5U4J Ribosome date Dec 04, 2016
title Structural Basis Of Co-Translational Quality Control By Arfa Bound To Ribosome
authors F.Zeng, Y.Chen, J.Remis, M.Shekhar, J.C.Phillips, E.Tajkhorshid, H
compound source
Molecule: 16s Rrna
Chain: a
 Organism_scientific: Escherichia Coli
Organism_taxid: 562
Strain: Mre600

Molecule: 23s Rrna
Chain: A
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Strain: Mre600

Molecule: 30s Ribosomal Protein S3
Chain: c
Other_details: Gene Name(S): Rpsc B3314 Jw3276
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Strain: Mre600

Molecule: 30s Ribosomal Protein S4
Chain: d
Other_details: Gene Name(S): Rpsd Rama B3296 Jw3258
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Strain: Mre600

Molecule: 30s Ribosomal Protein S5
Chain: e
Other_details: Gene Name(S): Rpse Spc B3303 Jw3265
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Strain: Mre600

Molecule: Mrna
Chain: z
Engineered: Yes
Synthetic: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: P-Site Trna Fmet
Chain: x
Engineered: Yes
Synthetic: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Other_details: Rna Was Prepared By In Vitro Transcription

Molecule: 30s Ribosomal Protein S12
Chain: l
Other_details: Gene Name(S): Rpsl Stra B3342 Jw3304
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Strain: Mre600

Molecule: Peptide Chain Release Factor 2
Chain: v
Synonym: Rf-2
Engineered: Yes
Other_details: Gene Name(S): Prfb Eck2886 Jw5847 Supk
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Strain: Mre600
Gene: Prfb, Supk, B2891, Jw5847
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Alternative Ribosome-Rescue Factor A
Chain: w
Engineered: Yes
Other_details: Gene Name(S): Arfa Eck3278 Jw3253 Yhdl
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Strain: Mre600
Gene: Arfa, Yhdl, B4550, Jw3253
Expression_system: Escherichia Coli
Expression_system_taxid: 562
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 3.70 Å
ligand 2MG, 4OC, 5MC, G7M, MA6, PSU, UR3 enzyme
Gene
Ontology
ChainFunctionProcessComponent
c


d


e


l


v


w


Primary referenceStructural basis of co-translational quality control by ArfA and RF2 bound to ribosome., Zeng F, Chen Y, Remis J, Shekhar M, Phillips JC, Tajkhorshid E, Jin H, Nature. 2017 Jan 11. doi: 10.1038/nature21053. PMID:28077875
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (250 Kb) [Save to disk]
  • Biological Unit Coordinates (5u4j.pdb1.gz) 229 Kb
  • LPC: Ligand-Protein Contacts for 5U4J
  • CSU: Contacts of Structural Units for 5U4J
  • Retrieve 5U4J in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5U4J from S2C, [Save to disk]
    • View 5U4J 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 5U4J
  • 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: [5u4j_z] [5u4j_x] [5u4j_w] [5u4j_A] [5u4j_a] [5u4j_v] [5u4j_d] [5u4j_e] [5u4j_c] [5u4j_l] [5u4j]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5U4J
  • Community annotation for 5U4J at PDBWiki (http://pdbwiki.org)

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