1RY1

Structure of the signal recognition particle interacting with the elongation-arrested ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 12 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the signal recognition particle interacting with the elongation-arrested ribosome

Halic, M.Becker, T.Pool, M.R.Spahn, C.M.Grassucci, R.A.Frank, J.Beckmann, R.

(2004) Nature 427: 808-814

  • DOI: 10.1038/nature02342

  • PubMed Abstract: 
  • Cotranslational translocation of proteins across or into membranes is a vital process in all kingdoms of life. It requires that the translating ribosome be targeted to the membrane by the signal recognition particle (SRP), an evolutionarily conserved ...

    Cotranslational translocation of proteins across or into membranes is a vital process in all kingdoms of life. It requires that the translating ribosome be targeted to the membrane by the signal recognition particle (SRP), an evolutionarily conserved ribonucleoprotein particle. SRP recognizes signal sequences of nascent protein chains emerging from the ribosome. Subsequent binding of SRP leads to a pause in peptide elongation and to the ribosome docking to the membrane-bound SRP receptor. Here we present the structure of a targeting complex consisting of mammalian SRP bound to an active 80S ribosome carrying a signal sequence. This structure, solved to 12 A by cryo-electron microscopy, enables us to generate a molecular model of SRP in its functional conformation. The model shows how the S domain of SRP contacts the large ribosomal subunit at the nascent chain exit site to bind the signal sequence, and that the Alu domain reaches into the elongation-factor-binding site of the ribosome, explaining its elongation arrest activity.


    Organizational Affiliation

    Institute of Biochemistry, Charité, University Medical School, Humboldt University of Berlin, Monbijoustrasse 2, 10117 Berlin, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (Signal recognition particle 9 kDa protein)
C
85Homo sapiensGene Names: SRP9
Find proteins for P49458 (Homo sapiens)
Go to Gene View: SRP9
Go to UniProtKB:  P49458
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (Signal recognition particle 14 kDa protein)
D
106Homo sapiensGene Names: SRP14
Find proteins for P37108 (Homo sapiens)
Go to Gene View: SRP14
Go to UniProtKB:  P37108
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (Signal recognition particle 19 kDa protein)
B
108Homo sapiensGene Names: SRP19
Find proteins for P09132 (Homo sapiens)
Go to Gene View: SRP19
Go to UniProtKB:  P09132
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Signal recognition particle protein
U
296Thermus aquaticusGene Names: ffh
Find proteins for O07347 (Thermus aquaticus)
Go to UniProtKB:  O07347
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Signal recognition particle 54 kDa protein
W
109Mus musculusGene Names: Srp54
Find proteins for P14576 (Mus musculus)
Go to UniProtKB:  P14576
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Rhodopsin
S
18Tursiops truncatusGene Names: RHO
Find proteins for O62798 (Tursiops truncatus)
Go to Gene View: RHO
Go to UniProtKB:  O62798
Entity ID: 1
MoleculeChainsLengthOrganism
ALU DOMAIN (RNA FRAGMENTS)E50N/A
Entity ID: 2
MoleculeChainsLengthOrganism
ALU DOMAIN (SRP9, SRP14 + RNA)A128N/A
Entity ID: 3
MoleculeChainsLengthOrganism
fragment of 7S RNAM27N/A
Entity ID: 4
MoleculeChainsLengthOrganism
RNA (31-MER)N31N/A
Entity ID: 5
MoleculeChainsLengthOrganism
RNA (5'-R(P*GP*UP*UP*CP*UP*GP*GP*GP*CP*UP*GP*UP*AP*GP*UP*GP*CP*GP*CP*UP*AP*UP*GP*C)-3')O24N/A
Entity ID: 6
MoleculeChainsLengthOrganism
RNA (5'-R(*CP*AP*AP*UP*AP*GP*CP*CP*AP*CP*UP*GP*CP*AP*CP*UP*CP*CP*AP*G)-3')P20N/A
Entity ID: 7
MoleculeChainsLengthOrganism
RNA (5'-R(P*CP*GP*AP*UP*CP*GP*GP*GP*UP*GP*UP*C)-3')Q12N/A
Entity ID: 8
MoleculeChainsLengthOrganism
RNA (5'-R(P*AP*UP*CP*GP*CP*GP*CP*CP*UP*GP*UP*G)-3')R12N/A
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
GDP
Query on GDP
E
RNA LINKINGC10 H15 N5 O11 P2G
CCC
Query on CCC
A
RNA LINKINGC9 H13 N3 O10 P2C
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 12 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-04-20
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance