3KTV

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.291 
  • R-Value Observed: 0.293 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 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 D Biol Crystallogr 66: 295-303

  • DOI: https://doi.org/10.1107/S0907444910000879
  • Primary Citation of Related Structures:  
    3KTV, 3KTW

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Signal recognition particle 19 kDa protein
B, D
128Homo sapiensMutation(s): 0 
Gene Names: SRP19
UniProt & NIH Common Fund Data Resources
Find proteins for P09132 (Homo sapiens)
Explore P09132 
Go to UniProtKB:  P09132
PHAROS:  P09132
GTEx:  ENSG00000153037 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09132
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
SRP RNA108Homo sapiens
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains LengthOrganismImage
SRP RNA108Homo sapiens
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.291 
  • R-Value Observed: 0.293 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.12α = 90
b = 100.12β = 90
c = 293.3γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MxCuBEdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-02-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description