4D5L Ribosome date Nov 05, 2014
title Cryo-Em Structures Of Ribosomal 80s Complexes With Terminati And Cricket Paralysis Virus Ires Reveal The Ires In The Tra State
authors M.Muhs, T.Hilal, T.Mielke, M.A.Skabkin, K.Y.Sanbonmatsu, T.V.Pest C.M.T.Spahn
compound source
Molecule: 18s Rrna 2
Chain: 1
Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein Es26
Chain: A

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein Es27
Chain: B

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein Es28
Chain: C

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein Us14
Chain: D

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein Es30
Chain: E

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein Es31
Chain: F

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein Rack1
Chain: G

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein Es7
Chain: H

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein Es8
Chain: I

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein Us4
Chain: J

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein Es10
Chain: K

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein Us17
Chain: L

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein Es12
Chain: M

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein Us15
Chain: N

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein Us11
Chain: O

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein Us19
Chain: P

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein Us9
Chain: Q

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein Es17
Chain: R

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein Us13
Chain: S

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein Es19
Chain: T

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein Us10
Chain: U

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein Es21
Chain: V

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein Us8
Chain: W

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein Us12
Chain: X

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein Es24
Chain: Y

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein Es25
Chain: Z

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein Us2
Chain: a

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein Es1
Chain: b

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein Us5
Chain: c

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein Us3
Chain: d

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein Es4
Chain: e

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein Us7
Chain: f

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein Es6
Chain: g

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986
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 9.00 Å
Gene
Ontology
ChainFunctionProcessComponent
A


B


C


D


E


F


G


H


I


J


L


M


N


O


P


Q


R


S


T


U


V


W


X


Y


Z


a


b


c


d


e


f


Primary referenceCryo-EM of Ribosomal 80S Complexes with Termination Factors Reveals the Translocated Cricket Paralysis Virus IRES., Muhs M, Hilal T, Mielke T, Skabkin MA, Sanbonmatsu KY, Pestova TV, Spahn CM, Mol Cell. 2015 Feb 5;57(3):422-432. doi: 10.1016/j.molcel.2014.12.016. Epub 2015 , Jan 15. PMID:25601755
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1301 Kb) [Save to disk]
  • Biological Unit Coordinates (4d5l.pdb1.gz) 1291 Kb
  • CSU: Contacts of Structural Units for 4D5L
  • Retrieve 4D5L in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4D5L from S2C, [Save to disk]
  • View 4D5L 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 4D5L
  • 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
  • 3D motif for 4D5L, from MSDmotif at EBI
  • Fold representative 4d5l from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4d5l_K] [4d5l_B] [4d5l_S] [4d5l_O] [4d5l_Q] [4d5l_M] [4d5l_W] [4d5l_L] [4d5l_b] [4d5l_Y] [4d5l_P] [4d5l_I] [4d5l_D] [4d5l_A] [4d5l_U] [4d5l_X] [4d5l_g] [4d5l_T] [4d5l_d] [4d5l_c] [4d5l] [4d5l_R] [4d5l_f] [4d5l_J] [4d5l_V] [4d5l_C] [4d5l_a] [4d5l_H] [4d5l_Z] [4d5l_G] [4d5l_F] [4d5l_1] [4d5l_E] [4d5l_N] [4d5l_e]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4D5L: [KH] [Ribosomal_S10] [Ribosomal_S13_N] [Ribosomal_S15] [Ribosomal_S19e] [Ribosomal_S27] [Ribosomal_S3Ae] [Ribosomal_S4] [Ribosomal_S6e] [S4] [UBQ] [WD40 ] by SMART
  • Other resources with information on 4D5L
  • Community annotation for 4D5L at PDBWiki (http://pdbwiki.org)

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