3U4M

Crystal structure of ribosomal protein tthl1 in complex with 80nt 23s rna from thermus thermophilus

• PDB DOI: https://doi.org/10.2210/pdb3U4M/pdb
• NAKB: 3U4M

• Classification: RNA/RNA BINDING PROTEIN
• Organism(s): Thermus thermophilus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-10-10 Released: 2012-08-08 
• Deposition Author(s): Gabdulkhakov, A.G., Nevskaya, N.A., NIkonov, S.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.208 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 

Literature

High-resolution crystal structure of the isolated ribosomal L1 stalk.

Tishchenko, S., Gabdulkhakov, A., Nevskaya, N., Sarskikh, A., Kostareva, O., Nikonova, E., Sycheva, A., Moshkovskii, S., Garber, M., Nikonov, S.

(2012) Acta Crystallogr D Biol Crystallogr 68: 1051-1057

• PubMed: 22868771 
• DOI: https://doi.org/10.1107/S0907444912020136
• Primary Citation of Related Structures:  
  3U4M


• PubMed Abstract: 
  

  The crystal structure of the isolated full-length ribosomal L1 stalk, consisting of Thermus thermophilus ribosomal protein L1 in complex with a specific 80-nucleotide fragment of 23S rRNA, has been solved for the first time at high resolution. The structure revealed details of protein-RNA interactions in the L1 stalk. Analysis of the crystal packing enabled the identification of sticky sites on the protein and the 23S rRNA which may be important for ribosome assembly and function. The structure was used to model different conformational states of the ribosome. This approach provides an insight into the roles of domain II of L1 and helix 78 of rRNA in ribosome function.

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Organizational Affiliation: 

Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russian Federation.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 52.06 kDa 
• Atom Count: 3,763 
• Modelled Residue Count: 308 
• Deposited Residue Count: 309 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L1	A	229	Thermus thermophilus	Mutation(s): 0  Gene Names: rplA, rpl1
UniProt
Find proteins for P27150 (Thermus thermophilus) Explore P27150  Go to UniProtKB:  P27150

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (80-MER)	B	80	Thermus thermophilus

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLI	D [auth A], E [auth A], F [auth A], O [auth B], P [auth B], Q [auth B], R [auth B]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
SO4	C [auth A], N [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	H [auth A], I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	G [auth A], S [auth B], T [auth B], U [auth B], V [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	J [auth A], K [auth A], L [auth A], M [auth A], W [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.208 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.55	α = 90
b = 68.9	β = 90
c = 117.56	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
PHASER	phasing
PHENIX	refinement
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-08 
Deposition Author(s): Gabdulkhakov, A.G., Nevskaya, N.A., NIkonov, S.V.

Revision History  

• Version 1.0: 2012-08-08
  Type: Initial release
  
• Version 1.1: 2013-01-23
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description