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- PDB-6du4: Crystal structure of hMettl16 catalytic domain in complex with MA... -

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Basic information

Entry
Database: PDB / ID: 6du4
TitleCrystal structure of hMettl16 catalytic domain in complex with MAT2A 3'UTR hairpin 1
Components
  • U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase
  • hp1x-RNA (29-MER)
KeywordsTransferase/RNA / RNA methylation / Methyltransferase / protein-RNA complex / m6A and n6-methyladenosine / Transferase-RNA complex
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 / rRNA base methylation ...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 / mRNA processing / 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 / RNA (> 10) / RNA N6-adenosine-methyltransferase METTL16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsDoxtader, K. / Wang, P. / Nam, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
United States
CitationJournal: Mol. Cell / Year: 2018
Title: Structural Basis for Regulation of METTL16, an S-Adenosylmethionine Homeostasis Factor.
Authors: Doxtader, K.A. / Wang, P. / Scarborough, A.M. / Seo, D. / Conrad, N.K. / Nam, Y.
History
DepositionJun 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase
B: hp1x-RNA (29-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5856
Polymers45,1562
Non-polymers4284
Water6,936385
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-13 kcal/mol
Surface area16320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.979, 74.979, 93.213
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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


Mass: 35754.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METTL16, METT10D / Production host: Escherichia coli (E. coli)
References: UniProt: Q86W50, U6 snRNA m6A methyltransferase, mRNA (2'-O-methyladenosine-N6-)-methyltransferase
#2: RNA chain hp1x-RNA (29-MER)


Mass: 9401.684 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 2.9 Å3/Da / Density % sol: 57.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Tris (pH 8.5), 20% glycerol, and 19% polyethylene (PEG) 10000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 56305 / % possible obs: 100 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 15.9
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 1.421 / Mean I/σ(I) obs: 4.29 / Num. unique obs: 5609

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: our own model

Resolution: 1.7→35.004 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 15.43
RfactorNum. reflection% reflection
Rfree0.1726 2859 5.08 %
Rwork0.1519 --
obs0.1529 56303 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→35.004 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2303 623 28 385 3339
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073180
X-RAY DIFFRACTIONf_angle_d0.9624464
X-RAY DIFFRACTIONf_dihedral_angle_d22.91318
X-RAY DIFFRACTIONf_chiral_restr0.23511
X-RAY DIFFRACTIONf_plane_restr0.007458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6965-1.72570.2031350.17962354X-RAY DIFFRACTION88
1.7257-1.75710.1841220.17812617X-RAY DIFFRACTION96
1.7571-1.79090.19911590.1692607X-RAY DIFFRACTION98
1.7909-1.82750.1721390.16392656X-RAY DIFFRACTION98
1.8275-1.86720.18681630.15812645X-RAY DIFFRACTION99
1.8672-1.91060.17821300.15522692X-RAY DIFFRACTION100
1.9106-1.95840.14561550.14772708X-RAY DIFFRACTION100
1.9584-2.01140.2068880.14382717X-RAY DIFFRACTION100
2.0114-2.07050.15991720.14692680X-RAY DIFFRACTION100
2.0705-2.13740.15791690.14782681X-RAY DIFFRACTION100
2.1374-2.21370.19061310.15182707X-RAY DIFFRACTION100
2.2137-2.30240.17721350.14842694X-RAY DIFFRACTION100
2.3024-2.40710.1641480.1482686X-RAY DIFFRACTION100
2.4071-2.5340.19881380.15612700X-RAY DIFFRACTION100
2.534-2.69270.16951280.15212726X-RAY DIFFRACTION100
2.6927-2.90050.18731330.16422723X-RAY DIFFRACTION100
2.9005-3.19220.16891390.15922708X-RAY DIFFRACTION100
3.1922-3.65370.16951590.1422701X-RAY DIFFRACTION100
3.6537-4.60170.14311600.13332709X-RAY DIFFRACTION100
4.6017-35.01180.18861560.15682733X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -29.3993 Å / Origin y: 13.0023 Å / Origin z: -9.6505 Å
111213212223313233
T0.0379 Å20.0493 Å20.0028 Å2-0.0308 Å2-0.0331 Å2--0.0372 Å2
L1.1452 °20.1138 °20.4353 °2-2.0169 °2-0.2441 °2--1.9701 °2
S0.0702 Å °0.1268 Å °-0.1638 Å °0.0387 Å °-0.0209 Å °0.0138 Å °0.2493 Å °0.1018 Å °0.0199 Å °
Refinement TLS groupSelection details: all

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