3J16

Models of ribosome-bound Dom34p and Rli1p and their ribosomal binding partners

Structural Biology Knowledgebase: 3J16 SBKB.org


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.2 Å
  • Aggregation State: Particle
  • Specimen Type: Vitreous Ice (cryo Em)
  • Reconstruction Method: Single Particle

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3J16

Classification: RIBOSOME

Total Structure Weight: 400150.13


Macromolecule Entities
Molecule Chains Length Organism Details
Dom34p A 386 Saccharomyces cerevisiae EC#: 3.1 IUBMB
Gene Name(s): DOM34 YNL001W N2016
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Rli1p B 608 Saccharomyces cerevisiae Gene Name(s): RLI1 YDR091C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein L6 F 191 Saccharomyces cerevisiae Gene Name(s): RPL9A RPL8A RPL9 Gene View YGL147C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein S30E E 63 Saccharomyces cerevisiae Gene Name(s): RPS30A YLR287C-A L8003.23 YLR287BC
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein L10 G 312 Saccharomyces cerevisiae Gene Name(s): RPP0 L10E RPA0 RPL10E RPLA0 YLR340W L8300.8
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein S6E C 236 Saccharomyces cerevisiae Gene Name(s): RPS6A RPS101 RPS10B YPL090C LPG18C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein L11 H 165 Saccharomyces cerevisiae Gene Name(s): RPL12A RPL15B YEL054C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein S24E I 137 Saccharomyces cerevisiae Gene Name(s): RPL23A Gene View RPL17A RPL17AA YBL087C YBL0713
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein S24-A D 135 Saccharomyces cerevisiae Gene Name(s): RPS24A RPS24EA YER074W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
28S ribosomal RNA J 233 Saccharomyces cerevisiae
18S ribosomal RNA K 155 Saccharomyces cerevisiae
P-site tRNA L 75 Saccharomyces cerevisiae

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ATP
Query on ATP

B ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SF4
Query on SF4

B IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.2 Å
  • Aggregation State: Particle
  • Specimen Type: Vitreous Ice (cryo Em)
  • Reconstruction Method: Single Particle

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-12-12
  • Released Date: 2012-02-22
  • Deposition author(s): Becker, T., Franckenberg, S., Wickles, S., Shoemaker, C.J., Anger, A.M., Armache, J.-P., Sieber, H., Ungewickell, C., Berninghausen, O., Daberkow, I., Karcher, A., Thomm, M., Hopfner, K.-P., Green, R., Beckmann, R.

Revision History

  • 2012-05-30
    Type: Refinement description | Details: Added map resolution
  • 2012-05-30
    Type: Polymer description | Details: Added entity name
  • 2012-04-18
    Type: Citation | Details: Citation update
  • 2012-03-28
    Type: Citation | Details: Citation update
  • 2012-02-29
    Type: Citation | Details: Citation update