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- PDB-6b92: Crystal Structure of the N-terminal domain of human METTL16 in co... -

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Basic information

Entry
Database: PDB / ID: 6b92
TitleCrystal Structure of the N-terminal domain of human METTL16 in complex with SAH
ComponentsU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase
KeywordsTRANSFERASE / methyltransferase-like protein 16 / RNA methylation / N6-methyladenosine / S-adenosylmethionine / S-adenosylhomocysteine
Function / homology
Function and homology information


snRNA (adenine-N6)-methylation / U6 snRNA m6A methyltransferase / U6 snRNA (adenine-(43)-N(6))-methyltransferase activity / negative regulation of 3'-UTR-mediated mRNA stabilization / 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 / U6 snRNA m6A methyltransferase / U6 snRNA (adenine-(43)-N(6))-methyltransferase activity / negative regulation of 3'-UTR-mediated mRNA stabilization / 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
S-ADENOSYL-L-HOMOCYSTEINE / RNA N6-adenosine-methyltransferase METTL16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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)34,2506
Polymers33,6181
Non-polymers6335
Water3,261181
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)190.351, 190.351, 190.351
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-579-

HOH

21A-580-

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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 4.77 Å3/Da / Density % sol: 74.23 %
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; 0.2 uL of 200 mM SAM solution (buffered in 50 mM Hepes pH7.5) was added to the ...Details: 1.3 M K2HPO4, 45 mM NaH2PO4; drop contained 4 uL of protein solution (27 mg/mL) and 2 uL of reservoir solution; 0.2 uL of 200 mM SAM solution (buffered in 50 mM Hepes pH7.5) was added to the drop with mature crystals. 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: 2.1→50 Å / Num. obs: 34224 / % possible obs: 99.3 % / Redundancy: 17.3 % / CC1/2: 1 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.066 / Net I/σ(I): 28.7
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 14.2 % / Rmerge(I) obs: 1.36 / Mean I/σ(I) obs: 2 / Num. unique obs: 5267 / CC1/2: 0.72 / Rrim(I) all: 1.41 / % possible all: 95.9

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Processing

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

2h00


Resolution: 2.1→44.87 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / SU B: 7.465 / SU ML: 0.098 / Cross valid method: FREE R-VALUE / ESU R: 0.122 / ESU R Free: 0.125
Details: HYDROGENS WERE ADDED IN THE RIDING POSITIONS FOR REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1027 3 %RANDOM
Rwork0.181 ---
obs0.182 33194 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 54.009 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.1→44.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2113 0 42 181 2336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022257
X-RAY DIFFRACTIONr_bond_other_d0.0020.022174
X-RAY DIFFRACTIONr_angle_refined_deg1.6761.9513052
X-RAY DIFFRACTIONr_angle_other_deg1.0162.9975015
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4585270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.47623.654104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.23215407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3631517
X-RAY DIFFRACTIONr_chiral_restr0.1010.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212503
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02516
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_it2.2733.7561068
X-RAY DIFFRACTIONr_mcbond_other2.2583.7551068
X-RAY DIFFRACTIONr_mcangle_it3.4985.6051339
X-RAY DIFFRACTIONr_mcangle_other3.4965.6081340
X-RAY DIFFRACTIONr_scbond_it2.844.221189
X-RAY DIFFRACTIONr_scbond_other2.8424.2181187
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6066.1281713
X-RAY DIFFRACTIONr_long_range_B_refined7.76631.1092583
X-RAY DIFFRACTIONr_long_range_B_other7.76431.1182584
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 68 -
Rwork0.363 2197 -
obs--91.29 %
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)
11.2211.0683-0.2749.01830.26160.4952-0.1736-0.0742-0.0248-0.05340.0983-0.50190.08080.0070.07530.16430.03510.01940.02790.02420.13776.887-2.94837.369
20.2617-0.5677-0.02551.3997-0.12840.368-0.01410.0781-0.02250.047-0.13180.04950.00940.00010.14590.17810.0265-0.03530.0470.02670.143-3.5942.88633.298
31.4484-2.22131.06673.5183-0.77317.6508-0.33490.2213-0.42310.5316-0.40160.7939-0.1613-0.43430.73650.0849-0.04480.12940.1231-0.10890.3414-17.1466.54536.65
40.69030.6511-0.56770.6661-0.44070.9604-0.05470.12250.0756-0.01460.09220.01150.0163-0.0266-0.03760.17580.042-0.02150.11190.10920.1587-4.05721.93124.697
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 29
2X-RAY DIFFRACTION2A30 - 141
3X-RAY DIFFRACTION3A142 - 161
4X-RAY DIFFRACTION4A162 - 291

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