6DZP Ribosome date Jul 05, 2018
title Cryo-Em Structure Of Mycobacterium Smegmatis C(Minus) 50s Ri Subunit
authors M.R.Sharma, Y.Li, R.Korripella, Y.Yang, P.S.Kaushal, Q.Lin, J.T.Wa A.G.Gray, K.M.Derbyshire, R.K.Agrawal, A.Ojha
compound source
Molecule: 23s Rrna
Chain: A
 Organism_scientific: Mycobacterium Smegmatis Str. Mc2 155
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 5s Rrna
Chain: B
Organism_scientific: Mycobacterium Smegmatis Str. Mc2 155
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L2
Chain: C
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L3
Chain: D
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L4
Chain: E
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L5
Chain: F
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L6
Chain: G
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L9
Chain: H
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L10
Chain: I
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L11
Chain: J
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L13
Chain: K
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L14
Chain: L
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L15
Chain: M
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L16
Chain: N
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L17
Chain: O
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L18
Chain: P
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L19
Chain: Q
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L20
Chain: R
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L21
Chain: S
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L22
Chain: T
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L23
Chain: U
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L24
Chain: V
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L25
Chain: W
Synonym: General Stress Protein Ctc
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L27
Chain: X
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L29
Chain: Z
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L30
Chain: a
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L32
Chain: b
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L33 2
Chain: c
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L34
Chain: d
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L35
Chain: e
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L36
Chain: f
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L31
Chain: g
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L28
Chain: y
Organism_scientific: Mycobacterium Smegmatis Str. Mc2 155
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: Uncharacterized Protein
Chain: 3
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155
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 3.42 Å
Gene
Ontology
ChainFunctionProcessComponent
C


D


E


F


G


H


I


J


K


L


M


N


O


P


Q


R


S


T


U


V


W


X


Z


a


b


c


d


e


f


g


y


Primary referenceZinc depletion induces ribosome hibernation in mycobacteria., Li Y, Sharma MR, Koripella RK, Yang Y, Kaushal PS, Lin Q, Wade JT, Gray TA, Derbyshire KM, Agrawal RK, Ojha AK, Proc Natl Acad Sci U S A. 2018 Aug 7;115(32):8191-8196. doi:, 10.1073/pnas.1804555115. Epub 2018 Jul 23. PMID:30038002
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1685 Kb) [Save to disk]
  • Biological Unit Coordinates (6dzp.pdb1.gz) 1676 Kb
  • CSU: Contacts of Structural Units for 6DZP
  • Retrieve 6DZP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6DZP from S2C, [Save to disk]
    • View 6DZP in 3D
  • Proteopedia, because life has more than 2D.
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  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 6DZP
  • 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: [6dzp_B] [6dzp_A] [6dzp_H] [6dzp_V] [6dzp_I] [6dzp_E] [6dzp_F] [6dzp_y] [6dzp_X] [6dzp_e] [6dzp_W] [6dzp_D] [6dzp_M] [6dzp_g] [6dzp_J] [6dzp_C] [6dzp_O] [6dzp_a] [6dzp_P] [6dzp_c] [6dzp_3] [6dzp_Q] [6dzp_f] [6dzp_b] [6dzp_L] [6dzp_G] [6dzp_U] [6dzp_R] [6dzp_d] [6dzp_Z] [6dzp_T] [6dzp_S] [6dzp_N] [6dzp_K]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6DZP
  • Community annotation for 6DZP at PDBWiki (http://pdbwiki.org)

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