3J80 Ribosome date Aug 28, 2014
title Cryoem Structure Of 40s-Eif1-Eif1a Preinitiation Complex
authors T.Hussain, J.L.Llacer, I.S.Fernandez, C.G.Savva, V.Ramakrishnan
compound source
Molecule: 18s Rrna
Chain: 2
Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Us2
Chain: A

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Es1
Chain: B

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Us5
Chain: C

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Es4
Chain: E

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Es6
Chain: G

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Es7
Chain: H

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Es8
Chain: I

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Us4
Chain: J

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Us17
Chain: L

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Us15
Chain: N

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Us11
Chain: O

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Es21
Chain: V

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Us8
Chain: W

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Us12
Chain: X

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Es24
Chain: Y

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Es26
Chain: a

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Es27
Chain: b

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Es30
Chain: e

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Us3
Chain: D

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Us7
Chain: F

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Es10
Chain: K

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Es12
Chain: M

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Us19
Chain: P

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Us9
Chain: Q

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Es17
Chain: R

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Us13
Chain: S

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Es19
Chain: T

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Us10
Chain: U

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Es25
Chain: Z

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Es28
Chain: c

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Us14
Chain: d

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Es31
Chain: f

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Rack1
Chain: g

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: El41
Chain: h
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Eif1a
Chain: I
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Eif1
Chain: j
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932
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 3.75 Å
ligand MG, ZN enzyme
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


a, b


c


d


e


f


g
  • GDP-dissociation inhibitor a...


  • h


    i


    j


    Primary referenceStructural changes enable start codon recognition by the eukaryotic translation initiation complex., Hussain T, Llacer JL, Fernandez IS, Munoz A, Martin-Marcos P, Savva CG, Lorsch JR, Hinnebusch AG, Ramakrishnan V, Cell. 2014 Oct 23;159(3):597-607. doi: 10.1016/j.cell.2014.10.001. Epub 2014 Oct , 16. PMID:25417110
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1577 Kb) [Save to disk]
  • Biological Unit Coordinates (3j80.pdb1.gz) 1564 Kb
  • LPC: Ligand-Protein Contacts for 3J80
  • CSU: Contacts of Structural Units for 3J80
  • Retrieve 3J80 in mmCIF format [Save to disk]
  • View 3J80 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 3J80
  • 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 3J80, from MSDmotif at EBI
  • Fold representative 3j80 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3j80_N] [3j80_Y] [3j80_A] [3j80_L] [3j80_O] [3j80_C] [3j80_W] [3j80_I] [3j80_f] [3j80_Q] [3j80_R] [3j80] [3j80_G] [3j80_K] [3j80_g] [3j80_e] [3j80_Z] [3j80_j] [3j80_b] [3j80_J] [3j80_F] [3j80_X] [3j80_S] [3j80_2] [3j80_T] [3j80_d] [3j80_P] [3j80_M] [3j80_H] [3j80_B] [3j80_U] [3j80_E] [3j80_a] [3j80_D] [3j80_i] [3j80_h] [3j80_c] [3j80_V]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3J80: [KH] [KOW] [Ribosomal_S10] [Ribosomal_S13_N] [Ribosomal_S15] [Ribosomal_S19e] [Ribosomal_S27] [Ribosomal_S3Ae] [Ribosomal_S4] [Ribosomal_S6e] [S4] [UBQ] [WD40] [eIF1a ] by SMART
  • Other resources with information on 3J80
  • Community annotation for 3J80 at PDBWiki (http://pdbwiki.org)

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