2RDO Ribosome date Sep 24, 2007
title 50s Subunit With Ef-G(Gdpnp) And Rrf Bound
authors N.Gao, A.V.Zavialov, M.Ehrenberg, J.Frank
compound source
Molecule: 5s Ribosomal Rna
Chain: A
 Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 23s Ribosomal Rna
Chain: B
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L25
Chain: V
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L2
Chain: C
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L3
Chain: D
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L4
Chain: E
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L5
Chain: F
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L6
Chain: G
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L13
Chain: J
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L14
Chain: K
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L15
Chain: L
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L16
Chain: M
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L17
Chain: N
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L18
Chain: O
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L19
Chain: P
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L20
Chain: Q
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L21
Chain: R
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L22
Chain: S
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L23
Chain: T
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L24
Chain: U
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L27
Chain: W
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L29
Chain: X
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L30
Chain: Y
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L31
Chain: Z
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L32
Chain
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L33
Chain: 1
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L34
Chain: 2
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L35
Chain: 3
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L36
Chain: 4
Synonym: Ribosomal Protein B
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L11
Chain: I
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L9
Chain: H
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L1
Chain: 9
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: Elongation Factor G
Chain: 7
Synonym: Ef-G
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: Ribosome Recycling Factor
Chain: 8
Synonym: Ribosome-Releasing Factor, Rrf
Organism_scientific: Escherichia Coli
Organism_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 9.10 Å
Gene
Ontology
ChainFunctionProcessComponent
0


1


2


3


4


7


8


9


C


D


E


F


G


H


I


J


K


L


M


N


O


P


Q
  • translation repressor activi...


    • R


    S


    T


    U


    V


    W


    X


    Y


    Z


    Primary referenceSpecific interaction between EF-G and RRF and its implication for GTP-dependent ribosome splitting into subunits., Gao N, Zavialov AV, Ehrenberg M, Frank J, J Mol Biol. 2007 Dec 14;374(5):1345-58. Epub 2007 Oct 16. PMID:17996252
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (144 Kb) [Save to disk]
  • Biological Unit Coordinates (2rdo.pdb1.gz) 140 Kb
  • CSU: Contacts of Structural Units for 2RDO
  • Likely Quarternary Molecular Structure file(s) for 2RDO
  • Retrieve 2RDO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2RDO from S2C, [Save to disk]
    • View 2RDO 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 2RDO
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2RDO, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2rdo_V] [2rdo_A] [2rdo_J] [2rdo_H] [2rdo_U] [2rdo_9] [2rdo_R] [2rdo_1] [2rdo_M] [2rdo_L] [2rdo_S] [2rdo_8] [2rdo_X] [2rdo_T] [2rdo_Q] [2rdo_I] [2rdo_2] [2rdo_Y] [2rdo_B] [2rdo_O] [2rdo] [2rdo_C] [2rdo_E] [2rdo_N] [2rdo_4] [2rdo_K] [2rdo_P] [2rdo_G] [2rdo_3] [2rdo_D] [2rdo_Z] [2rdo_W] [2rdo_7] [2rdo_F] [2rdo_0]
  • SWISS-PROT database: [P0A6M8] [P0A7J7] [P0AA10] [P0ADY3] [P02413] [P0ADY7] [P0AG44] [P0C018] [P0A7K6] [P0A7L0] [P0A7L3] [P0AG48] [P61175] [P0ADZ0] [P60624] [P68919] [P0A7L8] [P0A7M6] [P60422] [P0AG51] [P0A7M9] [P0A7N4] [P0A7N9] [P0A7P5] [P0A7Q1] [P0A7Q6] [P60438] [P60723] [P62399] [P0AG55] [P0A7R1] [P0A805]
  • Domain organization of [EFG_ECOLI] [RL11_ECOLI] [RL13_ECOLI] [RL14_ECOLI] [RL15_ECOLI] [RL16_ECOLI] [RL17_ECOLI] [RL18_ECOLI] [RL19_ECOLI] [RL1_ECOLI] [RL20_ECOLI] [RL21_ECOLI] [RL22_ECOLI] [RL23_ECOLI] [RL24_ECOLI] [RL25_ECOLI] [RL27_ECOLI] [RL29_ECOLI] [RL2_ECOLI] [RL30_ECOLI] [RL31_ECOLI] [RL32_ECOLI] [RL33_ECOLI] [RL34_ECOLI] [RL35_ECOLI] [RL36_ECOLI] [RL3_ECOLI] [RL4_ECOLI] [RL5_ECOLI] [RL6_ECOLI] [RL9_ECOLI] [RRF_ECOLI] by SWISSPFAM
  • Domains found in 2RDO: [EFG_C] [EFG_IV] [KOW] [RL11] [Ribosomal_L14] [Ribosomal_L2] [Ribosomal_L2_C ] by SMART
    • Other resources with information on 2RDO
  • Community annotation for 2RDO 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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