1LNG

Crystal Structure of the SRP19-7S.S SRP RNA Complex of M. jannaschii

• PDB DOI:  https://doi.org/10.2210/pdb1LNG/pdb
• NAKB: 1LNG

• Classification: SIGNALING PROTEIN/RNA
• Organism(s): Methanocaldococcus jannaschii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-05-03 Released: 2002-06-07 
• Deposition Author(s): Hainzl, T., Huang, S., Sauer-Eriksson, A.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.273 
• R-Value Work: 0.224 
• R-Value Observed: 0.227 

Literature

Structure of the SRP19 RNA complex and implications for signal recognition particle assembly.

Hainzl, T., Huang, S., Sauer-Eriksson, A.E.

(2002) Nature 417: 767-771

• PubMed: 12050674 
• DOI: https://doi.org/10.1038/nature00768
• Primary Citation of Related Structures:  
  1LNG


• PubMed Abstract: 
  

The signal recognition particle (SRP) is a phylogenetically conserved ribonucleoprotein. It associates with ribosomes to mediate co-translational targeting of membrane and secretory proteins to biological membranes. In mammalian cells, the SRP consists of a 7S RNA and six protein components. The S domain of SRP comprises the 7S.S part of RNA bound to SRP19, SRP54 and the SRP68/72 heterodimer; SRP54 has the main role in recognizing signal sequences of nascent polypeptide chains and docking SRP to its receptor. During assembly of the SRP, binding of SRP19 precedes and promotes the association of SRP54 (refs 4, 5). Here we report the crystal structure at 2.3 A resolution of the complex formed between 7S.S RNA and SRP19 in the archaeon Methanococcus jannaschii. SRP19 bridges the tips of helices 6 and 8 of 7S.S RNA by forming an extensive network of direct protein RNA interactions. Helices 6 and 8 pack side by side; tertiary RNA interactions, which also involve the strictly conserved tetraloop bases, stabilize helix 8 in a conformation competent for SRP54 binding. The structure explains the role of SRP19 and provides a molecular framework for SRP54 binding and SRP assembly in Eukarya and Archaea.

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Organizational Affiliation: 

Umeå Centre for Molecular Pathogenesis, Umeå University, SE-901 87 Umeå, Sweden. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 41.85 kDa 
• Atom Count: 3,017 
• Modelled Residue Count: 184 
• Deposited Residue Count: 184 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Signal recognition particle 19 kDa protein	B [auth A]	87	Methanocaldococcus jannaschii	Mutation(s): 0
UniProt
Find proteins for Q58440 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q58440  Go to UniProtKB:  Q58440

Entity ID: 1
Molecule	Chains	Length	Organism	Image
7S.S SRP RNA	A [auth B]	97	Methanocaldococcus jannaschii

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth B], D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.273 
• R-Value Work: 0.224 
• R-Value Observed: 0.227 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.521	α = 90
b = 61.405	β = 90
c = 155.978	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CNS	refinement
DENZO	data reduction
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-06-07 
Deposition Author(s): Hainzl, T., Huang, S., Sauer-Eriksson, A.E.

Revision History  

• Version 1.0: 2002-06-07
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-03-07
  Changes: Data collection
• Version 1.4: 2019-07-24
  Changes: Data collection, Refinement description
• Version 1.5: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description