1DUL

STRUCTURE OF THE RIBONUCLEOPROTEIN CORE OF THE E. COLI SIGNAL RECOGNITION PARTICLE

• PDB DOI:  https://doi.org/10.2210/pdb1DUL/pdb
• NAKB: 1DUL

• Classification: SIGNALING PROTEIN/RNA
• Organism(s): synthetic construct, Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2000-01-17 Released: 2000-02-28 
• Deposition Author(s): Batey, R.T., Rambo, R.P., Lucast, L., Rha, B., Doudna, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.221 
• R-Value Work: 0.199 
• R-Value Observed: 0.199 

Literature

Crystal structure of the ribonucleoprotein core of the signal recognition particle.

Batey, R.T., Rambo, R.P., Lucast, L., Rha, B., Doudna, J.A.

(2000) Science 287: 1232-1239

• PubMed: 10678824 
• DOI: https://doi.org/10.1126/science.287.5456.1232
• Primary Citation of Related Structures:  
  1DUL


• PubMed Abstract: 
  

  The signal recognition particle (SRP), a protein-RNA complex conserved in all three kingdoms of life, recognizes and transports specific proteins to cellular membranes for insertion or secretion. We describe here the 1.8 angstrom crystal structure of the universal core of the SRP, revealing protein recognition of a distorted RNA minor groove. Nucleotide analog interference mapping demonstrates the biological importance of observed interactions, and genetic results show that this core is functional in vivo. The structure explains why the conserved residues in the protein and RNA are required for SRP assembly and defines a signal sequence recognition surface composed of both protein and RNA.

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Organizational Affiliation: 

Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University, New Haven, CT 06511, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 28.84 kDa 
• Atom Count: 1,892 
• Modelled Residue Count: 118 
• Deposited Residue Count: 154 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Signal recognition particle protein	B [auth A]	105	Escherichia coli	Mutation(s): 1  Gene Names: ffh
UniProt
Find proteins for P0AGD7 (Escherichia coli (strain K12)) Explore P0AGD7  Go to UniProtKB:  P0AGD7

Entity ID: 1
Molecule	Chains	Length	Organism	Image
4.5 S RNA DOMAIN IV	A [auth B]	49	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K	C [auth B], D [auth B], E [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG	F [auth B], G [auth B], H [auth B], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	B [auth A]	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.221 
• R-Value Work: 0.199 
• R-Value Observed: 0.199 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.567	α = 90
b = 78.291	β = 96.14
c = 32.849	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-02-28 
Deposition Author(s): Batey, R.T., Rambo, R.P., Lucast, L., Rha, B., Doudna, J.A.

Revision History  

• Version 1.0: 2000-02-28
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2019-11-06
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Experimental preparation, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary
• Version 2.1: 2020-10-14
  Changes: Derived calculations, Structure summary