3KTV

Crystal structure of the human SRP19/S-domain SRP RNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.8 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.291 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural insights into the assembly of the human and archaeal signal recognition particles.

Wild, K.Bange, G.Bozkurt, G.Segnitz, B.Hendricks, A.Sinning, I.

(2010) Acta Crystallogr.,Sect.D 66: 295-303

  • DOI: 10.1107/S0907444910000879
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The signal recognition particle (SRP) is a conserved ribonucleoprotein (RNP) complex that co-translationally targets membrane and secretory proteins to membranes. The assembly of the particle depends on the proper folding of the SRP RNA, which in mam ...

    The signal recognition particle (SRP) is a conserved ribonucleoprotein (RNP) complex that co-translationally targets membrane and secretory proteins to membranes. The assembly of the particle depends on the proper folding of the SRP RNA, which in mammalia and archaea involves an induced-fit mechanism within helices 6 and 8 in the S domain of SRP. The two helices are juxtaposed and clamped together upon binding of the SRP19 protein to their apices. In the current assembly paradigm, archaeal SRP19 causes the asymmetric loop of helix 8 to bulge out and expose the binding platform for the key player SRP54. Based on a heterologous archaeal SRP19-human SRP RNA structure, mammalian SRP19 was thought not to be able to induce this change, thus explaining the different requirements of SRP19 for SRP54 recruitment. In contrast, the crystal structures of a crenarchaeal and the all-human SRP19-SRP RNA binary complexes presented here show that the asymmetric loop is bulged out in both binary complexes. Differences in SRP assembly between mammalia and archaea are therefore independent of SRP19 and are based on differences in SRP RNA itself. A new SRP-assembly scheme is presented.


    Organizational Affiliation

    Heidelberg University Biochemistry Center (BZH), University of Heidelberg, INF328, 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
B, D
128Homo sapiensMutation(s): 0 
Gene Names: SRP19
Find proteins for P09132 (Homo sapiens)
Go to Gene View: SRP19
Go to UniProtKB:  P09132
Entity ID: 1
MoleculeChainsLengthOrganism
SRP RNAA108Homo sapiens
Entity ID: 3
MoleculeChainsLengthOrganism
SRP RNAC108Homo sapiens
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, C, D
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
GDP
Query on GDP
C
RNA LINKINGC10 H15 N5 O11 P2G
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.8 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.291 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 100.120α = 90.00
b = 100.120β = 90.00
c = 293.300γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOSFLMdata reduction
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MxCuBEdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-02-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance