylmethionine biosynthetic process / : / rRNA base methylation / regulation of mRNA splicing, via spliceosome / post-transcriptional regulation of gene expression / mRNA destabilization / mRNA catabolic process / RNA stem-loop binding / RNA binding / nucleus / cytoplasm
Similarity search - Function
Methyltransferase METTL16/PsiM / RNA methyltransferase / METTL16/RlmF family / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
RNA N6-adenosine-methyltransferase METTL16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.791 Å
AuthorsAoyama, T. / Yamashita, S. / Tomita, K.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H03980 Japan
Japan Society for the Promotion of Science (JSPS)18J23142 Japan
Japan Society for the Promotion of Science (JSPS)26113002 Japan
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Mechanistic insights into m6A modification of U6 snRNA by human METTL16.
Authors: Aoyama, T. / Yamashita, S. / Tomita, K.
History
DepositionFeb 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1May 27, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.2Mar 27, 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

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Assembly

Deposited unit
A: RNA N6-adenosine-methyltransferase METTL16,RNA N6-adenosine-methyltransferase METTL16


Theoretical massNumber of molelcules
Total (without water)19,1791
Polymers19,1791
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.610, 139.610, 53.130
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein RNA N6-adenosine-methyltransferase METTL16,RNA N6-adenosine-methyltransferase METTL16 / Methyltransferase 10 domain-containing protein / Methyltransferase-like protein 16 / N6-adenosine- ...Methyltransferase 10 domain-containing protein / Methyltransferase-like protein 16 / N6-adenosine-methyltransferase METTL16 / U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase


Mass: 19179.477 Da / Num. of mol.: 1 / Mutation: delta_1-309,delta_411-508
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METTL16, METT10D / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q86W50, mRNA m6A methyltransferase, U6 snRNA m6A methyltransferase

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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: 2.62 Å3/Da / Density % sol: 52.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM Tris-HCl, pH 7.4, 20% (w/v) PEG3350, 200 mM sodium citrate, 4% (w/v) formamide and 5 mM dextran sulfate sodium salt.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.79→48.641 Å / Num. obs: 5022 / % possible obs: 99.8 % / Redundancy: 81.688 % / Biso Wilson estimate: 85.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.343 / Rrim(I) all: 0.346 / Χ2: 0.862 / Net I/σ(I): 17.68 / Num. measured all: 410237 / Scaling rejects: 32
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.79-2.8681.7924.7611.26291183633560.6344.79198.1
2.86-2.9484.0813.721.76311943713710.753.743100
2.94-3.0383.683.0332.28282003373370.8283.052100
3.03-3.1283.32423.53285803433430.9262.012100
3.12-3.2281.1331.6784.37256383163160.9291.688100
3.22-3.3479.3711.265.8258753263260.9671.268100
3.34-3.4673.6431.0277.16226823083080.9761.034100
3.46-3.675.8950.66411.26223892952950.9850.669100
3.6-3.7686.1580.5913.45245552852850.9920.593100
3.76-3.9587.1590.41118.79236202712710.9970.413100
3.95-4.1686.6860.33922.22226252612610.9970.341100
4.16-4.4186.5670.23430.13218152522520.9990.236100
4.41-4.7285.9460.15939.17189942212210.9990.16100
4.72-5.183.1490.15638.82183762212210.9990.157100
5.1-5.5882.1710.17734.98163521991990.9990.178100
5.58-6.2477.7660.2329.2143091841840.9970.232100
6.24-7.2169.4750.1634.71109771581580.9990.161100
7.21-8.8381.9730.10449.771196814614610.105100
8.83-12.4881.7940.06274.47875210710710.063100
12.48-48.64164.8920.06566.17421867650.9990.06597

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.791→48.641 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.75
RfactorNum. reflection% reflection
Rfree0.263 251 5.01 %
Rwork0.2336 --
obs0.2349 5013 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 234.79 Å2 / Biso mean: 87.7021 Å2 / Biso min: 50.97 Å2
Refinement stepCycle: final / Resolution: 2.791→48.641 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms987 0 0 0 987
Num. residues----122
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7911-3.51630.31011240.3161235099
3.5163-48.640.2481270.21052412100
Refinement TLS params.Method: refined / Origin x: 24.4936 Å / Origin y: 64 Å / Origin z: 18.062 Å
111213212223313233
T0.4674 Å2-0.0327 Å20.0211 Å2-0.51 Å2-0.0143 Å2--0.507 Å2
L4.2908 °2-0.8019 °20.5164 °2-3.5085 °2-0.3153 °2--5.1619 °2
S0.1142 Å °0.435 Å °0.2573 Å °-0.2474 Å °-0.0931 Å °0.0384 Å °0.2383 Å °-0.4737 Å °-0.017 Å °
Refinement TLS groupSelection details: all

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