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: 52707.01 
• Atom Count: 3459 
• Residue Count: 215 
• 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 (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
• Expression System: Escherichia coli
• Mutation(s): 8 


• 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: 2.9 Å
• R-Value Free: 0.296 
• R-Value Work: 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 


• 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
SIGNAL RECOGNITION PARTICLE 19 KDA PROTEIN	A	87	Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)	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 & Interactions
MMC	A	METHYL MERCURY ION C H3 Hg DBUXSCUEGJMZAE-UHFFFAOYSA-N
MG	A, B	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CCC	B	RNA LINKING	C9 H13 N3 O10 P2		C

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.9 Å
• R-Value Free: 0.296 
• R-Value Work: 0.264 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 70.765	α = 90.00
b = 223.875	β = 90.00
c = 43.024	γ = 90.00

Software Package:

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

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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2019-07-24
  Type: Data collection, Derived calculations, Refinement description