4P3E

Structure of the human SRP S domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.246 

Starting Models: experimental
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This is version 1.5 of the entry. See complete history


Literature

SRP RNA remodeling by SRP68 explains its role in protein translocation.

Grotwinkel, J.T.Wild, K.Segnitz, B.Sinning, I.

(2014) Science 344: 101-104

  • DOI: https://doi.org/10.1126/science.1249094
  • Primary Citation of Related Structures:  
    4P3E, 4P3F, 4P3G

  • PubMed Abstract: 

    The signal recognition particle (SRP) is central to membrane protein targeting; SRP RNA is essential for SRP assembly, elongation arrest, and activation of SRP guanosine triphosphatases. In eukaryotes, SRP function relies on the SRP68-SRP72 heterodimer. We present the crystal structures of the RNA-binding domain of SRP68 (SRP68-RBD) alone and in complex with SRP RNA and SRP19. SRP68-RBD is a tetratricopeptide-like module that binds to a RNA three-way junction, bends the RNA, and inserts an α-helical arginine-rich motif (ARM) into the major groove. The ARM opens the conserved 5f RNA loop, which in ribosome-bound SRP establishes a contact to ribosomal RNA. Our data provide the structural basis for eukaryote-specific, SRP68-driven RNA remodeling required for protein translocation.


  • Organizational Affiliation

    Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Signal recognition particle 19 kDa protein128Homo 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
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Signal recognition particle subunit SRP68216Homo sapiensMutation(s): 1 
Gene Names: SRP68
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UHB9 (Homo sapiens)
Explore Q9UHB9 
Go to UniProtKB:  Q9UHB9
PHAROS:  Q9UHB9
GTEx:  ENSG00000167881 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UHB9
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
SRP RNA (124-mer)125Homo sapiens
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.246 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.649α = 90
b = 70.53β = 100.46
c = 106.493γ = 90
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySFB638

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-16
    Type: Initial release
  • Version 1.1: 2014-04-23
    Changes: Data collection
  • Version 1.2: 2014-07-09
    Changes: Structure summary
  • Version 1.3: 2017-09-27
    Changes: Author supporting evidence, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
  • Version 1.4: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.5: 2023-09-27
    Changes: Data collection, Database references, Refinement description