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- PDB-6gt5: METTL16 MTase domain (crystal form 2) -

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Basic information

Entry
Database: PDB / ID: 6gt5
TitleMETTL16 MTase domain (crystal form 2)
ComponentsU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase
KeywordsTRANSFERASE / RNA 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
RNA N6-adenosine-methyltransferase METTL16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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
DepositionJun 15, 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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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


Theoretical massNumber of molelcules
Total (without water)66,6912
Polymers66,6912
Non-polymers00
Water45025
1
A: U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase


Theoretical massNumber of molelcules
Total (without water)33,3461
Polymers33,3461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase


Theoretical massNumber of molelcules
Total (without water)33,3461
Polymers33,3461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.550, 89.550, 179.130
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 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: 33345.543 Da / Num. of mol.: 2
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 BL21(DE3) (bacteria)
References: UniProt: Q86W50, U6 snRNA m6A methyltransferase, mRNA (2'-O-methyladenosine-N6-)-methyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.7 Å3/Da / Density % sol: 54.5 % / Description: Rod shaped
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-Tris propane, 0.2 M pottassium-sodium tartrate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 2, 2018 / Details: Be CRL and Multilayer mirror
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 2.45→80.1 Å / Num. obs: 12391 / % possible obs: 93.3 % / Redundancy: 6.9 % / Biso Wilson estimate: 63.09 Å2 / CC1/2: 0.967 / Rmerge(I) obs: 0.36 / Rpim(I) all: 0.124 / Rrim(I) all: 0.331 / Net I/σ(I): 4.5
Reflection shellResolution: 2.45→2.8 Å / Redundancy: 10.8 % / Rmerge(I) obs: 1.58 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 619 / CC1/2: 0.65 / Rpim(I) all: 0.5 / Rrim(I) all: 1.66 / % possible all: 79.9

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Processing

Software
NameVersionClassification
MxCuBEv2.2data collection
XDSBUILT 20171111data reduction
Aimless0.6.2data scaling
autoPROC1.0.5data scaling
STARANISO1.10.9data scaling
PHASER2.7.17phasing
BUSTER2.10.3refinement
Coot0.8.9.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GFN

6gfn


Resolution: 2.45→80.1 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.877 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.432
RfactorNum. reflection% reflectionSelection details
Rfree0.24 617 4.98 %RANDOM
Rwork0.182 ---
obs0.185 12391 45 %-
Displacement parametersBiso mean: 57.14 Å2
Baniso -1Baniso -2Baniso -3
1-2.9738 Å20 Å20 Å2
2--2.9738 Å20 Å2
3----5.9476 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: 1 / Resolution: 2.45→80.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4011 0 0 25 4036
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0094104HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.15564HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1405SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes680HARMONIC5
X-RAY DIFFRACTIONt_it4104HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.61
X-RAY DIFFRACTIONt_other_torsion22.11
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion533SEMIHARMONIC5
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_contact4520SEMIHARMONIC4
LS refinement shellResolution: 2.45→2.75 Å / Total num. of bins used: 30
RfactorNum. reflection% reflection
Rfree0.3054 -5.07 %
Rwork0.2336 393 -
all0.2375 414 -
obs--5.22 %
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)
12.40930.3239-1.28530.90090.67147.8845-0.13710.11920.0182-0.05880.17130.14720.22670.0644-0.0342-0.1930.09980.0468-0.17010.0531-0.0865-4.8022-25.6985-18.2369
21.4894-0.0072-1.28012.12780.03335.09110.2726-0.03720.01580.4874-0.194-0.13220.44760.6091-0.0786-0.250.1229-0.0460.2552-0.1059-0.284116.3742-33.736512.4419
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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