3IY9 Ribosome date Apr 20, 2009
title Leishmania Tarentolae Mitochondrial Large Ribosomal Subunit
authors M.R.Sharma, T.M.Booth, L.Simpson, D.A.Maslov, R.K.Agrawal
compound source
Molecule: Leishmania Tarentolae Mitochondrial Large Ribosom Subunit;
Chain: A
Organism_scientific: Leishmania Tarentolae
Organism_taxid: 5689

Molecule: 39s Ribosomal Protein L2, Mitochondrial
Chain: B

Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: 50s Ribosomal Protein L3
Chain: C

Organism_scientific: Escherichia Coli
Organism_taxid: 83333

Molecule: 39s Ribosomal Protein L4, Mitochondrial
Chain: D

Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: 50s Ribosomal Protein L9
Chain: H

Organism_scientific: Escherichia Coli
Organism_taxid: 83333

Molecule: 39s Ribosomal Protein L11, Mitochondrial
Chain: G

Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: 50s Ribosomal Protein L13
Chain: J

Organism_scientific: Escherichia Coli
Organism_taxid: 83333

Molecule: 50s Ribosomal Protein L14
Chain: K

Organism_scientific: Escherichia Coli
Organism_taxid: 83333

Molecule: 50s Ribosomal Protein L15
Chain: L

Organism_scientific: Escherichia Coli
Organism_taxid: 83333

Molecule: 39s Ribosomal Protein L16, Mitochondrial
Chain: I

Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: 39s Ribosomal Protein L17, Mitochondrial
Chain: S

Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: 50s Ribosomal Protein L20
Chain: Q

Organism_scientific: Escherichia Coli
Organism_taxid: 83333

Molecule: 50s Ribosomal Protein L21
Chain: R

Organism_scientific: Escherichia Coli
Organism_taxid: 83333

Molecule: 39s Ribosomal Protein L22, Mitochondrial
Chain: M

Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: 50s Ribosomal Protein L23
Chain: T

Organism_scientific: Escherichia Coli
Organism_taxid: 83333

Molecule: 39s Ribosomal Protein L24, Mitochondrial
Chain: N

Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: 39s Ribosomal Protein L27, Mitochondrial
Chain: O

Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: 50s Ribosomal Protein L29
Chain: X

Organism_scientific: Escherichia Coli
Organism_taxid: 83333

Molecule: 50s Ribosomal Protein L30
Chain: Y

Organism_scientific: Escherichia Coli
Organism_taxid: 83333

Molecule: 39s Ribosomal Protein L33, Mitochondrial
Chain: P

Organism_scientific: Homo Sapiens
Organism_taxid: 9606
symmetry Space Group
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 14.10 Å
Gene
Ontology
ChainFunctionProcessComponent
B


C


D


G


H


I


J


K


L


M


N


O


P


Q


R


S


T


X


Y


Primary referenceStructure of a mitochondrial ribosome with minimal RNA., Sharma MR, Booth TM, Simpson L, Maslov DA, Agrawal RK, Proc Natl Acad Sci U S A. 2009 Jun 16;106(24):9637-42. Epub 2009 Jun 3. PMID:19497863
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (69 Kb) [Save to disk]
  • Biological Unit Coordinates (3iy9.pdb1.gz) 65 Kb
  • CSU: Contacts of Structural Units for 3IY9
  • Likely Quarternary Molecular Structure file(s) for 3IY9
  • Retrieve 3IY9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3IY9 from S2C, [Save to disk]
  • View 3IY9 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 3IY9
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3IY9, from MSDmotif at EBI
  • Fold representative 3iy9 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3iy9_L] [3iy9_Q] [3iy9_N] [3iy9_X] [3iy9_T] [3iy9_D] [3iy9_R] [3iy9_M] [3iy9_H] [3iy9_G] [3iy9_K] [3iy9_S] [3iy9_I] [3iy9_Y] [3iy9_J] [3iy9_B] [3iy9_C] [3iy9_O] [3iy9] [3iy9_P] [3iy9_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3IY9: [KOW] [RL11] [Ribosomal_L14] [Ribosomal_L2] [Ribosomal_L2_C ] by SMART
  • Other resources with information on 3IY9
  • Community annotation for 3IY9 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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