3J81 Ribosome date Aug 29, 2014
title Cryoem Structure Of A Partial Yeast 48s Preinitiation Comple
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: Us3
Chain: D
Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Es4
Chain: E
Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Us7
Chain: F
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: Es10
Chain: K
Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Us17
Chain: L
Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Es12
Chain: M
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: 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: 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: Es25
Chain: Z
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: Es28
Chain: c
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: Us14
Chain: d
Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Es30
Chain: e
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: Met-Trnai
Chain: 1
Engineered: Yes
Synthetic: Yes
Other_details: In Vitro Transcribed Trna, Aminoacylated

Molecule: Mrna
Chain: 3
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

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: Eif2 Alpha
Chain: j
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932
Expression_system: Saccharomyces Cerevisiae
Expression_system_common: Yeast
Expression_system_taxid: 4932

Molecule: Eif1
Chain: m
Engineered: Yes
Mutation: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Eif2 Gamma
Chain: k
Engineered: Yes
Mutation: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932
Expression_system: Saccharomyces Cerevisiae
Expression_system_common: Yeast
Expression_system_taxid: 4932

Molecule: Eif2 Beta
Chain: l
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932
Expression_system: Saccharomyces Cerevisiae
Expression_system_common: Yeast
Expression_system_taxid: 4932
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 4.00 Å
ligand MET, MG, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


B


C


D


E


F


G


H


I


J


K, Z


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


    k


    l


    m


    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] (1669 Kb) [Save to disk]
  • Biological Unit Coordinates (3j81.pdb1.gz) 1653 Kb
  • LPC: Ligand-Protein Contacts for 3J81
  • CSU: Contacts of Structural Units for 3J81
  • Retrieve 3J81 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3J81 from S2C, [Save to disk]
    • View 3J81 in 3D
  • Proteopedia, because life has more than 2D.
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  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 3J81
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3J81, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3j81_M] [3j81_W] [3j81_V] [3j81_l] [3j81_f] [3j81_k] [3j81_X] [3j81_m] [3j81_N] [3j81_E] [3j81_T] [3j81_D] [3j81_R] [3j81_O] [3j81_a] [3j81] [3j81_Q] [3j81_S] [3j81_2] [3j81_3] [3j81_i] [3j81_B] [3j81_L] [3j81_H] [3j81_e] [3j81_U] [3j81_J] [3j81_I] [3j81_g] [3j81_F] [3j81_G] [3j81_K] [3j81_d] [3j81_Y] [3j81_j] [3j81_A] [3j81_C] [3j81_P] [3j81_b] [3j81_h] [3j81_c] [3j81_Z] [3j81_1]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3J81: [KH] [KOW] [Ribosomal_S10] [Ribosomal_S13_N] [Ribosomal_S15] [Ribosomal_S19e] [Ribosomal_S27] [Ribosomal_S3Ae] [Ribosomal_S4] [Ribosomal_S6e] [S1] [S4] [UBQ] [WD40] [eIF1a] [eIF2B_5 ] by SMART
    • Other resources with information on 3J81
  • Community annotation for 3J81 at PDBWiki (http://pdbwiki.org)

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