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- PDB-6b91: Crystal structure of the N-terminal domain of human METTL16 -

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Basic information

Entry
Database: PDB / ID: 6b91
TitleCrystal structure of the N-terminal domain of human METTL16
ComponentsU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase
KeywordsTRANSFERASE / Methyltransferase-like protein 16 / RNA methylation / N6-methyladenosine
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 N6-adenosine-methyltransferase METTL16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsRuszkowska, A. / Ruszkowski, M. / Dauter, Z. / Brown, J.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R00GM111430 United States
CitationJournal: Sci Rep / Year: 2018
Title: Structural insights into the RNA methyltransferase domain of METTL16.
Authors: Ruszkowska, A. / Ruszkowski, M. / Dauter, Z. / Brown, J.A.
History
DepositionOct 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _citation.page_first ..._chem_comp.name / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_audit_support / pdbx_entity_nonpoly
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_audit_support.funding_organization / _pdbx_entity_nonpoly.name
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8275
Polymers33,6181
Non-polymers2094
Water3,729207
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)190.050, 190.050, 190.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132
Components on special symmetry positions
IDModelComponents
11A-600-

HOH

21A-606-

HOH

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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: 33617.797 Da / Num. of mol.: 1 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METTL16, METT10D
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q86W50, Transferases; Transferring one-carbon groups; Methyltransferases, mRNA (2'-O-methyladenosine-N6-)-methyltransferase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 207 / 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: 4.66 Å3/Da / Density % sol: 73.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.3 M K2HPO4, 45 mM NaH2PO4; drop contained 4 uL of protein solution (27 mg/mL) and 2 uL of reservoir solution, 25% ethylene glycol was used for cryo-protection

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 25, 2017
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 43441 / % possible obs: 99.7 % / Redundancy: 16.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.067 / Rrim(I) all: 0.069 / Net I/σ(I): 25
Reflection shellResolution: 1.94→2.05 Å / Redundancy: 14.2 % / Rmerge(I) obs: 1.37 / Mean I/σ(I) obs: 2 / Num. unique obs: 6791 / CC1/2: 0.72 / Rrim(I) all: 1.42 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
ARP/wARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2h00

2h00


Resolution: 1.94→47.51 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / SU B: 6.275 / SU ML: 0.087 / Cross valid method: FREE R-VALUE / ESU R: 0.096 / ESU R Free: 0.098
Details: HYDROGENS WERE ADDED IN THE RIDING POSITIONS FOR REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1000 2.3 %RANDOM
Rwork0.181 ---
obs0.182 42441 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 48.654 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.94→47.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2142 0 13 207 2362
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192264
X-RAY DIFFRACTIONr_bond_other_d0.0020.022178
X-RAY DIFFRACTIONr_angle_refined_deg1.6241.933059
X-RAY DIFFRACTIONr_angle_other_deg1.0193.0015025
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3395276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.88623.75104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.90715411
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7151516
X-RAY DIFFRACTIONr_chiral_restr0.10.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212534
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02520
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7062.9461086
X-RAY DIFFRACTIONr_mcbond_other1.7012.9441085
X-RAY DIFFRACTIONr_mcangle_it2.754.391365
X-RAY DIFFRACTIONr_mcangle_other2.7524.3931366
X-RAY DIFFRACTIONr_scbond_it2.4813.3221178
X-RAY DIFFRACTIONr_scbond_other2.4813.3221178
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7814.8311694
X-RAY DIFFRACTIONr_long_range_B_refined7.81724.9762623
X-RAY DIFFRACTIONr_long_range_B_other7.81624.9852624
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.94→1.99 Å
RfactorNum. reflection% reflection
Rfree0.372 70 -
Rwork0.368 2974 -
obs--95.96 %
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)
10.23750.22940.16395.2181-0.78780.537-0.1035-0.01930.0085-0.0153-0.0208-0.38420.09080.04720.12430.1760.04790.01640.03610.05020.16657.771-2.03936.753
26.6897-2.53153.79724.8476-1.55162.16820.59051.0618-0.2323-0.1347-0.46740.32450.27490.6062-0.12310.37720.0833-0.08440.17-0.03930.03735.324-12.86126.201
31.4386-1.51860.88132.18450.83025.9223-0.0303-0.0069-0.18250.1764-0.05860.23750.4658-0.16370.08890.16490.01530.0070.04030.04770.1611-4.839-4.49434.528
40.2132-0.3677-0.0641.36760.26510.37480.05480.0703-0.02990.0951-0.0180.0072-0.0479-0.0524-0.03680.14950.0249-0.03320.06750.02930.1399-6.3310.46335.564
50.0569-0.47640.02364.1603-1.32079.2806-0.05150.0268-0.10270.4698-0.12880.8024-0.081-0.52070.18020.07410.00580.06520.1476-0.00330.3054-17.146.24737.265
60.26810.5156-0.55351.8445-0.21425.2549-0.00330.12240.1629-0.07220.0260.02380.1038-0.5451-0.02270.17950.04070.01160.11630.12450.315-14.50220.63331.42
70.8809-0.98650.40544.7909-8.912819.6112-0.3857-0.0292-0.0485-0.24330.4710.07641.3446-0.9749-0.08530.3759-0.15130.07770.1783-0.0160.0939-2.05618.1036.004
82.3664-5.2148-4.037414.455812.095210.373-0.1370.127-0.0958-0.3673-0.01010.232-0.514-0.01750.14710.2274-0.0214-0.00130.27360.1150.0725-8.16423.29320.854
93.3598-1.4041-1.15573.80252.14781.28230.53081.23860.82460.7481-0.2886-0.41480.3386-0.3485-0.24220.37590.22850.14410.50910.22580.3426-4.00922.88529.505
101.2837-0.9232-0.39741.7188-0.02590.54610.01050.2690.04460.2324-0.1846-0.1524-0.14730.14290.17410.1723-0.02180.00760.22040.13010.13113.19822.15924.949
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 29
2X-RAY DIFFRACTION2A30 - 51
3X-RAY DIFFRACTION3A52 - 72
4X-RAY DIFFRACTION4A73 - 142
5X-RAY DIFFRACTION5A143 - 161
6X-RAY DIFFRACTION6A162 - 188
7X-RAY DIFFRACTION7A214 - 222
8X-RAY DIFFRACTION8A223 - 237
9X-RAY DIFFRACTION9A238 - 252
10X-RAY DIFFRACTION10A253 - 291

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