1JRI

The Crystal Structure of an Sm-like Archaeal Protein with Two Heptamers in the Asymmetric Unit.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.199 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.5 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: https://doi.org/10.1110/ps.0224703
  • Primary Citation of Related Structures:  
    1JBM, 1JRI, 1LNX, 1LOJ

  • 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). 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sm-like Archaeal Protein 1 (SmAP1)
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N
85Methanothermobacter thermautotrophicusMutation(s): 0 
Gene Names: Mth0649
UniProt
Find proteins for O26745 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H))
Explore O26745 
Go to UniProtKB:  O26745
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO26745
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth M]
BA [auth N]
CA [auth N]
DA [auth N]
P [auth C]
AA [auth M],
BA [auth N],
CA [auth N],
DA [auth N],
P [auth C],
Q [auth D],
R [auth E],
S [auth F],
U [auth G],
V [auth H],
W [auth H],
X [auth I],
Z [auth L]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
O [auth B],
T [auth G],
Y [auth L]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.371α = 90
b = 114.698β = 90
c = 238.6γ = 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: 2002-02-13
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-31
    Changes: Experimental preparation
  • Version 1.4: 2021-07-21
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2023-08-16
    Changes: Data collection, Database references, Refinement description