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- PDB-5wws: Crystal structure of human NSun6/tRNA/SAM -

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Basic information

Entry
Database: PDB / ID: 5wws
TitleCrystal structure of human NSun6/tRNA/SAM
Components
  • Putative methyltransferase NSUN6
  • tRNATransfer RNA
KeywordsTRANSFERASE/RNA / RNA modification / m5C methyltransferase / NSun / TRANSFERASE-RNA complex
Function / homology
Function and homology information


tRNA C5-cytosine methylation / tRNA (cytidine-5-)-methyltransferase activity / tRNA modification in the nucleus and cytosol / tRNA methylation / RNA methylation / tRNA modification / Transferases; Transferring one-carbon groups; Methyltransferases / tRNA binding / cytosol / cytoplasm
Similarity search - Function
Bacterial Fmu (Sun)/eukaryotic nucleolar NOL1/Nop2p, conserved site / NOL1/NOP2/sun family signature. / : / SAM-dependent methyltransferase RsmB/NOP2-type / RNA (C5-cytosine) methyltransferase / 16S rRNA methyltransferase RsmB/F / SAM-dependent MTase RsmB/NOP-type domain profile. / PUA domain profile. / PUA domain superfamily / PUA-like superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / RNA / RNA (> 10) / tRNA (cytosine(72)-C(5))-methyltransferase NSUN6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.247 Å
AuthorsLiu, R.J. / Long, T. / Wang, E.D.
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Structural basis for substrate binding and catalytic mechanism of a human RNA:m5C methyltransferase NSun6
Authors: Liu, R.J. / Long, T. / Li, J. / Li, H. / Wang, E.D.
History
DepositionJan 4, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Sep 20, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 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
C: tRNA
D: tRNA
A: Putative methyltransferase NSUN6
B: Putative methyltransferase NSUN6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,9546
Polymers154,1574
Non-polymers7972
Water0
1
C: tRNA
A: Putative methyltransferase NSUN6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4773
Polymers77,0792
Non-polymers3981
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-27 kcal/mol
Surface area28860 Å2
MethodPISA
2
D: tRNA
B: Putative methyltransferase NSUN6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4773
Polymers77,0792
Non-polymers3981
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-25 kcal/mol
Surface area28320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)205.236, 170.262, 76.883
Angle α, β, γ (deg.)90.000, 108.630, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid A
21chain B and segid B
12chain C and segid C
22chain D and segid D

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segid AA0
211chain B and segid BB0
112chain C and segid CC0
212chain D and segid DD0

NCS ensembles :
ID
1
2

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Components

#1: RNA chain tRNA / Transfer RNA


Mass: 24173.365 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Protein Putative methyltransferase NSUN6 / NOL1/NOP2/Sun and PUA domain-containing protein 1 / NOL1/NOP2/Sun domain family member 6


Mass: 52905.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NSUN6, NOPD1
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: Q8TEA1, Transferases; Transferring one-carbon groups; Methyltransferases
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S

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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: 4.13 Å3/Da / Density % sol: 70.21 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 8.8 / Details: 0.1 M SPG, 26% (w/v) PEG 1500, 50 mM NaF

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 3.247→50 Å / Num. obs: 39477 / % possible obs: 94.6 % / Redundancy: 6.5 % / Biso Wilson estimate: 53.82 Å2 / Net I/σ(I): 26.9

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000data scaling
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.22data extraction
SCALEPACKdata reduction
PHASERphasing
HKLdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WWR

5wwr


Resolution: 3.247→42.702 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.25
RfactorNum. reflection% reflection
Rfree0.2221 1655 5.08 %
Rwork0.1934 --
obs0.1949 32578 82.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 172.74 Å2 / Biso mean: 53.9884 Å2 / Biso min: 6.52 Å2
Refinement stepCycle: final / Resolution: 3.247→42.702 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7083 3052 54 0 10189
Biso mean--45.6 --
Num. residues----1060
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610691
X-RAY DIFFRACTIONf_angle_d0.78315151
X-RAY DIFFRACTIONf_chiral_restr0.2311837
X-RAY DIFFRACTIONf_plane_restr0.0031413
X-RAY DIFFRACTIONf_dihedral_angle_d14.1184457
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4488X-RAY DIFFRACTION1.643TORSIONAL
12B4488X-RAY DIFFRACTION1.643TORSIONAL
21C1692X-RAY DIFFRACTION1.643TORSIONAL
22D1692X-RAY DIFFRACTION1.643TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2466-3.34210.2735510.26771066111734
3.3421-3.44990.3723630.27821308137142
3.4499-3.57320.2854940.26041788188258
3.5732-3.71620.21281100.22242280239073
3.7162-3.88520.22731380.21282705284386
3.8852-4.08990.25351720.20033011318397
4.0899-4.34590.20381450.174831473292100
4.3459-4.68110.1781670.163731143281100
4.6811-5.15140.21361710.17131293300100
5.1514-5.89520.2291650.184531263291100
5.8952-7.4210.23091760.198631313307100
7.421-42.70540.20142030.18093118332199

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