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- PDB-7ntn: The structure of RRM domain of human TRMT2A at 2 A resolution -

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Basic information

Entry
Database: PDB / ID: 7ntn
TitleThe structure of RRM domain of human TRMT2A at 2 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: 2.016 Å
AuthorsDavydova, E. / Janowski, R. / Witzenberger, M. / 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

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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)9,7279
Polymers9,2141
Non-polymers5148
Water55831
1
A: tRNA (uracil-5-)-methyltransferase homolog A
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)233,458216
Polymers221,13124
Non-polymers12,326192
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation14_665-y+1,-x+1,-z1
crystal symmetry operation15_565y,-x+1,z1
crystal symmetry operation16_655-y+1,x,z1
crystal symmetry operation33_554y,z+1/2,x-1/21
crystal symmetry operation34_655-y+1,z+1/2,-x+1/21
crystal symmetry operation35_555y,-z+1/2,-x+1/21
crystal symmetry operation36_654-y+1,-z+1/2,x-1/21
crystal symmetry operation41_555x,z+1/2,-y+1/21
crystal symmetry operation42_654-x+1,z+1/2,y-1/21
crystal symmetry operation43_655-x+1,-z+1/2,-y+1/21
crystal symmetry operation44_554x,-z+1/2,y-1/21
crystal symmetry operation53_554z+1/2,x,y-1/21
crystal symmetry operation54_565z+1/2,-x+1,-y+1/21
crystal symmetry operation55_564-z+1/2,-x+1,y-1/21
crystal symmetry operation56_555-z+1/2,x,-y+1/21
crystal symmetry operation69_555z+1/2,y,-x+1/21
crystal symmetry operation70_564z+1/2,-y+1,x-1/21
crystal symmetry operation71_554-z+1/2,y,x-1/21
crystal symmetry operation72_565-z+1/2,-y+1,-x+1/21
Buried area44210 Å2
ΔGint-1069 kcal/mol
Surface area82210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.450, 131.450, 131.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-201-

SO4

21A-205-

CL

31A-322-

HOH

41A-329-

HOH

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Components

#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
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
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: 2.57 Å3/Da / Density % sol: 52.1 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.22M lithium sulfate, 0.1M sodium acetate (pH 4.5) and 26 % PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0093 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0093 Å / Relative weight: 1
ReflectionResolution: 2.016→50 Å / Num. obs: 6872 / % possible obs: 100 % / Redundancy: 29.45 % / CC1/2: 1 / Net I/σ(I): 36.42
Reflection shellResolution: 2.016→2.07 Å / Mean I/σ(I) obs: 3.85 / Num. unique obs: 1079 / CC1/2: 0.92

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: sequence

Resolution: 2.016→46.475 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2514 360 5.24 %
Rwork0.2051 6512 -
obs0.2072 6872 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 160.09 Å2 / Biso mean: 52.1131 Å2 / Biso min: 24.3 Å2
Refinement stepCycle: final / Resolution: 2.016→46.475 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms624 0 29 31 684
Biso mean--84.23 53.2 -
Num. residues----77
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006689
X-RAY DIFFRACTIONf_angle_d0.975938
X-RAY DIFFRACTIONf_chiral_restr0.04898
X-RAY DIFFRACTIONf_plane_restr0.005118
X-RAY DIFFRACTIONf_dihedral_angle_d15.363564
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.0161-2.30780.30221320.22292072
2.3078-2.90760.27891190.26052128
Refinement TLS params.Method: refined / Origin x: 55.576 Å / Origin y: 34.0871 Å / Origin z: 15.2121 Å
111213212223313233
T0.3167 Å20.0548 Å2-0.0767 Å2-0.3005 Å2-0.0165 Å2--0.2542 Å2
L2.2568 °2-0.184 °2-1.638 °2-1.2317 °20.8929 °2--1.6543 °2
S0.0467 Å °-0.1747 Å °-0.0441 Å °-0.007 Å °0.0877 Å °-0.0661 Å °0.0527 Å °0.2028 Å °0.0005 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA70 - 146
2X-RAY DIFFRACTION1allZ4 - 107
3X-RAY DIFFRACTION1allB1 - 4
4X-RAY DIFFRACTION1allD6 - 11
5X-RAY DIFFRACTION1allC1

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