5IT9 Ribosome date Mar 16, 2016
title Structure Of The Yeast Kluyveromyces Lactis Small Ribosomal Complex With The Cricket Paralysis Virus Ires.
authors J.Murray, C.G.Savva, B.S.Shin, T.E.Dever, V.Ramakrishnan, I.S.Fer
compound source
Molecule: Ribosomal Protein Us2
Chain: A
Synonym: 40s Ribosomal Protein S0
 Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Ribosomal Protein Es1
Chain: B
Synonym: 40s Ribosomal Protein S1
Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Ribosomal Protein Us5
Chain: C
Synonym: Klla0f09812p
Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Ribosomal Protein Us3
Chain: D
Synonym: Klla0d08305p
Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Ribosomal Protein Es4
Chain: E
Synonym: 40s Ribosomal Protein S4
Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Ribosomal Protein Us7
Chain: F
Synonym: Klla0d10659p
Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Ribosomal Protein Es6
Chain: G
Synonym: 40s Ribosomal Protein S6
Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Ribosomal Protein Es7
Chain: H
Synonym: Klla0c13519p
Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Ribosomal Protein Es8
Chain: I
Synonym: 40s Ribosomal Protein S8
Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Ribosomal Protein Us4
Chain: J
Synonym: Klla0e23673p
Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Ribosomal Protein Es10
Chain: K
Synonym: Klla0b08173p
Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Ribosomal Protein Us17
Chain: L
Synonym: Klla0a10483p
Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Ribosomal Protein Es12
Chain: M
Synonym: 40s Ribosomal Protein S12
Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Ribosomal Protein Us15
Chain: N
Synonym: Klla0f18040p
Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Ribosomal Protein Us14
Chain: O
Synonym: 40s Ribosomal Protein S14, Rp59
Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Ribosomal Protein Us19
Chain: P
Synonym: Klla0f07843p
Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Ribosomal Protein Us9
Chain: Q
Synonym: 40s Ribosomal Protein S16
Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Ribosomal Protein Es17
Chain: R
Synonym: Klla0b01474p
Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Ribosomal Protein Us13
Chain: S
Synonym: Klla0b01562p
Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Ribosomal Protein Es19
Chain: T
Synonym: Klla0a07194p
Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Ribosomal Protein Us10
Chain: U
Synonym: Klla0f25542p
Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Ribosomal Protein Es21
Chain: V
Synonym: 40s Ribosomal Protein S21
Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Ribosomal Protein Us8
Chain: W
Synonym: 40s Ribosomal Protein S22
Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Ribosomal Protein Us21
Chain: X
Synonym: Rps23
Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Ribosomal Protein Es24
Chain: Y
Synonym: 40s Ribosomal Protein S24
Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Ribosomal Protein Es25
Chain: Z
Synonym: Klla0b06182p
Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Ribosomal Protein Es26
Chain: a
Synonym: Klla0d05115p
Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Ribosomal Protein Es27
Chain: b
Synonym: 40s Ribosomal Protein S27
Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Ribosomal Protein Es28
Chain: c
Synonym: 40s Ribosomal Protein S28, S33
Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Ribosomal Protein Es29
Chain: d
Synonym: 40s Ribosomal Protein S29
Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Ribosomal Protein Es30
Chain: e
Synonym: Klla0c04809p
Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Ribosomal Protein Es31
Chain: f
Synonym: Ubiquitin-40s Ribosomal Protein S27a
Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Ribosomal Protein Rack1
Chain: g
Synonym: Klla0e12277p
Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: 18s Ribosomal Rna
Chain: 2
Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Cricket Paralysis Virus Ires Rna
Chain: I
Engineered: Yes
Organism_scientific: Cricket Paralysis Virus
Organism_taxid: 12136
Expression_system: Escherichia Coli
Expression_system_taxid: 562
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 3.80 Å
ligand MG, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


B


C


D


E


F


G


H


I


J


K


L


M


N


O


P


Q


R


S


T


U


V


W


X


Y


a


b


c


d


e


f


g
  • GDP-dissociation inhibitor a...


    • Primary referenceStructural characterization of ribosome recruitment and translocation by type IV IRES., Murray J, Savva CG, Shin BS, Dever TE, Ramakrishnan V, Fernandez IS, Elife. 2016 May 9;5. pii: e13567. doi: 10.7554/eLife.13567. PMID:27159451
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1588 Kb) [Save to disk]
  • Biological Unit Coordinates (5it9.pdb1.gz) 1577 Kb
  • LPC: Ligand-Protein Contacts for 5IT9
  • CSU: Contacts of Structural Units for 5IT9
  • Retrieve 5IT9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5IT9 from S2C, [Save to disk]
    • View 5IT9 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 5IT9
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5it9_f] [5it9_c] [5it9_T] [5it9_S] [5it9_g] [5it9_E] [5it9_a] [5it9_e] [5it9_C] [5it9_i] [5it9_M] [5it9_b] [5it9_I] [5it9_R] [5it9_Y] [5it9_P] [5it9_W] [5it9_K] [5it9] [5it9_D] [5it9_F] [5it9_U] [5it9_d] [5it9_G] [5it9_2] [5it9_H] [5it9_O] [5it9_L] [5it9_Q] [5it9_J] [5it9_V] [5it9_X] [5it9_Z] [5it9_B] [5it9_N] [5it9_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5IT9: [KH] [KOW] [Ribosomal_S10] [Ribosomal_S13_N] [Ribosomal_S15] [Ribosomal_S19e] [Ribosomal_S27] [Ribosomal_S3Ae] [Ribosomal_S4] [Ribosomal_S6e] [S4] [WD40 ] by SMART
    • Other resources with information on 5IT9
  • Community annotation for 5IT9 at PDBWiki (http://pdbwiki.org)

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