7F0D Ribosome date Jun 03, 2021
title Cryo-Em Structure Of Mycobacterium Tuberculosis 50s Ribosome Bound With Clarithromycin
authors W.Zhang, Y.Sun, N.Gao, Z.Li
compound source
Molecule: 50s Ribosomal Protein L32
Chain
Engineered: Yes
 Organism_scientific: Mycobacterium Tuberculosis H37ra
Organism_taxid: 419947
Gene: Rpmf, Rpmf_1, Rpmf_2
Expression_system: Mycobacterium Tuberculosis
Expression_system_taxid: 1773

Molecule: 50s Ribosomal Protein L33
Chain: 1
Engineered: Yes
Organism_scientific: Mycobacterium Tuberculosis H37ra
Organism_taxid: 419947
Gene: Rpmg2, Rpmg
Expression_system: Mycobacterium Tuberculosis
Expression_system_taxid: 1773

Molecule: 50s Ribosomal Protein L34
Chain: 2
Engineered: Yes
Organism_scientific: Mycobacterium Tuberculosis H37ra
Organism_taxid: 419947
Gene: Rpmh
Expression_system: Mycobacterium Tuberculosis
Expression_system_taxid: 1773

Molecule: 50s Ribosomal Protein L35
Chain: 3
Engineered: Yes
Organism_scientific: Mycobacterium Tuberculosis H37ra
Organism_taxid: 419947
Gene: Rpmi
Expression_system: Mycobacterium Tuberculosis
Expression_system_taxid: 1773

Molecule: 50s Ribosomal Protein L36
Chain: 4
Engineered: Yes
Organism_scientific: Mycobacterium Tuberculosis H37ra
Organism_taxid: 419947
Gene: Rpmj
Expression_system: Mycobacterium Tuberculosis
Expression_system_taxid: 1773

Molecule: 50s Ribosomal Protein L31
Chain: 6
Engineered: Yes
Organism_scientific: Mycobacterium Tuberculosis H37ra
Organism_taxid: 419947
Gene: Rpme
Expression_system: Mycobacterium Tuberculosis
Expression_system_taxid: 1773

Molecule: 23s Rrna
Chain: A
Engineered: Yes
Organism_scientific: Mycobacterium Tuberculosis H37ra
Organism_taxid: 419947
Expression_system: Mycobacterium Tuberculosis
Expression_system_taxid: 1773

Molecule: 5s Ribosomal Rna
Chain: B
Engineered: Yes
Organism_scientific: Mycobacterium Tuberculosis H37ra
Organism_taxid: 419947
Expression_system: Mycobacterium Tuberculosis
Expression_system_taxid: 1773

Molecule: 50s Ribosomal Protein L2
Chain: C
Engineered: Yes
Organism_scientific: Mycobacterium Tuberculosis H37ra
Organism_taxid: 419947
Gene: Rplb
Expression_system: Mycobacterium Tuberculosis
Expression_system_taxid: 1773

Molecule: 50s Ribosomal Protein L3
Chain: D
Engineered: Yes
Organism_scientific: Mycobacterium Tuberculosis H37ra
Organism_taxid: 419947
Gene: Rplc
Expression_system: Mycobacterium Tuberculosis
Expression_system_taxid: 1773

Molecule: 50s Ribosomal Protein L4
Chain: E
Engineered: Yes
Organism_scientific: Mycobacterium Tuberculosis H37ra
Organism_taxid: 419947
Gene: Rpld
Expression_system: Mycobacterium Tuberculosis
Expression_system_taxid: 1773

Molecule: 50s Ribosomal Protein L5
Chain: F
Engineered: Yes
Organism_scientific: Mycobacterium Tuberculosis H37ra
Organism_taxid: 419947
Gene: Rple
Expression_system: Mycobacterium Tuberculosis
Expression_system_taxid: 1773

Molecule: 50s Ribosomal Protein L6
Chain: G
Engineered: Yes
Organism_scientific: Mycobacterium Tuberculosis H37ra
Organism_taxid: 419947
Gene: Rplf
Expression_system: Mycobacterium Tuberculosis
Expression_system_taxid: 1773

Molecule: 50s Ribosomal Protein L9
Chain: H
Engineered: Yes
Organism_scientific: Mycobacterium Tuberculosis H37ra
Organism_taxid: 419947
Gene: Rpli
Expression_system: Mycobacterium Tuberculosis
Expression_system_taxid: 1773

Molecule: 50s Ribosomal Protein L13
Chain: J
Engineered: Yes
Organism_scientific: Mycobacterium Tuberculosis H37ra
Organism_taxid: 419947
Gene: Rplm
Expression_system: Mycobacterium Tuberculosis
Expression_system_taxid: 1773

Molecule: 50s Ribosomal Protein L14
Chain: K
Engineered: Yes
Organism_scientific: Mycobacterium Tuberculosis H37ra
Organism_taxid: 419947
Gene: Rpln
Expression_system: Mycobacterium Tuberculosis
Expression_system_taxid: 1773

Molecule: 50s Ribosomal Protein L15
Chain: L
Engineered: Yes
Organism_scientific: Mycobacterium Tuberculosis H37ra
Organism_taxid: 419947
Gene: Rplo
Expression_system: Mycobacterium Tuberculosis
Expression_system_taxid: 1773

Molecule: 50s Ribosomal Protein L16
Chain: M
Engineered: Yes
Organism_scientific: Mycobacterium Tuberculosis H37ra
Organism_taxid: 419947
Gene: Rplp
Expression_system: Mycobacterium Tuberculosis
Expression_system_taxid: 1773

Molecule: 50s Ribosomal Protein L17
Chain: N
Engineered: Yes
Organism_scientific: Mycobacterium Tuberculosis H37ra
Organism_taxid: 419947
Gene: Rplq
Expression_system: Mycobacterium Tuberculosis
Expression_system_taxid: 1773

Molecule: 50s Ribosomal Protein L18
Chain: O
Engineered: Yes
Organism_scientific: Mycobacterium Tuberculosis H37ra
Organism_taxid: 419947
Gene: Rplr
Expression_system: Mycobacterium Tuberculosis
Expression_system_taxid: 1773

Molecule: 50s Ribosomal Protein L19
Chain: P
Engineered: Yes
Organism_scientific: Mycobacterium Tuberculosis H37ra
Organism_taxid: 419947
Gene: Rpls
Expression_system: Mycobacterium Tuberculosis
Expression_system_taxid: 1773

Molecule: 50s Ribosomal Protein L20
Chain: Q
Engineered: Yes
Organism_scientific: Mycobacterium Tuberculosis H37ra
Organism_taxid: 419947
Gene: Rplt
Expression_system: Mycobacterium Tuberculosis
Expression_system_taxid: 1773

Molecule: 50s Ribosomal Protein L21
Chain: R
Engineered: Yes
Organism_scientific: Mycobacterium Tuberculosis H37ra
Organism_taxid: 419947
Gene: Rplu
Expression_system: Mycobacterium Tuberculosis
Expression_system_taxid: 1773

Molecule: 50s Ribosomal Protein L22
Chain: S
Engineered: Yes
Organism_scientific: Mycobacterium Tuberculosis H37ra
Organism_taxid: 419947
Gene: Rplv
Expression_system: Mycobacterium Tuberculosis
Expression_system_taxid: 1773

Molecule: 50s Ribosomal Protein L23
Chain: T
Engineered: Yes
Organism_scientific: Mycobacterium Tuberculosis H37ra
Organism_taxid: 419947
Gene: Rplw
Expression_system: Mycobacterium Tuberculosis
Expression_system_taxid: 1773

Molecule: 50s Ribosomal Protein L24
Chain: U
Engineered: Yes
Organism_scientific: Mycobacterium Tuberculosis H37ra
Organism_taxid: 419947
Gene: Rplx
Expression_system: Mycobacterium Tuberculosis
Expression_system_taxid: 1773

Molecule: 50s Ribosomal Protein L25
Chain: V
Synonym: General Stress Protein Ctc
Engineered: Yes
Organism_scientific: Mycobacterium Tuberculosis H37ra
Organism_taxid: 419947
Gene: Rply
Expression_system: Mycobacterium Tuberculosis
Expression_system_taxid: 1773

Molecule: 50s Ribosomal Protein L27
Chain: W
Engineered: Yes
Organism_scientific: Mycobacterium Tuberculosis H37ra
Organism_taxid: 419947
Gene: Rpma
Expression_system: Mycobacterium Tuberculosis
Expression_system_taxid: 1773

Molecule: 50s Ribosomal Protein L28
Chain: X
Engineered: Yes
Organism_scientific: Mycobacterium Tuberculosis H37ra
Organism_taxid: 419947
Gene: Rpmb
Expression_system: Mycobacterium Tuberculosis
Expression_system_taxid: 1773

Molecule: 50s Ribosomal Protein L29
Chain: Y
Engineered: Yes
Organism_scientific: Mycobacterium Tuberculosis H37ra
Organism_taxid: 419947
Gene: Rpmc
Expression_system: Mycobacterium Tuberculosis
Expression_system_taxid: 1773

Molecule: 50s Ribosomal Protein L30
Chain: Z
Engineered: Yes
Organism_scientific: Mycobacterium Tuberculosis H37ra
Organism_taxid: 419947
Gene: Rpmd
Expression_system: Mycobacterium Tuberculosis
Expression_system_taxid: 1773
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 3.30 Å
ligand CTY, MG enzyme
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1613 Kb) [Save to disk]
  • Biological Unit Coordinates (7f0d.pdb1.gz) 1604 Kb
  • LPC: Ligand-Protein Contacts for 7F0D
  • CSU: Contacts of Structural Units for 7F0D
  • Retrieve 7F0D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 7F0D from S2C, [Save to disk]
    • View 7F0D 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 7F0D
  • 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: [7f0d_C] [7f0d_E] [7f0d_T] [7f0d_Z] [7f0d_K] [7f0d_3] [7f0d_R] [7f0d_H] [7f0d_U] [7f0d_B] [7f0d_D] [7f0d_0] [7f0d_4] [7f0d_X] [7f0d_N] [7f0d_6] [7f0d_W] [7f0d_F] [7f0d_V] [7f0d_2] [7f0d_L] [7f0d_M] [7f0d_S] [7f0d_Y] [7f0d_Q] [7f0d_O] [7f0d_G] [7f0d_J] [7f0d_1] [7f0d_P] [7f0d_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 7F0D
  • Community annotation for 7F0D at PDBWiki (http://pdbwiki.org)

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