3J5L Ribosome Antibiotic date Oct 23, 2013
title Structure Of The E. Coli 50s Subunit With Ermbl Nascent Chai
authors S.Arenz, H.Ramu, P.Gupta, O.Berninghausen, R.Beckmann, N.Vazquez- A.S.Mankin, D.N.Wilson
compound source
Molecule: 50s Ribosomal Protein L32
Chain
Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K-12

Molecule: 50s Ribosomal Protein L33
Chain: 1

Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K-12

Molecule: 50s Ribosomal Protein L34
Chain: 2

Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K-12

Molecule: 50s Ribosomal Protein L35
Chain: 3

Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K-12

Molecule: 50s Ribosomal Protein L36
Chain: 4

Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K-12

Molecule: 5'-R(Cp(Ma6))-3'
Chain: 5
Engineered: Yes
Other_details: 3'-End Of A-Site Trna

Synthetic: Yes

Molecule: Erythromycin Resistance Leader Peptide
Chain: 6
Fragment: Nascent Chain
Synonym: Ermbl

Organism_scientific: Streptococcus Sanguinis
Organism_taxid: 1305

Molecule: 5'-R(Cpcpa)-3'
Chain: 7
Engineered: Yes
Other_details: 3'-End Of P-Site Trna

Synthetic: Yes

Molecule: 23s Ribsomal Rna
Chain: A

Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K-12

Molecule: 5s Ribosomal Rna
Chain: B

Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K-12

Molecule: 50s Ribosomal Protein L2
Chain: C

Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K-12

Molecule: 50s Ribosomal Protein L3
Chain: D

Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K-12

Molecule: 50s Ribosomal Protein L4
Chain: E

Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K-12

Molecule: 50s Ribosomal Protein L5
Chain: F

Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K-12

Molecule: 50s Ribosomal Protein L6
Chain: G

Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K-12

Molecule: 50s Ribosomal Protein L9
Chain: H
Fragment: See Remark 999

Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K-12

Molecule: 50s Ribosomal Protein L11
Chain: I

Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K-12

Molecule: 50s Ribosomal Protein L13
Chain: J

Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K-12

Molecule: 50s Ribosomal Protein L14
Chain: K

Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K-12

Molecule: 50s Ribosomal Protein L15
Chain: L

Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K-12

Molecule: 50s Ribosomal Protein L16
Chain: M

Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K-12

Molecule: 50s Ribosomal Protein L17
Chain: N

Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K-12

Molecule: 50s Ribosomal Protein L18
Chain: O

Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K-12

Molecule: 50s Ribosomal Protein L19
Chain: P

Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K-12

Molecule: 50s Ribosomal Protein L20
Chain: Q

Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K-12

Molecule: 50s Ribosomal Protein L21
Chain: R

Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K-12

Molecule: 50s Ribosomal Protein L22
Chain: S

Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K-12

Molecule: 50s Ribosomal Protein L23
Chain: T

Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K-12

Molecule: 50s Ribosomal Protein L24
Chain: U

Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K-12

Molecule: 50s Ribosomal Protein L25
Chain: V

Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K-12

Molecule: 50s Ribosomal Protein L27
Chain: W

Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K-12

Molecule: 50s Ribosomal Protein L28
Chain: X

Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K-12

Molecule: 50s Ribosomal Protein L29
Chain: Y

Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K-12

Molecule: 50s Ribosomal Protein L30
Chain: Z

Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K-12
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
ligand ERY, MA6, UNL enzyme
Gene
Ontology
ChainFunctionProcessComponent
0


1


2


3


4


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 referenceMolecular basis for erythromycin-dependent ribosome stalling during translation of the ErmBL leader peptide., Arenz S, Ramu H, Gupta P, Berninghausen O, Beckmann R, Vazquez-Laslop N, Mankin AS, Wilson DN, Nat Commun. 2014 Mar 24;5:3501. doi: 10.1038/ncomms4501. PMID:24662426
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1771 Kb) [Save to disk]
  • Biological Unit Coordinates (3j5l.pdb1.gz) 1763 Kb
  • LPC: Ligand-Protein Contacts for 3J5L
  • CSU: Contacts of Structural Units for 3J5L
  • Retrieve 3J5L in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3J5L from S2C, [Save to disk]
  • View 3J5L in 3D
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  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3J5L
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  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3J5L, from MSDmotif at EBI
  • Fold representative 3j5l from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3j5l_2] [3j5l_5] [3j5l_F] [3j5l_0] [3j5l_V] [3j5l_X] [3j5l] [3j5l_N] [3j5l_T] [3j5l_A] [3j5l_M] [3j5l_6] [3j5l_J] [3j5l_P] [3j5l_G] [3j5l_4] [3j5l_H] [3j5l_I] [3j5l_L] [3j5l_D] [3j5l_1] [3j5l_R] [3j5l_Q] [3j5l_W] [3j5l_C] [3j5l_3] [3j5l_S] [3j5l_U] [3j5l_7] [3j5l_O] [3j5l_B] [3j5l_E] [3j5l_K] [3j5l_Z] [3j5l_Y]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3J5L: [KOW] [RL11] [Ribosomal_L14] [Ribosomal_L2] [Ribosomal_L2_C ] by SMART
  • Other resources with information on 3J5L
  • Community annotation for 3J5L at PDBWiki (http://pdbwiki.org)

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