1RY1 Translation date Dec 19, 2003
title Structure Of The Signal Recognition Particle Interacting Wit Elongation-Arrested Ribosome
authors M.Halic, T.Becker, M.R.Pool, C.M.Spahn, R.A.Grassucci, J.Frank, R.
compound source
Molecule: Srp Alu Domain
Chain: E
 Organism_scientific: Canis Lupus Familiaris
Organism_common: Dog
Organism_taxid: 9615

Molecule: Srp S Domain
Chain: A
Organism_scientific: Canis Lupus Familiaris
Organism_common: Dog
Organism_taxid: 9615

Molecule: Srp Rna
Chain: M
Organism_scientific: Canis Lupus Familiaris
Organism_common: Dog
Organism_taxid: 9615

Molecule: Srp Rna
Chain: N
Organism_scientific: Canis Lupus Familiaris
Organism_common: Dog
Organism_taxid: 9615

Molecule: Srp Rna
Chain: O
Organism_scientific: Canis Lupus Familiaris
Organism_common: Dog
Organism_taxid: 9615

Molecule: Srp Rna
Chain: P
Organism_scientific: Canis Lupus Familiaris
Organism_common: Dog
Organism_taxid: 9615

Molecule: Srp Rna
Chain: Q
Organism_scientific: Canis Lupus Familiaris
Organism_common: Dog
Organism_taxid: 9615

Molecule: Srp Rna
Chain: R
Organism_scientific: Canis Lupus Familiaris
Organism_common: Dog
Organism_taxid: 9615

Molecule: Srp9
Chain: C
Organism_scientific: Canis Lupus Familiaris
Organism_common: Dog
Organism_taxid: 9615

Molecule: Srp14
Chain: D
Organism_scientific: Canis Lupus Familiaris
Organism_common: Dog
Organism_taxid: 9615

Molecule: Srp19
Chain: B
Organism_scientific: Canis Lupus Familiaris
Organism_common: Dog
Organism_taxid: 9615

Molecule: Srp54ng
Chain: U
Organism_scientific: Canis Lupus Familiaris
Organism_common: Dog
Organism_taxid: 9615

Molecule: Srp54m
Chain: W
Organism_scientific: Canis Lupus Familiaris
Organism_common: Dog
Organism_taxid: 9615

Molecule: Signal Sequence Peptide
Chain: S
Engineered: Yes
Synthetic: Yes
Organism_scientific: Triticum Aestivum
Organism_common: Wheat
Organism_taxid: 4565
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 12.00 Å
ligand CCC enzyme
Gene
Ontology
ChainFunctionProcessComponent
B


C


D


U


W


Primary referenceStructure of the signal recognition particle interacting with the elongation-arrested ribosome., Halic M, Becker T, Pool MR, Spahn CM, Grassucci RA, Frank J, Beckmann R, Nature 2004 Feb 26;427(6977):808-14. PMID:14985753
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (231 Kb) [Save to disk]
  • Biological Unit Coordinates (1ry1.pdb1.gz) 225 Kb
  • LPC: Ligand-Protein Contacts for 1RY1
  • CSU: Contacts of Structural Units for 1RY1
  • Likely Quarternary Molecular Structure file(s) for 1RY1
  • Retrieve 1RY1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1RY1 from S2C, [Save to disk]
    • View 1RY1 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 1RY1
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1RY1, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ry1a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1ry1b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1ry1c_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1ry1d_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1ry1e_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1ry1m_, region M [Jmol] [rasmolscript] [script source]
        - Domain d1ry1n_, region N [Jmol] [rasmolscript] [script source]
        - Domain d1ry1o_, region O [Jmol] [rasmolscript] [script source]
        - Domain d1ry1p_, region P [Jmol] [rasmolscript] [script source]
        - Domain d1ry1q_, region Q [Jmol] [rasmolscript] [script source]
        - Domain d1ry1r_, region R [Jmol] [rasmolscript] [script source]
        - Domain d1ry1s_, region S [Jmol] [rasmolscript] [script source]
        - Domain d1ry1u_, region U [Jmol] [rasmolscript] [script source]
        - Domain d1ry1w_, region W [Jmol] [rasmolscript] [script source]
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1ry1_P] [1ry1_B] [1ry1_U] [1ry1_A] [1ry1_O] [1ry1_D] [1ry1_N] [1ry1] [1ry1_Q] [1ry1_M] [1ry1_R] [1ry1_E] [1ry1_C] [1ry1_S] [1ry1_W]
  • SWISS-PROT database: [O62798] [P49458] [P37108] [P09132] [P14576] [O07347]
  • Belongs to the general secretory pathway (sec) family according to TCDB.
  • Domain organization of [OPSD_TURTR] [SRP09_HUMAN] [SRP14_HUMAN] [SRP19_HUMAN] [SRP54_MOUSE] [SRP54_THEAQ] by SWISSPFAM
  • Domains found in 1RY1: [AAA] [SRP54] [SRP54_N ] by SMART
    • Other resources with information on 1RY1
  • Community annotation for 1RY1 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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