1I8F | pdb_00001i8f

THE CRYSTAL STRUCTURE OF A HEPTAMERIC ARCHAEAL SM PROTEIN: IMPLICATIONS FOR THE EUKARYOTIC SNRNP CORE

• PDB DOI: https://doi.org/10.2210/pdb1I8F/pdb

• Classification: STRUCTURAL GENOMICS
• Organism(s): Pyrobaculum aerophilum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2001-03-14 Released: 2001-05-16 
• Deposition Author(s): Mura, C., Cascio, D., Sawaya, M.R., Eisenberg, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.266 (Depositor) 
• R-Value Work: 
  0.235 (Depositor), 0.249 (DCC) 

Literature

The crystal structure of a heptameric archaeal Sm protein: Implications for the eukaryotic snRNP core.

Mura, C., Cascio, D., Sawaya, M.R., Eisenberg, D.S.

(2001) Proc Natl Acad Sci U S A 98: 5532-5537

• PubMed: 11331747 
• DOI: https://doi.org/10.1073/pnas.091102298
• Primary Citation Related Structures: 
  1I8F


• PubMed Abstract: 
  

  Sm proteins form the core of small nuclear ribonucleoprotein particles (snRNPs), making them key components of several mRNA-processing assemblies, including the spliceosome. We report the 1.75-A crystal structure of SmAP, an Sm-like archaeal protein that forms a heptameric ring perforated by a cationic pore. In addition to providing direct evidence for such an assembly in eukaryotic snRNPs, this structure (i) shows that SmAP homodimers are structurally similar to human Sm heterodimers, (ii) supports a gene duplication model of Sm protein evolution, and (iii) offers a model of SmAP bound to single-stranded RNA (ssRNA) that explains Sm binding-site specificity. The pronounced electrostatic asymmetry of the SmAP surface imparts directionality to putative SmAP-RNA interactions.

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Organizational Affiliation: 
• University of California at Los Angeles-Department of Energy Laboratory of Structural Biology and Molecular Medicine, 201 Boyer Hall/Molecular Biology Institute, Box 951570, Los Angeles, CA 90095-1570, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C7  (Explore in 3D)
Global Stoichiometry: Homo 7-mer - A7 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 63.02 kDa 
• Atom Count: 3,975 
• Modeled Residue Count: 499 
• Deposited Residue Count: 567 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PUTATIVE SNRNP SM-LIKE PROTEIN	A, B, C, D, E, F, G	81	Pyrobaculum aerophilum	Mutation(s): 0
UniProt
Find proteins for Q8ZYG5 (Pyrobaculum aerophilum (strain ATCC 51768 / DSM 7523 / JCM 9630 / CIP 104966 / NBRC 100827 / IM2)) Explore Q8ZYG5  Go to UniProtKB:  Q8ZYG5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	H [auth A], I [auth C], J [auth D], K [auth G], L [auth G]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.266 (Depositor) 
• R-Value Work:  0.235 (Depositor), 0.249 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.261	α = 90
b = 95.738	β = 92.69
c = 62.157	γ = 90

Software Package:

Software Name	Purpose
MLPHARE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-05-16 
Deposition Author(s): Mura, C., Cascio, D., Sawaya, M.R., Eisenberg, D.

Revision History  

• Version 1.0: 2001-05-16
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2021-07-21
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2024-02-07
  Changes: Data collection, Database references