5NPM

CRYSTAL STRUCTURE OF MUTANT RIBOSOMAL PROTEIN TTHL1 LACKING 8 N-TERMINAL RESIDUES IN COMPLEX WITH 80NT 23S RNA FROM THERMUS THERMOPHILUS

• PDB DOI: https://doi.org/10.2210/pdb5NPM/pdb
• NAKB: 5NPM

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


• Deposited: 2017-04-17 Released: 2018-05-16 
• Deposition Author(s): Gabdulkhakov, A.G., Tishchenko, T.V., Nevskaya, N.A., Nikonov, S.V., Garber, M.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.249 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 

Literature

[Influence of Nonconserved Regions of L1 Protuberance of Thermus thermophilus Ribosome on the Affinity of L1 Protein to 23s rRNA].

Kostareva, O.S., Nevskaya, N.A., Tishchenko, S.V., Gabdulkhakov, A.G., Garber, M.B., Nikonov, S.V.

(2018) Mol Biol (Mosk) 52: 106-111

• PubMed: 29512642 
• DOI: https://doi.org/10.7868/S0026898418010147
• Primary Citation of Related Structures:  
  5NPM


• PubMed Abstract: 
  

  The L1 protuberance of the ribosome includes two domain ribosomal protein L1 and three helices of 23S rRNA (H76, H77, and H78) with interconnecting loops A and B. Helix 78 consists of two parts, i.e., H78a and H78b. A comparison of the available structural data of L1-RNA complexes with the obtained kinetic data made it possible to determine the influence of the nonconserved regions of Thermus thermophilus L1-protuberance on the mutual affinity of the L1 protein and 23S rRNA. It has been shown that the N-terminal helix of the protein and 78b helix of 23S rRNA are essential for the formation of an additional intermolecular contact, which is separated in the protein from the main site of L1-rRNA interaction by a flexible connection. This results in a rise in the TthL1-rRNA affinity. At the same time, the elongation of the 76 helix has no effect on rRNA-protein binding.

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Organizational Affiliation: 

Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow oblast, 142290 Russia.

Biological Assembly 1  

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

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

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 49.81 kDa 
• Atom Count: 3,340 
• Modelled Residue Count: 291 
• Deposited Residue Count: 300 
• 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	220	Thermus thermophilus	Mutation(s): 0  Gene Names: rplA, rpl1
UniProt
Find proteins for Q5SLP7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLP7  Go to UniProtKB:  Q5SLP7

Entity ID: 2
Molecule	Chains	Length	Organism	Image
23S ribosomal RNA	B	80	Thermus thermophilus

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLI	C [auth B]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
NA	D [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.249 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.127	α = 90
b = 65.532	β = 90
c = 119.925	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-05-16 
Deposition Author(s): Gabdulkhakov, A.G., Tishchenko, T.V., Nevskaya, N.A., Nikonov, S.V., Garber, M.B.

Revision History  

• Version 1.0: 2018-05-16
  Type: Initial release
  
• Version 1.1: 2019-05-29
  Changes: Data collection, Database references
• Version 1.2: 2019-10-16
  Changes: Data collection
• Version 1.3: 2024-01-17
  Changes: Data collection, Database references, Refinement description