3NVK

Structural basis for substrate placement by an archaeal box C/D ribonucleoprotein particle


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.236 

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Ligand Structure Quality Assessment 


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Literature

Structural basis for substrate placement by an archaeal box C/D ribonucleoprotein particle.

Xue, S.Wang, R.Yang, F.Terns, R.M.Terns, M.P.Zhang, X.Maxwell, E.S.Li, H.

(2010) Mol Cell 39: 939-949

  • DOI: 10.1016/j.molcel.2010.08.022
  • Primary Citation of Related Structures:  
    3NMU, 3NVI, 3NVK, 3NVM

  • PubMed Abstract: 
  • Box C/D small nucleolar and Cajal body ribonucleoprotein particles (sno/scaRNPs) direct site-specific 2'-O-methylation of ribosomal and spliceosomal RNAs and are critical for gene expression. Here we report crystal structures of an archaeal box C/D RNP containing three core proteins (fibrillarin, Nop56/58, and L7Ae) and a half-mer box C/D guide RNA paired with a substrate RNA ...

    Box C/D small nucleolar and Cajal body ribonucleoprotein particles (sno/scaRNPs) direct site-specific 2'-O-methylation of ribosomal and spliceosomal RNAs and are critical for gene expression. Here we report crystal structures of an archaeal box C/D RNP containing three core proteins (fibrillarin, Nop56/58, and L7Ae) and a half-mer box C/D guide RNA paired with a substrate RNA. The structure reveals a guide-substrate RNA duplex orientation imposed by a composite protein surface and the conserved GAEK motif of Nop56/58. Molecular modeling supports a dual C/D RNP structure that closely mimics that recently visualized by electron microscopy. The substrate-bound dual RNP model predicts an asymmetric protein distribution between the RNP that binds and methylates the substrate RNA. The predicted asymmetric nature of the holoenzyme is consistent with previous biochemical data on RNP assembly and provides a simple solution for accommodating base-pairing between the C/D guide RNA and large ribosomal and spliceosomal substrate RNAs.


    Organizational Affiliation

    Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NOP5/NOP56 related proteinA,
B [auth F]
376Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: PF0060
UniProt
Find proteins for Q8U4M1 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8U4M1 
Go to UniProtKB:  Q8U4M1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8U4M1
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L7AeC [auth E],
D [auth H]
129Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rpl7aePF1367
UniProt
Find proteins for Q8U160 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8U160 
Go to UniProtKB:  Q8U160
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8U160
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Fibrillarin-like rRNA/tRNA 2'-O-methyltransferaseE [auth I],
F [auth J]
234Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: flpAPF0059
EC: 2.1.1
UniProt
Find proteins for Q8U4M2 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8U4M2 
Go to UniProtKB:  Q8U4M2
Entity Groups  
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UniProt GroupQ8U4M2
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsLengthOrganismImage
RNA (5'-R(*GP*CP*CP*GP*UP*UP*GP*AP*AP*GP*CP*UP*CP*UP*GP*AP*CP*CP*GP*AP*AP*AP*GP*GP*CP*GP*UP*GP*AP*UP*GP*AP*GP*C)-3')G [auth K],
I [auth L]
34N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 5
MoleculeChainsLengthOrganismImage
RNA (5'-R(*GP*AP*GP*CP*UP*UP*CP*AP*AP*CP*GP*GP*C)-3')H [auth G],
J [auth S]
13N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAM
Query on SAM

Download Ideal Coordinates CCD File 
K [auth I],
L [auth J]
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.236 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 330.039α = 90
b = 94.548β = 90
c = 97.729γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

  • Deposited Date: 2010-07-08 
  • Released Date: 2011-07-20 
  • Deposition Author(s): Xue, S., Wang, R., Li, H.

Revision History  (Full details and data files)

  • Version 1.0: 2011-07-20
    Type: Initial release