3NMU

Crystal Structure of substrate-bound halfmer box C/D RNP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

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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, B379Pyrococcus furiosusMutation(s): 0 
Gene Names: PF0060
UniProt
Find proteins for Q8U4M1 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Go to UniProtKB:  Q8U4M1
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UniProt GroupQ8U4M1
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L7AeC, G129Pyrococcus furiosusMutation(s): 0 
Gene Names: rpl7ae, PF1367
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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UniProt GroupQ8U160
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Fibrillarin-like rRNA/tRNA 2'-O-methyltransferaseF,
H [auth J]		234Pyrococcus furiosusMutation(s): 0 
Gene Names: flpA, PF0059
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
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UniProt GroupQ8U4M2
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Entity ID: 3
MoleculeChainsLengthOrganismImage
RNA (34-MER)D, E34Pyrococcus furiosus
Protein Feature View
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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')I,
J [auth K]		13synthetic construct
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAM
Query on SAM
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K [auth F],
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: 2.73 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 293.506α = 90
b = 94.054β = 101.47
c = 96.81γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-05-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance