Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 24468.11 
• Atom Count: 1551 
• Residue Count: 157 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

1JID

Human SRP19 in complex with helix 6 of Human SRP RNA

• DOI: 10.2210/pdb1JID/pdb
• NDB: PR0054

• Classification: SIGNALING PROTEIN/RNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): 1 


• Deposited: 2001-07-02 Released: 2001-10-19 
• Deposition Author(s): Wild, K., Sinning, I., Cusack, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.222 
• R-Value Work: 0.186 

Literature

Crystal structure of an early protein-RNA assembly complex of the signal recognition particle.

Wild, K., Sinning, I., Cusack, S.

(2001) Science 294: 598-601

• PubMed: 11641499 
• DOI: 10.1126/science.1063839


• PubMed Abstract: 
  

The signal recognition particle (SRP) is a universally conserved ribonucleoprotein complex that mediates the cotranslational targeting of secretory and membrane proteins to cellular membranes. A crucial early step in SRP assembly in archaea and eukarya is the binding of protein SRP19 to specific sites on SRP RNA. Here we report the 1.8 angstrom resolution crystal structure of human SRP19 in complex with its primary binding site on helix 6 of SRP RNA, which consists of a stem-loop structure closed by an unusual GGAG tetraloop. Protein-RNA interactions are mediated by the specific recognition of a widened major groove and the tetraloop without any direct protein-base contacts and include a complex network of highly ordered water molecules. A model of the assembly of the SRP core comprising SRP19, SRP54, and SRP RNA based on crystallographic and biochemical data is proposed.

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Related Citations: 

• The 2 A structure of helix 6 of the human signal recognition particle RNA
  Wild, K.,Weichenrieder, O.,Leonard, G.A.,Cusack, S.
  (1999) Structure 7: 1345




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Organizational Affiliation: 

Biochemie-Zentrum (BZH), University of Heidelberg, Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
SIGNAL RECOGNITION PARTICLE 19 KDA PROTEIN	A	128	Homo sapiens	Mutation(s): 0  Gene Names: SRP19
Find proteins for P09132 (Homo sapiens) Go to Gene View: SRP19 Go to UniProtKB:  P09132

Entity ID: 1
Molecule	Chains	Length	Organism
HELIX 6 OF HUMAN SRP RNA	B	29	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MG	B	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
A23	B	RNA LINKING	C10 H13 N5 O9 P2		A
5BU	B	RNA LINKING	C9 H12 Br N2 O9 P		U

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.222 
• R-Value Work: 0.186 
• Space Group: C 2 2 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 55.813	α = 90.00
b = 109.782	β = 90.00
c = 89.461	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-07-02 
• Released Date: 2001-10-19 
• Deposition Author(s): Wild, K., Sinning, I., Cusack, S.

Revision History 

• Version 1.0: 2001-10-19
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance