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- PDB-4by9: The structure of the Box CD enzyme reveals regulation of rRNA met... -

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Basic information

Entry
Database: PDB / ID: 4by9
TitleThe structure of the Box CD enzyme reveals regulation of rRNA methylation
Components
  • 5'-R(*UP*CP*GP*CP*CP*CP*AP*UP*CP*AP*CP)-3'
  • 50S RIBOSOMAL PROTEIN L7AE
  • FIBRILLARIN-LIKE RRNA/TRNA 2'-O-METHYLTRANSFERASE
  • NOP5/NOP56 RELATED PROTEIN
  • SSR26
KeywordsTRANSFERASE/RNA / TRANSFERASE-RNA COMPLEX / RRNA MODIFICATION
Function / homology
Function and homology information


box C/D sno(s)RNA 3'-end processing / rRNA methyltransferase activity / box C/D methylation guide snoRNP complex / ribonuclease P activity / tRNA 5'-leader removal / histone H2AQ104 methyltransferase activity / tRNA processing / snoRNA binding / Transferases; Transferring one-carbon groups; Methyltransferases / rRNA processing ...box C/D sno(s)RNA 3'-end processing / rRNA methyltransferase activity / box C/D methylation guide snoRNP complex / ribonuclease P activity / tRNA 5'-leader removal / histone H2AQ104 methyltransferase activity / tRNA processing / snoRNA binding / Transferases; Transferring one-carbon groups; Methyltransferases / rRNA processing / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / RNA binding / cytoplasm
Similarity search - Function
Nucleotidyltransferase; domain 5 - #220 / Helix Hairpins - #4070 / Nop domain / : / Archaeal Nop5/56-rel, N-terminal domain / : / Helix hairpin bin domain superfamily / Nucleolar protein Nop56/Nop58 / rRNA 2'-O-methyltransferase fibrillarin-like / Fibrillarin, conserved site ...Nucleotidyltransferase; domain 5 - #220 / Helix Hairpins - #4070 / Nop domain / : / Archaeal Nop5/56-rel, N-terminal domain / : / Helix hairpin bin domain superfamily / 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. / Ribosomal protein L7Ae, archaea / Ribosomal protein L30/S12 / Serum Albumin; Chain A, Domain 1 / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / Ribosomal protein L7Ae/L8/Nhp2 family / : / Vaccinia Virus protein VP39 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / Nucleotidyltransferase; domain 5 / Helix Hairpins / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Large ribosomal subunit protein eL8 / NOP5/NOP56 related protein / Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
Similarity search - Component
Biological speciesPYROCOCCUS FURIOSUS (archaea)
MethodSOLUTION NMR / ARIA
AuthorsLapinaite, A. / Simon, B. / Skjaerven, L. / Rakwalska-Bange, M. / Gabel, F. / Carlomagno, T.
CitationJournal: Nature / Year: 2013
Title: The Structure of the Box C/D Enzyme Reveals Regulation of RNA Methylation.
Authors: Lapinaite, A. / Simon, B. / Skjaerven, L. / Rakwalska-Bange, M. / Gabel, F. / Carlomagno, T.
History
DepositionJul 18, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2013Group: Atomic model
Revision 1.2Oct 23, 2013Group: Database references
Revision 1.3Oct 30, 2013Group: Database references
Revision 1.4May 4, 2016Group: Atomic model / Other
Revision 1.5Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.6Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SSR26
B: SSR26
C: NOP5/NOP56 RELATED PROTEIN
D: 50S RIBOSOMAL PROTEIN L7AE
E: FIBRILLARIN-LIKE RRNA/TRNA 2'-O-METHYLTRANSFERASE
F: NOP5/NOP56 RELATED PROTEIN
G: 50S RIBOSOMAL PROTEIN L7AE
H: FIBRILLARIN-LIKE RRNA/TRNA 2'-O-METHYLTRANSFERASE
I: NOP5/NOP56 RELATED PROTEIN
J: 50S RIBOSOMAL PROTEIN L7AE
K: FIBRILLARIN-LIKE RRNA/TRNA 2'-O-METHYLTRANSFERASE
L: NOP5/NOP56 RELATED PROTEIN
M: 50S RIBOSOMAL PROTEIN L7AE
N: FIBRILLARIN-LIKE RRNA/TRNA 2'-O-METHYLTRANSFERASE
W: 5'-R(*UP*CP*GP*CP*CP*CP*AP*UP*CP*AP*CP)-3'
X: 5'-R(*UP*CP*GP*CP*CP*CP*AP*UP*CP*AP*CP)-3'
Y: 5'-R(*UP*CP*GP*CP*CP*CP*AP*UP*CP*AP*CP)-3'
Z: 5'-R(*UP*CP*GP*CP*CP*CP*AP*UP*CP*AP*CP)-3'


Theoretical massNumber of molelcules
Total (without water)385,92118
Polymers385,92118
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

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Components

#1: RNA chain SSR26


Mass: 23525.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) PYROCOCCUS FURIOSUS (archaea)
#2: Protein
NOP5/NOP56 RELATED PROTEIN / NOP5


Mass: 42302.547 Da / Num. of mol.: 4 / Fragment: RESIDUES 4-369
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PYROCOCCUS FURIOSUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8U4M1
#3: Protein
50S RIBOSOMAL PROTEIN L7AE / L7AE


Mass: 13212.391 Da / Num. of mol.: 4 / Fragment: RESIDUES 3-123
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PYROCOCCUS FURIOSUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2 / References: UniProt: Q8U160
#4: Protein
FIBRILLARIN-LIKE RRNA/TRNA 2'-O-METHYLTRANSFERASE / FIBRILLARIN


Mass: 25800.764 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PYROCOCCUS FURIOSUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8U4M2, Transferases; Transferring one-carbon groups; Methyltransferases
#5: RNA chain
5'-R(*UP*CP*GP*CP*CP*CP*AP*UP*CP*AP*CP)-3' / SUBSTRATE RNA


Mass: 3402.082 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) PYROCOCCUS FURIOSUS (archaea)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: NONE

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Sample preparation

DetailsContents: 99% D2O
Sample conditionspH: 6.6 / Temperature: 328.0 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON,WARRENrefinement
NMRViewstructure solution
RefinementMethod: ARIA / Software ordinal: 1
Details: THE STRUCTURE WAS DETERMINED USING A MULTI-STEP PROTOCOL. THE INITIAL COORDINATES OF THE ISOLATED DOMAINS WERE BASED ON PDB ID 3NMU BY XUE ET AL. 2010. MOL. CELL 39, 939-49. THE LINKERS ...Details: THE STRUCTURE WAS DETERMINED USING A MULTI-STEP PROTOCOL. THE INITIAL COORDINATES OF THE ISOLATED DOMAINS WERE BASED ON PDB ID 3NMU BY XUE ET AL. 2010. MOL. CELL 39, 939-49. THE LINKERS BETWEEN PROTEIN DOMAINS AND RNA SECONDARY STRUCTURE ELEMENTS WERE LEFT FLEXIBLE. PRE-BASED DISTANCE RESTRAINT AND MULTIPLE SANS DATA WERE USED EITHER FOR STRUCTURE CALCULATION OR FOR STRUCTURE SELECTION. PRE-DERIVED DISTANCE RESTRAINTS WERE BASED ON PARAMAGNETIC RELAXATION ENHANCEMENT DATA FROM FIVE INDEPENDENT CYSTEINE MUTANTS (NOP5: E68C, E199C, D250C. L7AE: Q47C, K73C) COVALENTLY MODIFIED BY 3-(2-IODOACETAMIDO)-2,2,5,5, TETRAMETHYL-1- PYRROLIDINYLOXY RADICAL (IODOACETAMIDO-PROXYL).
NMR ensembleConformers submitted total number: 1

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