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- PDB-7nto: The structure of RRM domain of human TRMT2A at 1.23 A resolution -

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Basic information

Entry
Database: PDB / ID: 7nto
TitleThe structure of RRM domain of human TRMT2A at 1.23 A resolution
ComponentstRNA (uracil-5-)-methyltransferase homolog A
KeywordsTRANSFERASE / tRNA binding / methyltransferase / TRMT2a / polyQ aggregation
Function / homology
Function and homology information


tRNA (uracil(54)-C5)-methyltransferase activity, S-adenosyl methionine-dependent / tRNA (uracil54-C5)-methyltransferase / C-methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / mRNA processing / RNA binding / cytosol
Similarity search - Function
TRMT2A, RNA recognition motif / tRNA (uracil(54)-C(5))-methyltransferase, metazoa type / (Uracil-5)-methyltransferase family / tRNA (Uracil-5-)-methyltransferase / SAM-dependent methyltransferase RNA m(5)U-type domain profile. / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
tRNA (uracil-5-)-methyltransferase homolog A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.23 Å
AuthorsWitzenberger, M. / Janowski, R. / Davydova, E. / Niessing, D.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research Germany
CitationJournal: Comput Struct Biotechnol J / Year: 2022
Title: Small-molecule modulators of TRMT2A decrease PolyQ aggregation and PolyQ-induced cell death.
Authors: Margreiter, M.A. / Witzenberger, M. / Wasser, Y. / Davydova, E. / Janowski, R. / Metz, J. / Habib, P. / Sahnoun, S.E.M. / Sobisch, C. / Poma, B. / Palomino-Hernandez, O. / Wagner, M. / ...Authors: Margreiter, M.A. / Witzenberger, M. / Wasser, Y. / Davydova, E. / Janowski, R. / Metz, J. / Habib, P. / Sahnoun, S.E.M. / Sobisch, C. / Poma, B. / Palomino-Hernandez, O. / Wagner, M. / Carell, T. / Jon Shah, N. / Schulz, J.B. / Niessing, D. / Voigt, A. / Rossetti, G.
History
DepositionMar 10, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA (uracil-5-)-methyltransferase homolog A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,94016
Polymers9,2141
Non-polymers72615
Water1,40578
1
A: tRNA (uracil-5-)-methyltransferase homolog A
hetero molecules

A: tRNA (uracil-5-)-methyltransferase homolog A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,88032
Polymers18,4282
Non-polymers1,45230
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3980 Å2
ΔGint-208 kcal/mol
Surface area10320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.880, 36.300, 39.100
Angle α, β, γ (deg.)90.000, 119.180, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-209-

NA

21A-325-

HOH

31A-349-

HOH

41A-372-

HOH

51A-375-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein tRNA (uracil-5-)-methyltransferase homolog A / HpaII tiny fragments locus 9c protein


Mass: 9213.796 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRMT2A, HTF9C / Production host: Escherichia coli (E. coli)
References: UniProt: Q8IZ69, Transferases; Transferring one-carbon groups; Methyltransferases

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Non-polymers , 5 types, 93 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 1.78 Å3/Da / Density % sol: 30.82 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 0.2 M cesium sulfate and 2.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.000033 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000033 Å / Relative weight: 1
ReflectionResolution: 1.23→50 Å / Num. obs: 17520 / % possible obs: 97 % / Redundancy: 6.62 % / CC1/2: 1 / Net I/σ(I): 18.2
Reflection shellResolution: 1.23→1.26 Å / Mean I/σ(I) obs: 1.95 / Num. unique obs: 1293 / CC1/2: 0.614

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7NTN

7ntn


Resolution: 1.23→34.14 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.059 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1716 872 4.7 %RANDOM
Rwork0.1271 ---
obs0.1292 17520 97.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 68.62 Å2 / Biso mean: 18.833 Å2 / Biso min: 9.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å2-0.57 Å2
2--0.78 Å20 Å2
3---0.08 Å2
Refinement stepCycle: final / Resolution: 1.23→34.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms634 0 34 81 749
Biso mean--32.08 35.49 -
Num. residues----78
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.013753
X-RAY DIFFRACTIONr_bond_other_d0.0020.017735
X-RAY DIFFRACTIONr_angle_refined_deg2.1291.6521027
X-RAY DIFFRACTIONr_angle_other_deg1.5181.5831694
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.387595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.60716.88945
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.44715133
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1331512
X-RAY DIFFRACTIONr_chiral_restr0.1180.287
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02858
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02194
X-RAY DIFFRACTIONr_rigid_bond_restr4.12331488
LS refinement shellResolution: 1.23→1.262 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 47 -
Rwork0.229 1239 -
all-1286 -
obs--94.77 %
Refinement TLS params.Method: refined / Origin x: 12.1626 Å / Origin y: 0.4148 Å / Origin z: 7.7038 Å
111213212223313233
T0.0026 Å2-0.0002 Å20.0033 Å2-0.0002 Å2-0.0001 Å2--0.0047 Å2
L0.0042 °2-0.0059 °2-0.0042 °2-0.0657 °2-0.0264 °2--0.0225 °2
S-0.0001 Å °-0.0007 Å °0 Å °0.0027 Å °-0.0011 Å °-0.0024 Å °-0.0015 Å °0.0018 Å °0.0012 Å °

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