3J3V Ribosome date Apr 28, 2013
title Atomic Model Of The Immature 50s Subunit From Bacillus Subti I-A)
authors N.Li, Q.Guo, Y.Zhang, Y.Yuan, C.Ma, J.Lei, N.Gao
compound source
Molecule: 50s Ribosomal Protein L32
Chain
 Organism_scientific: Bacillus Subtilis
Organism_taxid: 224308
Strain: 168

Molecule: 50s Ribosomal Protein L34
Chain: 2
Organism_scientific: Bacillus Subtilis
Organism_taxid: 224308
Strain: 168

Molecule: 50s Ribosomal Protein L1
Chain: 5
Synonym: Bl1
Organism_scientific: Bacillus Subtilis
Organism_taxid: 224308
Strain: 168

Molecule: 50s Ribosomal Protein L11
Chain: 6
Synonym: Bl11
Organism_scientific: Bacillus Subtilis
Organism_taxid: 224308
Strain: 168

Molecule: Ribosome Rna 23s
Chain: A
Organism_scientific: Bacillus Subtilis
Organism_taxid: 224308
Strain: 168

Molecule: Ribosome Rna 5s
Chain: B
Organism_scientific: Bacillus Subtilis
Organism_taxid: 224308
Strain: 168

Molecule: 50s Ribosomal Protein L2
Chain: C
Synonym: Bl2
Organism_scientific: Bacillus Subtilis
Organism_taxid: 224308
Strain: 168

Molecule: 50s Ribosomal Protein L3
Chain: D
Synonym: Bl3
Organism_scientific: Bacillus Subtilis
Organism_taxid: 224308
Strain: 168

Molecule: 50s Ribosomal Protein L4
Chain: E
Organism_scientific: Bacillus Subtilis
Organism_taxid: 224308
Strain: 168

Molecule: 50s Ribosomal Protein L5
Chain: F
Synonym: Bl6
Organism_scientific: Bacillus Subtilis
Organism_taxid: 224308
Strain: 168

Molecule: 50s Ribosomal Protein L6
Chain: G
Synonym: Bl10
Organism_scientific: Bacillus Subtilis
Organism_taxid: 224308
Strain: 168

Molecule: 50s Ribosomal Protein L13
Chain: J
Organism_scientific: Bacillus Subtilis
Organism_taxid: 224308
Strain: 168

Molecule: 50s Ribosomal Protein L14
Chain: K
Organism_scientific: Bacillus Subtilis
Organism_taxid: 224308
Strain: 168

Molecule: 50s Ribosomal Protein L15
Chain: L
Organism_scientific: Bacillus Subtilis
Organism_taxid: 224308
Strain: 168

Molecule: 50s Ribosomal Protein L17
Chain: N
Synonym: Bl15, Bl21
Organism_scientific: Bacillus Subtilis
Organism_taxid: 224308
Strain: 168

Molecule: 50s Ribosomal Protein L18
Chain: O
Synonym: Bl16
Organism_scientific: Bacillus Subtilis
Organism_taxid: 224308
Strain: 168

Molecule: 50s Ribosomal Protein L19
Chain: P
Organism_scientific: Bacillus Subtilis
Organism_taxid: 224308
Strain: 168

Molecule: 50s Ribosomal Protein L20
Chain: Q
Organism_scientific: Bacillus Subtilis
Organism_taxid: 224308
Strain: 168

Molecule: 50s Ribosomal Protein L21
Chain: R
Synonym: Bl20
Organism_scientific: Bacillus Subtilis
Organism_taxid: 224308
Strain: 168

Molecule: 50s Ribosomal Protein L22
Chain: S
Organism_scientific: Bacillus Subtilis
Organism_taxid: 224308
Strain: 168

Molecule: 50s Ribosomal Protein L23
Chain: T
Organism_scientific: Bacillus Subtilis
Organism_taxid: 224308
Strain: 168

Molecule: 50s Ribosomal Protein L24
Chain: U
Synonym: 12 Kda Dna-Binding Protein, Bl23, Hpb12
Organism_scientific: Bacillus Subtilis
Organism_taxid: 224308
Strain: 168

Molecule: 50s Ribosomal Protein L29
Chain: X
Organism_scientific: Bacillus Subtilis
Organism_taxid: 224308
Strain: 168

Molecule: 50s Ribosomal Protein L30
Chain: Y
Synonym: Bl27
Organism_scientific: Bacillus Subtilis
Organism_taxid: 224308
Strain: 168
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 13.30 Å
Gene
Ontology
ChainFunctionProcessComponent
0


2


5


6


C


D


E


F


G


J


K


L


N


O


P


Q


R


S


T


U


X


Y


Primary referenceCryo-EM structures of the late-stage assembly intermediates of the bacterial 50S ribosomal subunit., Li N, Chen Y, Guo Q, Zhang Y, Yuan Y, Ma C, Deng H, Lei J, Gao N, Nucleic Acids Res. 2013 May 21. PMID:23700310
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1426 Kb) [Save to disk]
  • Biological Unit Coordinates (3j3v.pdb1.gz) 1418 Kb
  • CSU: Contacts of Structural Units for 3J3V
  • Retrieve 3J3V in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3J3V from S2C, [Save to disk]
    • View 3J3V 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 3J3V
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3J3V, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3j3v_K] [3j3v_5] [3j3v_L] [3j3v_A] [3j3v_B] [3j3v_P] [3j3v_J] [3j3v_C] [3j3v_E] [3j3v_T] [3j3v_Q] [3j3v_Y] [3j3v_O] [3j3v_G] [3j3v_0] [3j3v] [3j3v_6] [3j3v_2] [3j3v_S] [3j3v_R] [3j3v_D] [3j3v_X] [3j3v_F] [3j3v_U] [3j3v_N]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3J3V: [KOW] [RL11] [Ribosomal_L14] [Ribosomal_L2] [Ribosomal_L2_C ] by SMART
    • Other resources with information on 3J3V
  • Community annotation for 3J3V at PDBWiki (http://pdbwiki.org)

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