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- PDB-5wwr: Crystal structure of human NSun6/tRNA/SFG -

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Basic information

Entry
Database: PDB / ID: 5wwr
TitleCrystal structure of human NSun6/tRNA/SFG
Components
  • Putative methyltransferase NSUN6
  • tRNA
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 / RNA methylation / tRNA modification in the nucleus and cytosol / tRNA modification / tRNA methylation / Transferases; Transferring one-carbon groups; Methyltransferases / tRNA binding / cytoplasm / cytosol
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 superfamily / PUA domain profile. / PUA-like superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
SINEFUNGIN / RNA / RNA (> 10) / tRNA (cytosine(72)-C(5))-methyltransferase NSUN6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.096 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
A: Putative methyltransferase NSUN6
B: Putative methyltransferase NSUN6
C: tRNA
D: tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,9206
Polymers154,1574
Non-polymers7632
Water00
1
A: Putative methyltransferase NSUN6
C: tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4603
Polymers77,0792
Non-polymers3811
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-22 kcal/mol
Surface area29060 Å2
MethodPISA
2
B: Putative methyltransferase NSUN6
D: tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4603
Polymers77,0792
Non-polymers3811
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-23 kcal/mol
Surface area28570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)206.908, 170.478, 76.999
Angle α, β, γ (deg.)90.000, 108.550, 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: 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
#2: RNA chain tRNA


Mass: 24173.365 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N7O5

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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: 4.18 Å3/Da / Density % sol: 70.56 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 8.5 / Details: 0.1 M SPG, 25% (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: 0.97776 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 3.096→50 Å / Num. obs: 45890 / % possible obs: 98.2 % / Redundancy: 6.7 % / Biso Wilson estimate: 61.73 Å2 / Net I/σ(I): 19.7

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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: 5WWQ, 2DU3

5wwq

2du3


Resolution: 3.096→42.892 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.81
RfactorNum. reflection% reflection
Rfree0.2352 1793 4.95 %
Rwork0.1953 --
obs0.1973 36230 78.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 179.41 Å2 / Biso mean: 55.2541 Å2 / Biso min: 8.94 Å2
Refinement stepCycle: final / Resolution: 3.096→42.892 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7091 3072 54 0 10217
Biso mean--41.06 --
Num. residues----1062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310721
X-RAY DIFFRACTIONf_angle_d0.59315196
X-RAY DIFFRACTIONf_chiral_restr0.0241844
X-RAY DIFFRACTIONf_plane_restr0.0031415
X-RAY DIFFRACTIONf_dihedral_angle_d13.234472
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4407X-RAY DIFFRACTION6.049TORSIONAL
12B4407X-RAY DIFFRACTION6.049TORSIONAL
21C1716X-RAY DIFFRACTION6.049TORSIONAL
22D1716X-RAY DIFFRACTION6.049TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0959-3.17950.4637360.3154981101729
3.1795-3.27310.4471500.29921294134438
3.2731-3.37870.3781910.26621682177350
3.3787-3.49940.30571050.26562039214461
3.4994-3.63940.30311370.24032328246570
3.6394-3.8050.27281330.22682723285681
3.805-4.00540.24721700.21713156332694
4.0054-4.25620.22681810.191233663547100
4.2562-4.58450.20731840.168333663550100
4.5845-5.04520.2051620.166133703532100
5.0452-5.77370.23341700.174433743544100
5.7737-7.26850.21821730.188733723545100
7.2685-42.89580.19082010.16953386358799

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