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- PDB-6gfk: delta-N METTL16 MTase domain -

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Basic information

Entry
Database: PDB / ID: 6gfk
Titledelta-N METTL16 MTase domain
ComponentsU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase
KeywordsTRANSFERASE / SAM 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
S-ADENOSYL-L-HOMOCYSTEINE / RNA N6-adenosine-methyltransferase METTL16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChen, K.M. / Mendel, M. / Homolka, D. / McCarthy, A.A. / Pillai, R.S.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science FoundationGermMethylation and Origin-of-pi Switzerland
CitationJournal: Mol. Cell / Year: 2018
Title: Methylation of Structured RNA by the m6A Writer METTL16 Is Essential for Mouse Embryonic Development.
Authors: Mendel, M. / Chen, K.M. / Homolka, D. / Gos, P. / Pandey, R.R. / McCarthy, A.A. / Pillai, R.S.
History
DepositionApr 30, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 19, 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 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase
B: U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase
C: U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,65311
Polymers86,0203
Non-polymers1,6348
Water1,802100
1
A: U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2504
Polymers28,6731
Non-polymers5773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2504
Polymers28,6731
Non-polymers5773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1543
Polymers28,6731
Non-polymers4802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase
C: U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase
hetero molecules

A: U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase
C: U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase
hetero molecules

B: U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase
hetero molecules

B: U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,30622
Polymers172,0396
Non-polymers3,26716
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
crystal symmetry operation3_564-x+y,-x+1,z-1/31
crystal symmetry operation5_564x-y,-y+1,-z-1/31
Buried area20470 Å2
ΔGint-231 kcal/mol
Surface area48630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.768, 133.768, 78.701
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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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: 28673.184 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METTL16, METT10D / Plasmid: pETM-11-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q86W50, U6 snRNA m6A methyltransferase, mRNA (2'-O-methyladenosine-N6-)-methyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.35 Å3/Da / Density % sol: 47.6 % / Description: Nice blocks
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1.7M Ammonium Sulfate, 0.2M K/Na Tartrate, 0.1M Na Citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 24, 2017 / Details: Be CRL and elliptical mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.3→46 Å / Num. obs: 36074 / % possible obs: 99.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 62.8 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.037 / Rrim(I) all: 0.07 / Net I/σ(I): 10.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.721 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3538 / CC1/2: 0.996 / Rpim(I) all: 0.55 / Rrim(I) all: 1.03 / % possible all: 99.6

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Processing

Software
NameVersionClassification
MxCuBEv2.1data collection
XDSdata reduction
Aimless0.5.32data scaling
PHASERphasing
BUSTER2.10.3refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2h00

2h00


Resolution: 2.3→31.95 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.943 / SU R Cruickshank DPI: 0.281 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.274 / SU Rfree Blow DPI: 0.201 / SU Rfree Cruickshank DPI: 0.205
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1820 5.05 %RANDOM
Rwork0.195 ---
obs0.196 36037 99.2 %-
Displacement parametersBiso mean: 67.16 Å2
Baniso -1Baniso -2Baniso -3
1--4.3015 Å20 Å20 Å2
2---4.3015 Å20 Å2
3---8.603 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: 1 / Resolution: 2.3→31.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5281 0 103 100 5484
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0095528HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.047500HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1908SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes944HARMONIC5
X-RAY DIFFRACTIONt_it5528HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.18
X-RAY DIFFRACTIONt_other_torsion17.25
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion725SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6202SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.37 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.2351 153 5.24 %
Rwork0.2177 2765 -
all0.2186 2918 -
obs--99.53 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.83790.1394-0.56631.52250.36562.44250.1272-0.142-0.00080.2641-0.02630.15930.0952-0.0146-0.1009-0.0836-0.0567-0.01140.03490.0005-0.1551-25.995240.9468-8.5379
24.9535-0.0851-0.66231.3479-0.14011.6157-0.15950.0457-0.2406-0.27360.05060.01440.1838-0.21380.1089-0.0859-0.0602-0.044-0.0881-0.013-0.161817.540438.6714-14.6
34.45-1.8348-0.14062.58360.17291.6953-0.20990.0570.16470.0524-0.0864-0.4768-0.08080.25560.2962-0.1724-0.0391-0.0406-0.07520.1587-0.1235-16.221269.0567-9.5795
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }

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