1JID

Human SRP19 in complex with helix 6 of Human SRP RNA


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • 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 eukar ...

    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.


    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


    Organizational Affiliation

    Biochemie-Zentrum (BZH), University of Heidelberg, Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany. klemens.wild@bzh.uni-heidelberg.de




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
SIGNAL RECOGNITION PARTICLE 19 KDA PROTEIN
A
128Homo sapiensGene Names: SRP19
Find proteins for P09132 (Homo sapiens)
Go to Gene View: SRP19
Go to UniProtKB:  P09132
Entity ID: 1
MoleculeChainsLengthOrganism
HELIX 6 OF HUMAN SRP RNAB29N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
A23
Query on A23
B
RNA LINKINGC10 H13 N5 O9 P2A
5BU
Query on 5BU
B
RNA LINKINGC9 H12 Br N2 O9 PU
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 = 55.813α = 90.00
b = 109.782β = 90.00
c = 89.461γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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