6AZ1 Ribosome Antibiotic date Sep 09, 2017
title Cryo-Em Structure Of The Small Subunit Of Leishmania Ribosom Paromomycin
authors M.Shalev-Benami, Y.Zhang, H.Rozenberg, D.Matzov, E.Zimmerman, A.B C.L.Jaffe, A.Yonath, G.Skiniotis
compound source
Molecule: Ribosomal Protein S1e
Chain: A
 Organism_scientific: Leishmania Donovani
Organism_taxid: 5661

Molecule: Ribosomal Protein S2
Chain: B
Organism_scientific: Leishmania Donovani
Organism_taxid: 5661

Molecule: Ribosomal Protein S3
Chain: C
Organism_scientific: Leishmania Donovani
Organism_taxid: 5661

Molecule: Ribosomal Protein S4
Chain: D
Organism_scientific: Leishmania Donovani
Organism_taxid: 5661

Molecule: Ribosomal Protein S4e
Chain: E
Organism_scientific: Leishmania Donovani
Organism_taxid: 5661

Molecule: Ribosomal Protein S5
Chain: F
Organism_scientific: Leishmania Donovani
Organism_taxid: 5661

Molecule: Ribosomal Protein S6e
Chain: G
Organism_scientific: Leishmania Donovani
Organism_taxid: 5661

Molecule: Ribosomal Protein S7
Chain: H
Organism_scientific: Leishmania Donovani
Organism_taxid: 5661

Molecule: Ribosomal Protein S7e
Chain: I
Organism_scientific: Leishmania Donovani
Organism_taxid: 5661

Molecule: Ribosomal Protein S8
Chain: J
Organism_scientific: Leishmania Donovani
Organism_taxid: 5661

Molecule: Ribosomal Protein S8e
Chain: K
Organism_scientific: Leishmania Donovani
Organism_taxid: 5661

Molecule: Ribosomal Protein S9
Chain: L
Organism_scientific: Leishmania Donovani
Organism_taxid: 5661

Molecule: Ribosomal Protein S10
Chain: M
Organism_scientific: Leishmania Donovani
Organism_taxid: 5661

Molecule: Ribosomal Protein S10e
Chain: N
Organism_scientific: Leishmania Donovani
Organism_taxid: 5661

Molecule: Ribosomal Protein S11
Chain: O
Organism_scientific: Leishmania Donovani
Organism_taxid: 5661

Molecule: Ribosomal Protein S12
Chain: P
Organism_scientific: Leishmania Donovani
Organism_taxid: 5661

Molecule: Ribosomal Protein S12e
Chain: Q
Organism_scientific: Leishmania Donovani
Organism_taxid: 5661

Molecule: Ribosomal Protein S13
Chain: R
Organism_scientific: Leishmania Donovani
Organism_taxid: 5661

Molecule: Ribosomal Protein S14
Chain: S
Organism_scientific: Leishmania Donovani
Organism_taxid: 5661

Molecule: Ribosomal Protein S15
Chain: T
Organism_scientific: Leishmania Donovani
Organism_taxid: 5661

Molecule: Ribosomal Protein S17
Chain: U
Organism_scientific: Leishmania Donovani
Organism_taxid: 5661

Molecule: Ribosomal Protein S17e
Chain: V
Organism_scientific: Leishmania Donovani
Organism_taxid: 5661

Molecule: Ribosomal Protein S19
Chain: W
Organism_scientific: Leishmania Donovani
Organism_taxid: 5661

Molecule: Ribosomal Protein S19e
Chain: X
Organism_scientific: Leishmania Donovani
Organism_taxid: 5661

Molecule: Ribosomal Protein S21e
Chain: Y
Organism_scientific: Leishmania Donovani
Organism_taxid: 5661

Molecule: Ribosomal Protein S24e
Chain: Z
Organism_scientific: Leishmania Donovani
Organism_taxid: 5661

Molecule: Ribosomal Protein S25e
Chain: a
Organism_scientific: Leishmania Donovani
Organism_taxid: 5661

Molecule: Ribosomal Protein S26e
Chain: b
Organism_scientific: Leishmania Donovani
Organism_taxid: 5661

Molecule: Ribosomal Protein S27e
Chain: c
Organism_scientific: Leishmania Donovani
Organism_taxid: 5661

Molecule: Ribosomal Protein S28e
Chain: d
Organism_scientific: Leishmania Donovani
Organism_taxid: 5661

Molecule: Ribosomal Protein S30e
Chain: e
Organism_scientific: Leishmania Donovani
Organism_taxid: 5661

Molecule: Ribosomal Protein S31e
Chain: f
Organism_scientific: Leishmania Donovani
Organism_taxid: 5661

Molecule: Lack1
Chain: g
Organism_scientific: Leishmania Donovani
Organism_taxid: 5661

Molecule: Ribosomal Rna 18s
Chain: 1
Organism_scientific: Leishmania Donovani
Organism_taxid: 5661

Molecule: Trna-Phe
Chain: 2
Engineered: Yes
Synthetic: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: P-Site Trna
Chain: 3
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: E-Site Trna
Chain: 4
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: Mrna
Chain: 5
Engineered: Yes
Synthetic: Yes
Organism_scientific: Leishmania Donovani
Organism_taxid: 5661
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 2.70 Å
ligand 4OC, 5MC, 7MG, A2M, C4J, M1Y, MA6, MG, MIA, OMC, OMG, OMU, PAR enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


B


C


D


E


F


G


H


I


J


K


L


M


O


P


Q


R


S


T


U


V


W


X


Y


Z


a, N, g


b


c


d


e


f


Primary referenceAtomic resolution snapshot of Leishmania ribosome inhibition by the aminoglycoside paromomycin., Shalev-Benami M, Zhang Y, Rozenberg H, Nobe Y, Taoka M, Matzov D, Zimmerman E, Bashan A, Isobe T, Jaffe CL, Yonath A, Skiniotis G, Nat Commun. 2017 Nov 17;8(1):1589. doi: 10.1038/s41467-017-01664-4. PMID:29150609
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1444 Kb) [Save to disk]
  • Biological Unit Coordinates (6az1.pdb1.gz) 1420 Kb
  • LPC: Ligand-Protein Contacts for 6AZ1
  • CSU: Contacts of Structural Units for 6AZ1
  • Retrieve 6AZ1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6AZ1 from S2C, [Save to disk]
    • View 6AZ1 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 6AZ1
  • 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: [6az1_Z] [6az1_e] [6az1_S] [6az1_D] [6az1_K] [6az1_V] [6az1_g] [6az1_R] [6az1_f] [6az1_A] [6az1_a] [6az1_G] [6az1_2] [6az1_1] [6az1_E] [6az1_N] [6az1_B] [6az1_b] [6az1_X] [6az1_c] [6az1_M] [6az1_L] [6az1_5] [6az1_4] [6az1_C] [6az1_O] [6az1_U] [6az1_T] [6az1_d] [6az1_I] [6az1_F] [6az1_H] [6az1_3] [6az1_J] [6az1_Y] [6az1_Q] [6az1_P] [6az1_W]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6AZ1
  • Community annotation for 6AZ1 at PDBWiki (http://pdbwiki.org)

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