5K0Y Translation date May 17, 2016
title M48s Late-Stage Initiation Complex, Purified From Rabbit Ret Lysates, Displaying Eif2 Ternary Complex And Eif3 I And G S Relocated To The Intersubunit Face
authors A.Simonetti, J.Brito Querido, A.G.Myasnikov, E.Mancera-Martinez A.Renaud, L.Kuhn, Y.Hashem
compound source
Molecule: Trna
Chain: N
Engineered: Yes
Other_details: Trnaimet
Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986
Expression_system: Oryctolagus Cuniculus
Expression_system_taxid: 9986

Molecule: 18s Ribosomal Rna
Chain: A
Engineered: Yes

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986
Expression_system: Oryctolagus Cuniculus
Expression_system_taxid: 9986

Molecule: Mrna
Chain: F
Engineered: Yes
Other_details: Beta-Globin Mrna

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986
Expression_system: Oryctolagus Cuniculus
Expression_system_taxid: 9986

Molecule: Eukaryotic Translation Initiation Factor 2 Subuni
Chain: P
Engineered: Yes

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986
Gene: Eif2s1
Expression_system: Oryctolagus Cuniculus
Expression_system_taxid: 9986

Molecule: Ribosomal Protein Us17
Chain: G
Engineered: Yes

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986
Gene: Loc100347468
Expression_system: Oryctolagus Cuniculus
Expression_system_taxid: 9986

Molecule: Ribosomal Protein Us9
Chain: H
Engineered: Yes

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986
Gene: Rps16
Expression_system: Oryctolagus Cuniculus
Expression_system_taxid: 9986

Molecule: 40s Ribosomal Protein S4
Chain: I
Engineered: Yes

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986
Gene: Rps4x
Expression_system: Oryctolagus Cuniculus
Expression_system_taxid: 9986

Molecule: Ribosomal Protein Us14
Chain: J
Engineered: Yes

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986
Gene: Loc100337712
Expression_system: Oryctolagus Cuniculus
Expression_system_taxid: 9986

Molecule: Ribosomal Protein S9 (Predicted)
Chain: K
Engineered: Yes

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986
Gene: Rps9
Expression_system: Oryctolagus Cuniculus
Expression_system_taxid: 9986

Molecule: Ribosomal Protein Us13
Chain: L
Engineered: Yes

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986
Gene: Rps18
Expression_system: Oryctolagus Cuniculus
Expression_system_taxid: 9986

Molecule: Eukaryotic Translation Initiation Factor 3 Subuni
Chain: M
Synonym: Eif3g,Eukaryotic Translation Initiation Factor 3 R Subunit,Eif-3 Rna-Binding Subunit,Eukaryotic Translation In Factor 3 Subunit 4,Eif-3-Delta,Eif3 P42,Eif3 P44;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Eif3g, Eif3s4
Expression_system: Homo Sapiens
Expression_system_taxid: 9606

Molecule: Eukaryotic Translation Initiation Factor 3 Subuni
Chain: O
Synonym: Eif3g,Eukaryotic Translation Initiation Factor 3 R Subunit,Eif-3 Rna-Binding Subunit,Eukaryotic Translation In Factor 3 Subunit 4,Eif-3-Delta,Eif3 P42,Eif3 P44;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Eif3g, Eif3s4
Expression_system: Homo Sapiens
Expression_system_taxid: 9606

Molecule: Ribosomal Protein Us12
Chain: Q
Engineered: Yes

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986
Expression_system: Oryctolagus Cuniculus
Expression_system_taxid: 9986

Molecule: Ribosomal Protein Es19
Chain: R
Engineered: Yes

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986
Gene: Loc100345774
Expression_system: Oryctolagus Cuniculus
Expression_system_taxid: 9986

Molecule: Eukaryotic Initiation Factor 2 Gamma Subunit (Eif
Chain: S
Engineered: Yes

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986
Expression_system: Oryctolagus Cuniculus
Expression_system_taxid: 9986

Molecule: Eukaryotic Translation Initiation Factor 3 Subuni
Chain: T
Synonym: Eif3i,Eukaryotic Translation Initiation Factor 3 S Eif-3-Beta,Eif3 P36;
Engineered: Yes

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986
Gene: Eif3i, Eif3s2
Expression_system: Oryctolagus Cuniculus
Expression_system_taxid: 9986

Molecule: Ribosomal Protein Us7
Chain: U
Engineered: Yes

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986
Gene: Rps5
Expression_system: Oryctolagus Cuniculus
Expression_system_taxid: 9986

Molecule: Ribosomal Protein Es30
Chain: V
Engineered: Yes

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986
Gene: Fau
Expression_system: Oryctolagus Cuniculus
Expression_system_taxid: 9986

Molecule: Ribosomal Protein Es25
Chain: W
Engineered: Yes

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986
Gene: Rps25
Expression_system: Oryctolagus Cuniculus
Expression_system_taxid: 9986

Molecule: Ribosomal Protein Es7
Chain: X
Engineered: Yes

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986
Gene: Rps7
Expression_system: Oryctolagus Cuniculus
Expression_system_taxid: 9986

Molecule: 40s Ribosomal Protein S27
Chain: Y
Engineered: Yes

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986
Gene: Rps27
Expression_system: Oryctolagus Cuniculus
Expression_system_taxid: 9986

Molecule: Ribosomal Protein Us15
Chain: Z
Engineered: Yes

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986
Gene: Rps13
Expression_system: Oryctolagus Cuniculus
Expression_system_taxid: 9986

Molecule: Ribosomal Protein Us8
Chain: a
Engineered: Yes

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986
Gene: Rps15a
Expression_system: Oryctolagus Cuniculus
Expression_system_taxid: 9986

Molecule: 40s Ribosomal Protein S21
Chain: b
Engineered: Yes

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986
Gene: Rps21
Expression_system: Oryctolagus Cuniculus
Expression_system_taxid: 9986

Molecule: Ribosomal Protein Us5
Chain: c
Engineered: Yes

Organism_scientific: Oryctolagus Cuniculus
Organism_taxid: 9986
Expression_system: Oryctolagus Cuniculus
Expression_system_taxid: 9986

Molecule: Eukaryotic Initiation Factor 2 Subunit Beta (Eif2
Chain: d
Engineered: Yes

Organism_scientific: Oryctolagus Cuniculus
Organism_taxid: 9986
Expression_system: Oryctolagus Cuniculus
Expression_system_taxid: 9986

Molecule: Ribosomal Protein Es17
Chain: e
Engineered: Yes

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986
Gene: Rps17
Expression_system: Oryctolagus Cuniculus
Expression_system_taxid: 9986

Molecule: Ribosomal Protein Us2
Chain: f
Engineered: Yes

Organism_scientific: Oryctolagus Cuniculus
Organism_taxid: 9986
Expression_system: Oryctolagus Cuniculus
Expression_system_taxid: 9986

Molecule: Ribosomal Protein Us3
Chain: g
Engineered: Yes

Organism_scientific: Oryctolagus Cuniculus
Organism_taxid: 9986
Expression_system: Oryctolagus Cuniculus
Expression_system_taxid: 9986

Molecule: Ribosomal Protein Us10
Chain: h
Engineered: Yes

Organism_scientific: Oryctolagus Cuniculus
Organism_taxid: 9986
Expression_system: Oryctolagus Cuniculus
Expression_system_taxid: 9986

Molecule: Ribosomal Protein Es1
Chain: I
Engineered: Yes

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986
Gene: Rps3a
Expression_system: Oryctolagus Cuniculus
Expression_system_taxid: 9986

Molecule: Ribosomal Protein Us11
Chain: j
Engineered: Yes

Organism_scientific: Oryctolagus Cuniculus
Organism_taxid: 9986
Expression_system: Oryctolagus Cuniculus
Expression_system_taxid: 9986

Molecule: Ribosomal Protein Es26
Chain: k
Engineered: Yes

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986
Gene: Rps26
Expression_system: Oryctolagus Cuniculus
Expression_system_taxid: 9986

Molecule: Ribosomal Protein Es28
Chain: l
Engineered: Yes

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986
Gene: Rps28
Expression_system: Oryctolagus Cuniculus
Expression_system_taxid: 9986

Molecule: Ribosomal Protein Rack1
Chain: m
Engineered: Yes

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986
Gene: Gnb2l1
Expression_system: Oryctolagus Cuniculus
Expression_system_taxid: 9986

Molecule: Ribosomal Protein Us19
Chain: n
Engineered: Yes

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986
Gene: Loc103349305
Expression_system: Oryctolagus Cuniculus
Expression_system_taxid: 9986

Molecule: 40s Ribosomal Protein S8
Chain: o
Engineered: Yes

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986
Gene: Rps8
Expression_system: Oryctolagus Cuniculus
Expression_system_taxid: 9986

Molecule: Ribosomal Protein Es31
Chain: p
Engineered: Yes

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986
Gene: Loc100348379
Expression_system: Oryctolagus Cuniculus
Expression_system_taxid: 9986

Molecule: 40s Ribosomal Protein S6
Chain: q
Engineered: Yes

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986
Gene: Loc100339133, Rps6
Expression_system: Oryctolagus Cuniculus
Expression_system_taxid: 9986

Molecule: 40s Ribosomal Protein S12
Chain: r
Engineered: Yes

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986
Gene: Rps12
Expression_system: Oryctolagus Cuniculus
Expression_system_taxid: 9986

Molecule: 40s Ribosomal Protein S24
Chain: s
Engineered: Yes

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986
Gene: Rps24
Expression_system: Oryctolagus Cuniculus
Expression_system_taxid: 9986

Molecule: Ribosomal Protein Es10
Chain: t
Engineered: Yes

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986
Gene: Rps10
Expression_system: Oryctolagus Cuniculus
Expression_system_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 5.80 Å
Gene
Ontology
ChainFunctionProcessComponent
G


H


I


J


K


L


O


P


Q


R


S


T


U


V


X


Y


Z


a


b


c


e


f


g


h


i


j


k


l


n


o


p


q


r


s


Primary referenceeIF3 Peripheral Subunits Rearrangement after mRNA Binding and Start-Codon Recognition., Simonetti A, Brito Querido J, Myasnikov AG, Mancera-Martinez E, Renaud A, Kuhn L, Hashem Y, Mol Cell. 2016 Jun 29. pii: S1097-2765(16)30197-6. doi:, 10.1016/j.molcel.2016.05.033. PMID:27373335
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1503 Kb) [Save to disk]
  • Biological Unit Coordinates (5k0y.pdb1.gz) 1491 Kb
  • CSU: Contacts of Structural Units for 5K0Y
  • Retrieve 5K0Y in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5K0Y from S2C, [Save to disk]
  • View 5K0Y 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 5K0Y
  • 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 5k0y from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5k0y_W] [5k0y_e] [5k0y_k] [5k0y_q] [5k0y_I] [5k0y] [5k0y_T] [5k0y_P] [5k0y_c] [5k0y_S] [5k0y_Y] [5k0y_d] [5k0y_r] [5k0y_f] [5k0y_g] [5k0y_o] [5k0y_i] [5k0y_s] [5k0y_K] [5k0y_a] [5k0y_j] [5k0y_m] [5k0y_L] [5k0y_n] [5k0y_F] [5k0y_Z] [5k0y_p] [5k0y_V] [5k0y_H] [5k0y_h] [5k0y_b] [5k0y_R] [5k0y_l] [5k0y_U] [5k0y_J] [5k0y_X] [5k0y_O] [5k0y_A] [5k0y_Q] [5k0y_t] [5k0y_N] [5k0y_M] [5k0y_G]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5K0Y: [KH] [RRM] [Ribosomal_S10] [Ribosomal_S13_N] [Ribosomal_S15] [Ribosomal_S19e] [Ribosomal_S27] [Ribosomal_S3Ae] [Ribosomal_S4] [Ribosomal_S6e] [S1] [S4] [WD40 ] by SMART
  • Other resources with information on 5K0Y
  • Community annotation for 5K0Y at PDBWiki (http://pdbwiki.org)

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