Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 52.71 kDa 
• Atom Count: 3489 
• Residue Count: 213 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

1L9A

CRYSTAL STRUCTURE OF SRP19 IN COMPLEX WITH THE S DOMAIN OF SIGNAL RECOGNITION PARTICLE RNA

• DOI: 10.2210/pdb1L9A/pdb
• NDB: PR0067

• Classification: SIGNALING PROTEIN/RNA
• Organism(s): Methanocaldococcus jannaschii
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2002-03-22 Released: 2002-06-28 
• Deposition Author(s): Oubridge, C., Kuglstatter, A., Jovine, L., Nagai, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.296 
• R-Value Work: 0.264 
• R-Value Observed: 0.264 

Literature

Crystal structure of SRP19 in complex with the S domain of SRP RNA and its implication for the assembly of the signal recognition particle.

Oubridge, C., Kuglstatter, A., Jovine, L., Nagai, K.

(2002) Mol Cell 9: 1251-1261

• PubMed: 12086622 
• DOI: 10.1016/s1097-2765(02)00530-0
• Structures With Same Primary Citation


• PubMed Abstract: 
  

The signal recognition particle (SRP) is a ribonucleoprotein particle involved in GTP-dependent translocation of secretory proteins across membranes. In Archaea and Eukarya, SRP19 binds to 7SL RNA and promotes the incorporation of SRP54, which contains the binding sites for GTP, the signal peptide, and the membrane-bound SRP receptor. We have determined the crystal structure of Methanococcus jannaschii SRP19 bound to the S domain of human 7SL RNA at 2.9 A resolution. SRP19 clamps the tetraloops of two branched helices (helices 6 and 8) and allows them to interact side by side. Helix 6 acts as a splint for helix 8 and partially preorganizes the binding site for SRP54 in helix 8, thereby facilitating the binding of SRP54 in assembly.

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Organizational Affiliation: 

MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, United Kingdom.

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
SIGNAL RECOGNITION PARTICLE 19 KDA PROTEIN	A	87	Methanocaldococcus jannaschii	Mutation(s): 4  Gene Names: srp19
Find proteins for Q58440 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Go to UniProtKB:  Q58440

Entity ID: 1
Molecule	Chains	Length	Organism
signal recognition particle RNA S domain	B	128	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MMC	A	METHYL MERCURY ION C H3 Hg DBUXSCUEGJMZAE-UHFFFAOYSA-N
MG	A, B	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.296 
• R-Value Work: 0.264 
• R-Value Observed: 0.264 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.765	α = 90
b = 223.875	β = 90
c = 43.024	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
SHARP	phasing
SOLOMON	phasing
EDEN	model building
REFMAC	refinement
SOLVE	phasing
DENZO	data reduction
SCALEPACK	data scaling
EDEN	phasing
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-03-22 
• Released Date: 2002-06-28 
Deposition Author(s): Oubridge, C., Kuglstatter, A., Jovine, L., Nagai, K.

Revision History 

• Version 1.0: 2002-06-28
  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: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description