1JID | pdb_00001jid

Human SRP19 in complex with helix 6 of Human SRP RNA

• PDB DOI: https://doi.org/10.2210/pdb1JID/pdb
• NAKB: 1JID

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


• 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: 1.80 Å
• R-Value Free: 
  0.222 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.178 (DCC) 

Starting Model: experimental

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: https://doi.org/10.1126/science.1063839
• Primary Citation Related Structures: 
  1JID


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

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 24.47 kDa 
• Atom Count: 1,828 
• Modeled Residue Count: 143 
• Deposited Residue Count: 157 
• 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]	128	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P09132 (Homo sapiens) Explore P09132  Go to UniProtKB:  P09132
PHAROS:  P09132 GTEx:  ENSG00000153037

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

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: 1.80 Å
• R-Value Free:  0.222 (Depositor), 0.212 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.178 (DCC) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.813	α = 90
b = 109.782	β = 90
c = 89.461	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-27
  Changes: Database references, Derived calculations
• Version 1.4: 2023-08-16
  Changes: Data collection, Refinement description