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- PDB-7xpl: Crystal structure of a C/D-free RNA-guided RNA 2'-O-methyltransferase -

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Basic information

Entry
Database: PDB / ID: 7xpl
TitleCrystal structure of a C/D-free RNA-guided RNA 2'-O-methyltransferase
Components
  • (BMG3 RNA strand ...) x 2
  • C/D box methylation guide ribonucleoprotein complex aNOP56 subunit
  • Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
  • RNA (5'-R(*CP*CP*AP*UP*GP*AP*GP*UP*GP*UP*U)-3')
KeywordsRNA BINDING PROTEIN/RNA / 2'-O-methylation / guide RNA / RNP / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


box C/D methylation guide snoRNP complex / tRNA processing / snoRNA binding / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / rRNA processing / methylation / RNA binding
Similarity search - Function
: / Archaeal Nop5/56-rel, N-terminal domain / : / Nucleolar protein Nop56/Nop58 / rRNA 2'-O-methyltransferase fibrillarin-like / Fibrillarin, conserved site / Fibrillarin / Fibrillarin signature. / Fibrillarin / NOSIC ...: / Archaeal Nop5/56-rel, N-terminal domain / : / Nucleolar protein Nop56/Nop58 / rRNA 2'-O-methyltransferase fibrillarin-like / Fibrillarin, conserved site / Fibrillarin / Fibrillarin signature. / Fibrillarin / NOSIC / NOSIC (NUC001) domain / Nop domain / Nop domain superfamily / Nop, C-terminal domain / snoRNA binding domain, fibrillarin / Nop domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / RNA / RNA (> 10) / C/D box methylation guide ribonucleoprotein complex aNOP56 subunit / Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
Similarity search - Component
Biological speciesSaccharolobus solfataricus (archaea)
Saccharolobus solfataricus 98/2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.213 Å
AuthorsWang, J. / Ye, K.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)91940302 China
CitationJournal: Rna / Year: 2022
Title: Methylation guide RNAs without box C/D motifs.
Authors: Wang, J. / Yang, Z. / Ye, K.
History
DepositionMay 4, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 2023Group: 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: C/D box methylation guide ribonucleoprotein complex aNOP56 subunit
B: C/D box methylation guide ribonucleoprotein complex aNOP56 subunit
E: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
F: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
G: BMG3 RNA strand A
H: BMG3 RNA strand B
I: RNA (5'-R(*CP*CP*AP*UP*GP*AP*GP*UP*GP*UP*U)-3')
J: RNA (5'-R(*CP*CP*AP*UP*GP*AP*GP*UP*GP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,57610
Polymers166,8078
Non-polymers7692
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24750 Å2
ΔGint-169 kcal/mol
Surface area55350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.088, 76.185, 98.201
Angle α, β, γ (deg.)92.860, 94.080, 112.910
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 4 molecules ABEF

#1: Protein C/D box methylation guide ribonucleoprotein complex aNOP56 subunit / Pre mRNA splicing ribonucleoprotein / binding domain protein


Mass: 44168.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharolobus solfataricus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E3MJI1
#2: Protein Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase


Mass: 26455.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharolobus solfataricus 98/2 (archaea)
Strain: 98/2 / Gene: flpA, Ssol_1916 / Production host: Escherichia coli (E. coli)
References: UniProt: D0KTQ8, Transferases; Transferring one-carbon groups; Methyltransferases

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BMG3 RNA strand ... , 2 types, 2 molecules GH

#3: RNA chain BMG3 RNA strand A


Mass: 9252.516 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharolobus solfataricus (archaea)
#4: RNA chain BMG3 RNA strand B


Mass: 9338.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharolobus solfataricus (archaea)

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RNA chain , 1 types, 2 molecules IJ

#5: RNA chain RNA (5'-R(*CP*CP*AP*UP*GP*AP*GP*UP*GP*UP*U)-3')


Mass: 3484.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Substrate / Source: (synth.) Saccharolobus solfataricus (archaea)

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Non-polymers , 2 types, 255 molecules

#6: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 0.2M sodium citrate tribasic dehydrate, 20% (w/v) polyethylene glycol 3350 (pH 8.3)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.21→50 Å / Num. obs: 87481 / % possible obs: 97.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 11.73
Reflection shellResolution: 2.21→2.25 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.136 / Num. unique obs: 4361 / CC1/2: 0.561 / CC star: 0.848 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PLA

3pla


Resolution: 2.213→41.705 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 28.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2364 2000 2.29 %
Rwork0.1889 85431 -
obs0.19 87431 97.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.44 Å2 / Biso mean: 50.7864 Å2 / Biso min: 29.02 Å2
Refinement stepCycle: final / Resolution: 2.213→41.705 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9690 1523 52 253 11518
Biso mean--43.16 48.32 -
Num. residues----1283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811612
X-RAY DIFFRACTIONf_angle_d1.0116033
X-RAY DIFFRACTIONf_chiral_restr0.0521871
X-RAY DIFFRACTIONf_plane_restr0.0061799
X-RAY DIFFRACTIONf_dihedral_angle_d20.5016936
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.213-2.26840.34711360.2882578192
2.2684-2.32970.30941420.2671607797
2.3297-2.39820.31741430.2502614297
2.3982-2.47560.28391430.2444608897
2.4756-2.56410.2651450.234616198
2.5641-2.66670.32381440.2289617598
2.6667-2.78810.27121440.2191613398
2.7881-2.9350.26251450.2175620598
2.935-3.11890.25621420.2158611398
3.1189-3.35960.26711450.2026613598
3.3596-3.69750.21481430.1795611598
3.6975-4.23210.20721430.1625613897
4.2321-5.33020.18661400.1498600396
5.3302-41.7050.20641450.1584616598

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