1YI2 Ribosome date Jan 11, 2005
title Crystal Structure Of Erythromycin Bound To The G2099a Mutant Ribosomal Subunit Of Haloarcula Marismortui
authors D.Tu, G.Blaha, P.B.Moore, T.A.Steitz
compound source
Molecule: 23s Ribosomal Rna
Chain
Mutation: Yes
Other_details: Encoded By Rrna Operon
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Strain: Dt38

Molecule: 5s Ribosomal Rna
Chain: 9

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Strain: Dt38

Molecule: 50s Ribosomal Protein L2p
Chain: A

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Strain: Dt38

Molecule: 50s Ribosomal Protein L3p
Chain: B

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Strain: Dt38

Molecule: 50s Ribosomal Protein L4e
Chain: C

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Strain: Dt38

Molecule: 50s Ribosomal Protein L5p
Chain: D

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Strain: Dt38

Molecule: 50s Ribosomal Protein L6p
Chain: E

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Strain: Dt38

Molecule: 50s Ribosomal Protein L7ae
Chain: F

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Strain: Dt38

Molecule: Acidic Ribosomal Protein P0 Homolog
Chain: G

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Strain: Dt38

Molecule: 50s Ribosomal Protein L10e
Chain: H

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Strain: Dt38

Molecule: 50s Ribosomal Protein L11p
Chain: I

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Strain: Dt38

Molecule: 50s Ribosomal Protein L13p
Chain: J

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Strain: Dt38

Molecule: 50s Ribosomal Protein L14p
Chain: K

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Strain: Dt38

Molecule: 50s Ribosomal Protein L15p
Chain: L

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Strain: Dt38

Molecule: 50s Ribosomal Protein L15e
Chain: M

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Strain: Dt38

Molecule: 50s Ribosomal Protein L18p
Chain: N

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Strain: Dt38

Molecule: 50s Ribosomal Protein L18e
Chain: O

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Strain: Dt38

Molecule: 50s Ribosomal Protein L19e
Chain: P

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Strain: Dt38

Molecule: 50s Ribosomal Protein L21e
Chain: Q

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Strain: Dt38

Molecule: 50s Ribosomal Protein L22p
Chain: R

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Strain: Dt38

Molecule: 50s Ribosomal Protein L23p
Chain: S

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Strain: Dt38

Molecule: 50s Ribosomal Protein L24p
Chain: T

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Strain: Dt38

Molecule: 50s Ribosomal Protein L24e
Chain: U

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Strain: Dt38

Molecule: 50s Ribosomal Protein L29p
Chain: V

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Strain: Dt38

Molecule: 50s Ribosomal Protein L30p
Chain: W

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Strain: Dt38

Molecule: 50s Ribosomal Protein L31e
Chain: X

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Strain: Dt38

Molecule: 50s Ribosomal Protein L32e
Chain: Y

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Strain: Dt38

Molecule: 50s Ribosomal Protein L37ae
Chain: Z

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Strain: Dt38

Molecule: 50s Ribosomal Protein L37e
Chain: 1

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Strain: Dt38

Molecule: 50s Ribosomal Protein L39e
Chain: 2

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Strain: Dt38

Molecule: 50s Ribosomal Protein L44e
Chain: 3

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Strain: Dt38
symmetry Space Group: C 2 2 21
R_factor 0.176 R_Free 0.214
crystal
cell
length a length b length c angle alpha angle beta angle gamma
212.435 299.989 574.176 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.65 Å
ligand 1MA, CD, CL, ERY, K, MG, NA, OMG, OMU, PSU, UR3 enzyme
related structures by homologous chain: 1YIJ, 1YIT
Gene
Ontology
ChainFunctionProcessComponent
1


2


3


A


B


C


D


E


F
  • ribonuclease P activity


  • G


    H


    I


    J


    K


    L


    M


    N


    O


    P


    Q


    R


    S


    T


    U


    V


    W


    X


    Y


    Z


    Primary referenceStructures of MLSBK antibiotics bound to mutated large ribosomal subunits provide a structural explanation for resistance., Tu D, Blaha G, Moore PB, Steitz TA, Cell. 2005 Apr 22;121(2):257-70. PMID:15851032
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (2010 Kb) [Save to disk]
  • Biological Unit Coordinates (1yi2.pdb1.gz) 1972 Kb
  • LPC: Ligand-Protein Contacts for 1YI2
  • CSU: Contacts of Structural Units for 1YI2
  • Likely Quarternary Molecular Structure file(s) for 1YI2
  • Structure Factors (10711 Kb)
  • Retrieve 1YI2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YI2 from S2C, [Save to disk]
  • Re-refined 1yi2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1YI2 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 1YI2
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1YI2, from MSDmotif at EBI
  • Fold representative 1yi2 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1yi2_Z] [1yi2_B] [1yi2_U] [1yi2_S] [1yi2_3] [1yi2_H] [1yi2_K] [1yi2_9] [1yi2_1] [1yi2_V] [1yi2_2] [1yi2] [1yi2_T] [1yi2_L] [1yi2_M] [1yi2_W] [1yi2_X] [1yi2_A] [1yi2_N] [1yi2_E] [1yi2_R] [1yi2_J] [1yi2_Q] [1yi2_C] [1yi2_G] [1yi2_Y] [1yi2_0] [1yi2_D] [1yi2_P] [1yi2_F] [1yi2_I] [1yi2_O]
  • SWISS-PROT database: [P60617] [P14122] [P29198] [P22450] [P60618] [P12737] [P12733] [P14123] [P14119] [P12734] [P10970] [P12732] [P14116] [P10972] [P10971] [P20276] [P14121] [P18138] [P12736] [P60619] [P32410] [P22452] [P20279] [P32411] [P12735] [P14124] [P14135] [P12743] [P15825]
  • Domain organization of [RL10_HALMA] [RL11_HALMA] [RL13_HALMA] [RL14_HALMA] [RL15E_HALMA] [RL15_HALMA] [RL18E_HALMA] [RL18_HALMA] [RL19_HALMA] [RL21_HALMA] [RL22_HALMA] [RL23_HALMA] [RL24E_HALMA] [RL24_HALMA] [RL29_HALMA] [RL2_HALMA] [RL30_HALMA] [RL31_HALMA] [RL32_HALMA] [RL37A_HALMA] [RL37_HALMA] [RL39_HALMA] [RL3_HALMA] [RL44_HALMA] [RL4_HALMA] [RL5_HALMA] [RL6_HALMA] [RL7A_HALMA] [RLA0_HALMA] by SWISSPFAM
  • Domains found in 1YI2: [HhH1] [KOW] [RL11] [Ribosomal_L14] [Ribosomal_L15e] [Ribosomal_L19e] [Ribosomal_L2] [Ribosomal_L2_C] [Ribosomal_L31e] [Ribosomal_L32e] [TRASH ] by SMART
  • Other resources with information on 1YI2
  • Community annotation for 1YI2 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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