4ADX Ribosome date Jan 04, 2012
title The Cryo-Em Structure Of The Archaeal 50s Ribosomal Subunit With Initiation Factor 6
authors B.J.Greber, D.Boehringer, V.Godinic-Mikulcic, A.Crnkovic, M.Ibba I.Weygand-Durasevic, N.Ban
compound source
Molecule: 23s Ribosomal Rna
Chain
 Organism_scientific: Methanothermobacter Thermautotrophicus
Organism_taxid: 187420
Strain: Delta H
Cellular_location: Cytoplasm

Molecule: Rpl37e
Chain: 1
Organism_scientific: Methanothermobacter Thermautotrophicus
Organism_taxid: 187420
Strain: Delta H
Cellular_location: Cytoplasm

Molecule: Rpl39e
Chain: 2
Organism_scientific: Methanothermobacter Thermautotrophicus
Organism_taxid: 187420
Strain: Delta H
Cellular_location: Cytoplasm

Molecule: Rpl44e
Chain: 3
Organism_scientific: Methanothermobacter Thermautotrophicus
Organism_taxid: 187420
Strain: Delta H

Molecule: Rpl34e
Chain: 4
Organism_scientific: Methanothermobacter Thermautotrophicus
Organism_taxid: 187420
Strain: Delta H
Cellular_location: Cytoplasm

Molecule: Rpl40e
Chain: 5
Organism_scientific: Methanothermobacter Thermautotrophicus
Organism_taxid: 187420
Strain: Delta H
Cellular_location: Cytoplasm

Molecule: Rpl30e
Chain: 6
Organism_scientific: Methanothermobacter Thermautotrophicus
Organism_taxid: 187420
Strain: Delta H
Cellular_location: Cytoplasm

Molecule: Rpl14e
Chain: 7
Organism_scientific: Methanothermobacter Thermautotrophicus
Organism_taxid: 187420
Strain: Delta H
Cellular_location: Cytoplasm

Molecule: 23s Ribosomal Rna Expansion Segments
Chain: 8
Organism_scientific: Methanothermobacter Thermautotrophicus
Organism_taxid: 187420
Strain: Delta H
Cellular_location: Cytoplasm

Molecule: 5s Ribosomal Rna
Chain: 9
Organism_scientific: Methanothermobacter Thermautotrophicus
Organism_taxid: 187420
Strain: Delta H
Cellular_location: Cytoplasm

Molecule: Rpl2
Chain: A
Organism_scientific: Methanothermobacter Thermautotrophicus
Organism_taxid: 187420
Strain: Delta H
Cellular_location: Cytoplasm

Molecule: Rpl3
Chain: B
Organism_scientific: Methanothermobacter Thermautotrophicus
Organism_taxid: 187420
Strain: Delta H
Cellular_location: Cytoplasm

Molecule: Rpl4
Chain: C
Organism_scientific: Methanothermobacter Thermautotrophicus
Organism_taxid: 187420
Strain: Delta H
Cellular_location: Cytoplasm

Molecule: Rpl5
Chain: D
Organism_scientific: Methanothermobacter Thermautotrophicus
Organism_taxid: 187420
Strain: Delta H
Cellular_location: Cytoplasm

Molecule: Rpl6
Chain: E
Organism_scientific: Methanothermobacter Thermautotrophicus
Organism_taxid: 187420
Strain: Delta H
Cellular_location: Cytoplasm

Molecule: Rpl7ae
Chain: F
Organism_scientific: Methanothermobacter Thermautotrophicus
Organism_taxid: 187420
Strain: Delta H
Cellular_location: Cytoplasm

Molecule: Rplx
Chain: G
Organism_scientific: Methanothermobacter Thermautotrophicus
Organism_taxid: 187420
Strain: Delta H
Cellular_location: Cytoplasm

Molecule: Rpl10e
Chain: H
Organism_scientific: Methanothermobacter Thermautotrophicus
Organism_taxid: 187420
Strain: Delta H
Cellular_location: Cytoplasm

Molecule: Aif6
Chain: I
Organism_scientific: Methanothermobacter Thermautotrophicus
Organism_taxid: 187420
Strain: Delta H
Cellular_location: Cytoplasm

Molecule: Rpl13
Chain: J
Organism_scientific: Methanothermobacter Thermautotrophicus
Organism_taxid: 187420
Strain: Delta H
Cellular_location: Cytoplasm

Molecule: Rpl14
Chain: K
Organism_scientific: Methanothermobacter Thermautotrophicus
Organism_taxid: 187420
Strain: Delta H
Cellular_location: Cytoplasm

Molecule: Rpl15
Chain: L
Organism_scientific: Methanothermobacter Thermautotrophicus
Organism_taxid: 187420
Strain: Delta H
Cellular_location: Cytoplasm

Molecule: Rpl15e
Chain: M
Organism_scientific: Methanothermobacter Thermautotrophicus
Organism_taxid: 187420
Strain: Delta H
Cellular_location: Cytoplasm

Molecule: Rpl18
Chain: N
Organism_scientific: Methanothermobacter Thermautotrophicus
Organism_taxid: 187420
Strain: Delta H
Cellular_location: Cytoplasm

Molecule: Rpl18e
Chain: O
Organism_scientific: Methanothermobacter Thermautotrophicus
Organism_taxid: 187420
Strain: Delta H
Cellular_location: Cytoplasm

Molecule: Rpl19e
Chain: P
Organism_scientific: Methanothermobacter Thermautotrophicus
Organism_taxid: 187420
Strain: Delta H
Cellular_location: Cytoplasm

Molecule: Rpl21e
Chain: Q
Organism_scientific: Methanothermobacter Thermautotrophicus
Organism_taxid: 187420
Strain: Delta H
Cellular_location: Cytoplasm

Molecule: Rpl22
Chain: R
Organism_scientific: Methanothermobacter Thermautotrophicus
Organism_taxid: 187420
Strain: Delta H
Cellular_location: Cytoplasm

Molecule: Rpl23
Chain: S
Organism_scientific: Methanothermobacter Thermautotrophicus
Organism_taxid: 187420
Strain: Delta H
Cellular_location: Cytoplasm

Molecule: Rpl24
Chain: T
Organism_scientific: Methanothermobacter Thermautotrophicus
Organism_taxid: 187420
Strain: Delta H
Cellular_location: Cytoplasm

Molecule: Rpl24e
Chain: U
Organism_scientific: Methanothermobacter Thermautotrophicus
Organism_taxid: 187420
Strain: Delta H
Cellular_location: Cytoplasm

Molecule: Rpl29
Chain: V
Organism_scientific: Methanothermobacter Thermautotrophicus
Organism_taxid: 187420
Strain: Delta H
Cellular_location: Cytoplasm

Molecule: Rpl30
Chain: W
Organism_scientific: Methanothermobacter Thermautotrophicus
Organism_taxid: 187420
Strain: Delta H
Cellular_location: Cytoplasm

Molecule: Rpl31e
Chain: X
Organism_scientific: Methanothermobacter Thermautotrophicus
Organism_taxid: 187420
Strain: Delta H
Cellular_location: Cytoplasm

Molecule: Rpl32e
Chain: Y
Organism_scientific: Methanothermobacter Thermautotrophicus
Organism_taxid: 187420
Strain: Delta H
Cellular_location: Cytoplasm

Molecule: Rpl37ae
Chain: Z
Organism_scientific: Methanothermobacter Thermautotrophicus
Organism_taxid: 187420
Strain: Delta H
Cellular_location: Cytoplasm
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 6.60 Å
Gene
Ontology
ChainFunctionProcessComponent
1


2


3


4


5


6


7


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 referenceCryo-EM Structure of the Archaeal 50S Ribosomal Subunit in Complex with Initiation Factor 6 and Implications for Ribosome Evolution., Greber BJ, Boehringer D, Godinic-Mikulcic V, Crnkovic A, Ibba M, Weygand-Durasevic I, Ban N, J Mol Biol. 2012 May 4;418(3-4):145-60. Epub 2012 Jan 27. PMID:22306461
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (165 Kb) [Save to disk]
  • Biological Unit Coordinates (4adx.pdb1.gz) 158 Kb
  • CSU: Contacts of Structural Units for 4ADX
  • Retrieve 4ADX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4ADX from S2C, [Save to disk]
    • View 4ADX 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 4ADX
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 4ADX, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4adx_L] [4adx_3] [4adx_K] [4adx_M] [4adx_J] [4adx_9] [4adx_4] [4adx_Z] [4adx_F] [4adx_P] [4adx_E] [4adx_T] [4adx_S] [4adx_Q] [4adx_D] [4adx_O] [4adx_B] [4adx_A] [4adx_I] [4adx_6] [4adx_Y] [4adx_U] [4adx_V] [4adx_C] [4adx_0] [4adx_H] [4adx] [4adx_1] [4adx_R] [4adx_8] [4adx_N] [4adx_2] [4adx_X] [4adx_7] [4adx_W] [4adx_G] [4adx_5]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4ADX: [HhH1] [KOW] [Ribosomal_L14] [Ribosomal_L15e] [Ribosomal_L19e] [Ribosomal_L2] [Ribosomal_L2_C] [Ribosomal_L31e] [Ribosomal_L32e] [Ribosomal_L40e] [TRASH] [UBQ] [eIF6 ] by SMART
    • Other resources with information on 4ADX
  • Community annotation for 4ADX at PDBWiki (http://pdbwiki.org)
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