1LNX

Crystal structure of the P.aerophilum SmAP1 heptamer in a new crystal form (C2221)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The oligomerization and ligand-binding properties of Sm-like archaeal proteins (SmAPs)

Mura, C.Kozhukhovsky, A.Gingery, M.Phillips, M.Eisenberg, D.

(2003) Protein Sci 12: 832-847

  • DOI: 10.1110/ps.0224703
  • Primary Citation of Related Structures:  
    1JBM, 1JRI, 1LOJ, 1LNX

  • PubMed Abstract: 
  • Intron splicing is a prime example of the many types of RNA processing catalyzed by small nuclear ribonucleoprotein (snRNP) complexes. Sm proteins form the cores of most snRNPs, and thus to learn principles of snRNP assembly we characterized the oligomerization and ligand-binding properties of Sm-like archaeal proteins (SmAPs) from Pyrobaculum aerophilum (Pae) and Methanobacterium thermautotrophicum (Mth) ...

    Intron splicing is a prime example of the many types of RNA processing catalyzed by small nuclear ribonucleoprotein (snRNP) complexes. Sm proteins form the cores of most snRNPs, and thus to learn principles of snRNP assembly we characterized the oligomerization and ligand-binding properties of Sm-like archaeal proteins (SmAPs) from Pyrobaculum aerophilum (Pae) and Methanobacterium thermautotrophicum (Mth). Ultracentrifugation shows that Mth SmAP1 is exclusively heptameric in solution, whereas Pae SmAP1 forms either disulfide-bonded 14-mers or sub-heptameric states (depending on the redox potential). By electron microscopy, we show that Pae and Mth SmAP1 polymerize into bundles of well ordered fibers that probably form by head-to-tail stacking of heptamers. The crystallographic results reported here corroborate these findings by showing heptamers and 14-mers of both Mth and Pae SmAP1 in four new crystal forms. The 1.9 A-resolution structure of Mth SmAP1 bound to uridine-5'-monophosphate (UMP) reveals conserved ligand-binding sites. The likely RNA binding site in Mth agrees with that determined for Archaeoglobus fulgidus (Afu) SmAP1. Finally, we found that both Pae and Mth SmAP1 gel-shift negatively supercoiled DNA. These results distinguish SmAPs from eukaryotic Sm proteins and suggest that SmAPs have a generic single-stranded nucleic acid-binding activity.


    Related Citations: 
    • The crystal structure of a heptameric archaeal Sm protein: Implications for the eukaryotic snRNP core
      Mura, C., Cascio, D., Sawaya, M.R., Eisenberg, D.
      (2001) Proc Natl Acad Sci U S A 98: 5532

    Organizational Affiliation

    Howard Hughes Medical Institute, Molecular Biology Institute, Los Angeles, California 90095-1570, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
small nuclear ribonucleoprotein homolog (Sm-like)A, B, C, D, E, F, G81Pyrobaculum aerophilumMutation(s): 0 
Gene Names: SmAP1GPA2549
Find proteins for Q8ZYG5 (Pyrobaculum aerophilum (strain ATCC 51768 / IM2 / DSM 7523 / JCM 9630 / NBRC 100827))
Explore Q8ZYG5 
Go to UniProtKB:  Q8ZYG5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
URI
Query on URI

Download Ideal Coordinates CCD File 
H [auth A], J [auth B], N [auth D], O [auth D], R [auth E], V [auth F], Y [auth G]URIDINE
C9 H12 N2 O6
DRTQHJPVMGBUCF-XVFCMESISA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth A] , K [auth B] , M [auth C] , Q [auth D] , S [auth E] , T [auth E] , U [auth E] , W [auth F] , 
I [auth A],  K [auth B],  M [auth C],  Q [auth D],  S [auth E],  T [auth E],  U [auth E],  W [auth F],  X [auth F],  Z [auth G]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

Download Ideal Coordinates CCD File 
L [auth C], P [auth D]ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.182 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.829α = 90
b = 113.764β = 90
c = 126.594γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-03-25
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Atomic model