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- PDB-2nnw: Alternative conformations of Nop56/58-fibrillarin complex and imp... -

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Basic information

Entry
Database: PDB / ID: 2nnw
TitleAlternative conformations of Nop56/58-fibrillarin complex and implication for induced-fit assenly of box C/D RNPs
Components
  • Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
  • NOP5/NOP56 related protein
KeywordsTRANSFERASE / box C/D
Function / homology
Function and homology information


box C/D methylation guide snoRNP complex / tRNA processing / snoRNA binding / S-adenosylmethionine-dependent methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / small-subunit processome / rRNA processing / methylation / RNA binding
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. / Serum Albumin; Chain A, Domain 1 / Vaccinia Virus protein VP39 / Helix Hairpins / Nucleotidyltransferase; domain 5 / 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
NOP5/NOP56 related protein / Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsOruganti, S. / Zhang, Y. / Terns, R. / Terns, M.P. / Li, H.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Alternative Conformations of the Archaeal Nop56/58-Fibrillarin Complex Imply Flexibility in Box C/D RNPs.
Authors: Oruganti, S. / Zhang, Y. / Li, H. / Robinson, H. / Terns, M.P. / Terns, R.M. / Yang, W. / Li, H.
History
DepositionOct 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NOP5/NOP56 related protein
B: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
C: NOP5/NOP56 related protein
D: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase


Theoretical massNumber of molelcules
Total (without water)140,5544
Polymers140,5544
Non-polymers00
Water0
1
A: NOP5/NOP56 related protein
B: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase

A: NOP5/NOP56 related protein
B: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase


Theoretical massNumber of molelcules
Total (without water)140,5544
Polymers140,5544
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_775-y+2,-x+2,-z+2/31
Buried area11220 Å2
ΔGint-63 kcal/mol
Surface area49270 Å2
MethodPISA, PQS
2
C: NOP5/NOP56 related protein
D: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase

C: NOP5/NOP56 related protein
D: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase


Theoretical massNumber of molelcules
Total (without water)140,5544
Polymers140,5544
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_576x,x-y+2,-z+11
Buried area11320 Å2
ΔGint-56 kcal/mol
Surface area49270 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)120.712, 120.712, 297.741
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112
DetailsThe second part is generated by CNS

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Components

#1: Protein NOP5/NOP56 related protein


Mass: 43516.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U4M1
#2: Protein Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase


Mass: 26760.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: flpA / Production host: Escherichia coli (E. coli)
References: UniProt: Q8U4M2, Transferases; Transferring one-carbon groups; Methyltransferases

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.45 Å3/Da / Density % sol: 72.38 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.7→49.33 Å / Num. obs: 68534 / Rsym value: 0.07

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.7→49.33 Å
RfactorNum. reflection
Rfree0.2652 3233
Rwork0.2341 -
all-68544
obs-64131
Refinement stepCycle: LAST / Resolution: 2.7→49.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9336 0 0 0 9336

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