1LOJ

Crystal structure of a Methanobacterial Sm-like archaeal protein (SmAP1) bound to uridine-5'-monophosphate (UMP)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


This is version 1.2 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:  
    1LOJ, 1LNX, 1JBM, 1JRI

  • 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, G, H
A, B, C, D, E, F, G, H, I, J, K, L, M, N
87Methanothermobacter thermautotrophicus str. Delta HMutation(s): 0 
Gene Names: Mth649MTH_649
UniProt
Find proteins for O26745 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H))
Explore O26745 
Go to UniProtKB:  O26745
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
U
Query on U

Download Ideal Coordinates CCD File 
CA [auth H], EA [auth I], IA [auth K], O [auth A], OA [auth N], U [auth D]URIDINE-5'-MONOPHOSPHATE
C9 H13 N2 O9 P
DJJCXFVJDGTHFX-XVFCMESISA-N
 Ligand Interaction
URI
Query on URI

Download Ideal Coordinates CCD File 
AA [auth G], GA [auth J], KA [auth L], MA [auth M], Q [auth B], S [auth C], W [auth E], Y [auth F]URIDINE
C9 H12 N2 O6
DRTQHJPVMGBUCF-XVFCMESISA-N
 Ligand Interaction
MPD
Query on MPD

Download Ideal Coordinates CCD File 
BA [auth G] , DA [auth H] , FA [auth I] , HA [auth J] , JA [auth K] , LA [auth L] , NA [auth M] , P [auth A] , 
BA [auth G],  DA [auth H],  FA [auth I],  HA [auth J],  JA [auth K],  LA [auth L],  NA [auth M],  P [auth A],  PA [auth N],  R [auth B],  T [auth C],  V [auth D],  X [auth E],  Z [auth F]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.254α = 90
b = 109.956β = 95.81
c = 83.756γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNSrefinement

Structure Validation

View Full Validation Report



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: Version format compliance