4U67 Ribosome date Jul 28, 2014
title Crystal Structure Of The Large Ribosomal Subunit (50s) Of De Radiodurans Containing A Three Residue Insertion In L22
authors I.Wekselman, E.Zimmerman, H.Rozenberg, A.Bashan, A.Yonath
compound source
Molecule: 50s Ribosomal Protein L2
Chain: A
Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L3
Chain: B

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L4
Chain: C

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L5
Chain: D

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L6
Chain: E

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L13
Chain: G

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L14
Chain: H

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L15
Chain: I

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L16
Chain: J

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L17
Chain: K

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L18
Chain: L

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L19
Chain: M

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L20
Chain: N

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L21
Chain: O

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L22
Chain: P
Mutation: Yes

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L23
Chain: Q

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L24
Chain: R

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L25
Chain: S
Synonym: General Stress Protein Ctc

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L27
Chain: T

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L28
Chain: U

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L29
Chain: V

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L30
Chain: W

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L32
Chain: Z

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L33
Chain: 1

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L34
Chain: 2

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L35
Chain: 3

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 23s Rna
Chain: X

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 5s Rna
Chain: Y

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422
symmetry Space Group: I 2 2 2
R_factor 0.226 R_Free 0.270
crystal
cell
length a length b length c angle alpha angle beta angle gamma
169.720 412.591 696.974 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.65 Å
ligand MG enzyme
Gene
Ontology
ChainFunctionProcessComponent
1


2


3


A


B


C


D


E


G


H


I


J


K


L


M


N


O


P


Q


R


S


T


U


V


W


Z


Primary referenceThe Ribosomal Protein uL22 Modulates the Shape of the Protein Exit Tunnel., Wekselman I, Zimmerman E, Davidovich C, Belousoff M, Matzov D, Krupkin M, Rozenberg H, Bashan A, Friedlander G, Kjeldgaard J, Ingmer H, Lindahl L, Zengel JM, Yonath A, Structure. 2017 Aug 1;25(8):1233-1241.e3. doi: 10.1016/j.str.2017.06.004. Epub, 2017 Jul 6. PMID:28689968
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (3515 Kb) [Save to disk]
  • Biological Unit Coordinates (4u67.pdb1.gz) 3501 Kb
  • LPC: Ligand-Protein Contacts for 4U67
  • CSU: Contacts of Structural Units for 4U67
  • Structure Factors (4164 Kb)
  • Retrieve 4U67 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4U67 from S2C, [Save to disk]
  • Re-refined 4u67 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4U67 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 4U67
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 4u67 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4u67_X] [4u67_M] [4u67_R] [4u67_A] [4u67_Z] [4u67_C] [4u67_J] [4u67_1] [4u67_P] [4u67_O] [4u67_B] [4u67_L] [4u67_Q] [4u67_D] [4u67_2] [4u67_T] [4u67_H] [4u67_E] [4u67_3] [4u67_Y] [4u67_N] [4u67] [4u67_V] [4u67_G] [4u67_S] [4u67_K] [4u67_W] [4u67_U] [4u67_I]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4U67: [KOW] [Ribosomal_L14] [Ribosomal_L2] [Ribosomal_L2_C ] by SMART
  • Other resources with information on 4U67
  • Community annotation for 4U67 at PDBWiki (http://pdbwiki.org)

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science