Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 29267.49 
• Atom Count: 2022 
• Residue Count: 143 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

1DK1

DETAILED VIEW OF A KEY ELEMENT OF THE RIBOSOME ASSEMBLY: CRYSTAL STRUCTURE OF THE S15-RRNA COMPLEX

• DOI: 10.2210/pdb1DK1/pdb
• NDB: RR0005

• Classification: RIBOSOME
• Organism(s): Thermus thermophilus
• Expression System: Escherichia coli
• Mutation(s): 4 


• Deposited: 1999-12-06 Released: 2000-04-02 
• Deposition Author(s): Nikulin, A., Serganov, A., Ennifar, E., Tischenko, S., Nevskaya, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.291 
• R-Value Work: 0.213 

Literature

Crystal structure of the S15-rRNA complex.

Nikulin, A., Serganov, A., Ennifar, E., Tishchenko, S., Nevskaya, N., Shepard, W., Portier, C., Garber, M., Ehresmann, B., Ehresmann, C., Nikonov, S., Dumas, P.

(2000) Nat.Struct.Mol.Biol. 7: 273-277

• PubMed: 10742169 
• DOI: 10.1038/74028


• PubMed Abstract: 
  

In bacterial ribosomes, the small (30S) ribosomal subunit is composed of 16S rRNA and 21 distinct proteins. Ribosomal protein S15 is of particular interest because it binds primarily to 16S rRNA and is required for assembly of the small subunit and for intersubunit association, thus representing a key element in the assembly of a whole ribosome. Here we report the 2.8 ¿ resolution crystal structure of the highly conserved S15-rRNA complex. Protein S15 interacts in the minor groove with a G-U/G-C motif and a three-way junction. The latter is constrained by a conserved base triple and stacking interactions, and locked into place by magnesium ions and protein side chains, mainly through interactions with the unique three-dimensional geometry of the backbone. The present structure gives insights into the dual role of S15 in ribosome assembly and translational regulation.

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Organizational Affiliation: 

Institute of Protein Research, Pushchino, Moscow Region, 142292, Russia.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
30S RIBOSOMAL PROTEIN S15	A	86	Thermus thermophilus	Mutations: M57M, I11M, A79M, M58M Gene Names: rpsO (rps15)
Find proteins for P80378 (Thermus thermophilus) Go to UniProtKB:  P80378

Entity ID: 1
Molecule	Chains	Length	Organism
RRNA FRAGMENT	B	57	Thermus thermophilus

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
K	A	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
NA	B	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
MG	B	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.291 
• R-Value Work: 0.213 
• Space Group: P 6₄ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 128.800	α = 90.00
b = 128.800	β = 90.00
c = 65.100	γ = 120.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-12-06 
• Released Date: 2000-04-02 
• Deposition Author(s): Nikulin, A., Serganov, A., Ennifar, E., Tischenko, S., Nevskaya, N.

Revision History 

• Version 1.0: 2000-04-02
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2011-12-28
  Type: Advisory
• Version 1.4: 2018-01-31
  Type: Experimental preparation