2HVY

Crystal structure of an H/ACA box RNP from Pyrococcus furiosus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of an H/ACA box ribonucleoprotein particle

Li, L.Ye, K.

(2006) Nature 443: 302-307

  • DOI: 10.1038/nature05151
  • Primary Citation of Related Structures:  
    2HVY

  • PubMed Abstract: 
  • H/ACA ribonucleoprotein particles (RNPs) are a family of RNA pseudouridine synthases that specify modification sites through guide RNAs. They also participate in eukaryotic ribosomal RNA processing and are a component of vertebrate telomerases. Here we report the crystal structure, at 2 ...

    H/ACA ribonucleoprotein particles (RNPs) are a family of RNA pseudouridine synthases that specify modification sites through guide RNAs. They also participate in eukaryotic ribosomal RNA processing and are a component of vertebrate telomerases. Here we report the crystal structure, at 2.3 A resolution, of an entire archaeal H/ACA RNP consisting of proteins Cbf5, Nop10, Gar1 and L7ae, and a single-hairpin H/ACA RNA, revealing a modular organization of the complex. The RNA upper stem is bound to a composite surface formed by L7ae, Nop10 and Cbf5, and the RNA lower stem and ACA signature motif are bound to the PUA domain of Cbf5, thereby positioning middle guide sequences so that they are primed to pair with substrate RNA. Furthermore, Gar1 may regulate substrate loading and release. The structure rationalizes the consensus structure of H/ACA RNAs, suggests a functional role of each protein, and provides a framework for understanding the mechanism of RNA-guided pseudouridylation, as well as various cellular functions of H/ACA RNP.


    Organizational Affiliation

    National Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Probable tRNA pseudouridine synthase BB [auth A]346Pyrococcus furiosusMutation(s): 0 
Gene Names: truB
EC: 5.4.99 (PDB Primary Data), 5.4.99.25 (UniProt)
UniProt
Find proteins for Q7LWY0 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q7LWY0 
Go to UniProtKB:  Q7LWY0
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Small nucleolar rnp similar to gar1C [auth B]104Pyrococcus furiosusMutation(s): 0 
Gene Names: GAR1
UniProt
Find proteins for Q8U029 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8U029 
Go to UniProtKB:  Q8U029
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome biogenesis protein Nop10D [auth C]60Pyrococcus furiosusMutation(s): 1 
Gene Names: nop10
UniProt
Find proteins for Q8U1R4 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8U1R4 
Go to UniProtKB:  Q8U1R4
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L7AeE [auth D]130Pyrococcus furiosusMutation(s): 1 
Gene Names: rpl7ae
UniProt
Find proteins for Q8U160 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8U160 
Go to UniProtKB:  Q8U160
Protein Feature View
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
H/ACA RNAA [auth E]65N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
F [auth A]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth C]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.031α = 90
b = 90.95β = 90
c = 114.064γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2006-07-31 
  • Released Date: 2006-09-12 
  • Deposition Author(s): Ye, K.

Revision History  (Full details and data files)

  • Version 1.0: 2006-09-12
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance