3JAP Translation date Jun 18, 2015
title Structure Of A Partial Yeast 48s Preinitiation Complex In Cl Conformation
authors J.L.Llacer, T.Hussain, V.Ramakrishnan
compound source
Molecule: Met-Trnai (U31:A39 Variant)
Chain: 1
Engineered: Yes
Synthetic: Yes
Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: 18s Rrna
Chain: 2

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Mrna
Chain: 3
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

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: Us14
Chain: d

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Es30
Chain: e

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

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Eif1a
Chain: I
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Rosetta
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ptyb2

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: Eif2 Gamma
Chain: k
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: 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

Molecule: Eif1
Chain: m
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Rosetta
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ptyb2

Molecule: Eif3a
Chain: o
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: Eif3c
Chain: p
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: Eif3i
Chain: q
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: Eif3b
Chain: r
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: Eif3g
Chain: s
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 4.90 Å
ligand GCP, 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


    o


    p


    q


    Primary referenceConformational Differences between Open and Closed States of the Eukaryotic Translation Initiation Complex., Llacer JL, Hussain T, Marler L, Aitken CE, Thakur A, Lorsch JR, Hinnebusch AG, Ramakrishnan V, Mol Cell. 2015 Aug 6;59(3):399-412. doi: 10.1016/j.molcel.2015.06.033. Epub 2015 , Jul 23. PMID:26212456
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1683 Kb) [Save to disk]
  • Biological Unit Coordinates (3jap.pdb1.gz) 1633 Kb
  • LPC: Ligand-Protein Contacts for 3JAP
  • CSU: Contacts of Structural Units for 3JAP
  • Retrieve 3JAP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3JAP from S2C, [Save to disk]
  • View 3JAP 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 3JAP
  • 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
  • Fold representative 3jap from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3jap_U] [3jap_l] [3jap_s] [3jap_p] [3jap_Z] [3jap_K] [3jap_h] [3jap_H] [3jap_R] [3jap_1] [3jap_g] [3jap_E] [3jap_c] [3jap_o] [3jap_3] [3jap_N] [3jap_O] [3jap_W] [3jap_Y] [3jap_d] [3jap_P] [3jap_V] [3jap_L] [3jap_C] [3jap_G] [3jap_m] [3jap_F] [3jap_B] [3jap_a] [3jap_T] [3jap_r] [3jap_M] [3jap] [3jap_J] [3jap_I] [3jap_j] [3jap_X] [3jap_S] [3jap_2] [3jap_e] [3jap_q] [3jap_D] [3jap_k] [3jap_i] [3jap_f] [3jap_Q] [3jap_A] [3jap_b]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3JAP: [KH] [KOW] [PINT] [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 3JAP
  • Community annotation for 3JAP at PDBWiki (http://pdbwiki.org)

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