1S03

The Structure of a Ribosomal Protein S8/spc Operon mRNA Complex

• PDB DOI:  https://doi.org/10.2210/pdb1S03/pdb
• NAKB: 1S03

• Classification: TRANSCRIPTION/RNA
• Organism(s): Escherichia coli
• Mutation(s): No 


• Deposited: 2003-12-29 Released: 2004-05-25 
• Deposition Author(s): Merianos, H.J., Wang, J., Moore, P.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.273 
• R-Value Work: 0.237 
• R-Value Observed: 0.237 

Literature

The structure of a ribosomal protein S8/spc operon mRNA complex.

Merianos, H.J., Wang, J., Moore, P.B.

(2004) RNA 10: 954-964

• PubMed: 15146079 
• DOI: https://doi.org/10.1261/rna.7030704
• Primary Citation of Related Structures:  
  1S03


• PubMed Abstract: 
  

In bacteria, translation of all the ribosomal protein cistrons in the spc operon mRNA is repressed by the binding of the product of one of them, S8, to an internal sequence at the 5' end of the L5 cistron. The way in which the first two genes of the spc operon are regulated, retroregulation, is mechanistically distinct from translational repression by S8 of the genes from L5 onward. A 2.8 A resolution crystal structure has been obtained of Escherichia coli S8 bound to this site. Despite sequence differences, the structure of this complex is almost identical to that of the S8/helix 21 complex seen in the small ribosomal subunit, consistent with the hypothesis that autogenous regulation of ribosomal protein synthesis results from conformational similarities between mRNAs and rRNAs. S8 binding must repress the translation of its own mRNA by inhibiting the formation of a ribosomal initiation complex at the start of the L5 cistron.

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Organizational Affiliation: 

Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 59.37 kDa 
• Atom Count: 3,951 
• Modelled Residue Count: 347 
• Deposited Residue Count: 352 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S8	C [auth H], D [auth G]	129	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7W7 (Escherichia coli (strain K12)) Explore P0A7W7  Go to UniProtKB:  P0A7W7

Entity ID: 1
Molecule	Chains	Length	Organism	Image
47-MER	A, B	47	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth H], T [auth G], U [auth G]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.273 
• R-Value Work: 0.237 
• R-Value Observed: 0.237 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.22	α = 90
b = 61.22	β = 90
c = 332.52	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-05-25 
Deposition Author(s): Merianos, H.J., Wang, J., Moore, P.B.

Revision History  

• Version 1.0: 2004-05-25
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description