1E8S | pdb_00001e8s

Alu domain of the mammalian SRP (potential Alu retroposition intermediate)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Work: 
    0.388 (Depositor) 
  • R-Value Observed: 
    0.388 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history. 

Literature

Structure and Assembly of the Alu Domain of the Mammalian Signal Recognition Particle

Weichenrieder, O., Wild, K., Strub, K., Cusack, S.

(2000) Nature 408: 167

  • DOI: https://doi.org/10.1038/35041507
  • Primary Citation Related Structures: 
    1E8O, 1E8S

  • PubMed Abstract: 

    The Alu domain of the mammalian signal recognition particle (SRP) comprises the heterodimer of proteins SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. It retards the ribosomal elongation of signal-peptide-containing proteins before their engagement with the translocation machinery in the endoplasmic reticulum. Here we report two crystal structures of the heterodimer SRP9/14 bound either to the 5' domain or to a construct containing both 5' and 3' domains. We present a model of the complete Alu domain that is consistent with extensive biochemical data. SRP9/14 binds strongly to the conserved core of the 5' domain, which forms a U-turn connecting two helical stacks. Reversible docking of the more weakly bound 3' domain might be functionally important in the mechanism of translational regulation. The Alu domain structure is probably conserved in other cytoplasmic ribonucleoprotein particles and retroposition intermediates containing SRP9/14-bound RNAs transcribed from Alu repeats or related elements in genomic DNA.

    • Organizational Affiliation: 
    • European Molecular Laboratory Biology, Grenoble Outstation, France.

Macromolecule Content 

  • Total Structure Weight: 50.91 kDa 
  • Atom Count: 235 
  • Modeled Residue Count: 233 
  • Deposited Residue Count: 279 
  • Unique protein chains: 2
  • Unique nucleic acid chains: 1

Macromolecules


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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
SIGNAL RECOGNITION PARTICLE 9 KDA PROTEIN85Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P49458 (Homo sapiens)
Explore P49458 
Go to UniProtKB:  P49458
PHAROS:  P49458
GTEx:  ENSG00000143742 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49458
Sequence Annotations
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Reference Sequence
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|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
SIGNAL RECOGNITION PARTICLE 14 KDA PROTEIN106Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P37108 (Homo sapiens)
Explore P37108 
Go to UniProtKB:  P37108
PHAROS:  P37108
GTEx:  ENSG00000140319 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37108
Sequence Annotations
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Reference Sequence
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(by identity cutoff) 
Entity ID: 3
MoleculeChains LengthOrganismImage
7SL RNA, 88-MER88Homo sapiens
Sequence Annotations
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Work:  0.388 (Depositor) 
  • R-Value Observed: 0.388 (Depositor) 
Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.33α = 90
b = 143.33β = 90
c = 60.36γ = 90
Software Package:
Software NamePurpose
HKLdata reduction
MOSFLMdata reduction
HKLdata scaling
SCALAdata scaling
SHARPphasing
SOLOMONphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-11-08
    Type: Initial release
  • Version 1.1: 2024-05-08
    Changes: Data collection, Database references