4KZX Ribosome date May 30, 2013
title Rabbit 40s Ribosomal Subunit In Complex With Eif1.
authors I.B.Lomakin, T.A.Steitz
compound source
Molecule: 40s Ribosomal Protein Sa
Chain: A
Organism_scientific: Oryctolagus Cuniculus
Organism_common: European Rabbit,Japanese White Rabbit,Dome Rabbit,Rabbits;
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S3a
Chain: B

Organism_scientific: Oryctolagus Cuniculus
Organism_common: European Rabbit,Japanese White Rabbit,Dome Rabbit,Rabbits;
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S2
Chain: C

Organism_scientific: Oryctolagus Cuniculus
Organism_common: European Rabbit,Japanese White Rabbit,Dome Rabbit,Rabbits;
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S3
Chain: D

Organism_scientific: Oryctolagus Cuniculus
Organism_common: European Rabbit,Japanese White Rabbit,Dome Rabbit,Rabbits;
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S4x
Chain: E

Organism_scientific: Oryctolagus Cuniculus
Organism_common: European Rabbit,Japanese White Rabbit,Dome Rabbit,Rabbits;
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S5
Chain: F

Organism_scientific: Oryctolagus Cuniculus
Organism_common: European Rabbit,Japanese White Rabbit,Dome Rabbit,Rabbits;
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S6
Chain: G

Organism_scientific: Oryctolagus Cuniculus
Organism_common: European Rabbit,Japanese White Rabbit,Dome Rabbit,Rabbits;
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S7
Chain: H

Organism_scientific: Oryctolagus Cuniculus
Organism_common: European Rabbit,Japanese White Rabbit,Dome Rabbit,Rabbits;
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S8
Chain: I

Organism_scientific: Oryctolagus Cuniculus
Organism_common: European Rabbit,Japanese White Rabbit,Dome Rabbit,Rabbits;
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S9
Chain: J

Organism_scientific: Oryctolagus Cuniculus
Organism_common: European Rabbit,Japanese White Rabbit,Dome Rabbit,Rabbits;
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S10
Chain: K

Organism_scientific: Oryctolagus Cuniculus
Organism_common: European Rabbit,Japanese White Rabbit,Dome Rabbit,Rabbits;
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S11
Chain: L

Organism_scientific: Oryctolagus Cuniculus
Organism_common: European Rabbit,Japanese White Rabbit,Dome Rabbit,Rabbits;
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S12
Chain: M

Organism_scientific: Oryctolagus Cuniculus
Organism_common: European Rabbit,Japanese White Rabbit,Dome Rabbit,Rabbits;
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S13
Chain: N

Organism_scientific: Oryctolagus Cuniculus
Organism_common: European Rabbit,Japanese White Rabbit,Dome Rabbit,Rabbits;
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S14
Chain: O

Organism_scientific: Oryctolagus Cuniculus
Organism_common: European Rabbit,Japanese White Rabbit,Dome Rabbit,Rabbits;
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S15
Chain: P

Organism_scientific: Oryctolagus Cuniculus
Organism_common: European Rabbit,Japanese White Rabbit,Dome Rabbit,Rabbits;
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S16
Chain: Q

Organism_scientific: Oryctolagus Cuniculus
Organism_common: European Rabbit,Japanese White Rabbit,Dome Rabbit,Rabbits;
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S17
Chain: R

Organism_scientific: Oryctolagus Cuniculus
Organism_common: European Rabbit,Japanese White Rabbit,Dome Rabbit,Rabbits;
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S18
Chain: S

Organism_scientific: Oryctolagus Cuniculus
Organism_common: European Rabbit,Japanese White Rabbit,Dome Rabbit,Rabbits;
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S19
Chain: T

Organism_scientific: Oryctolagus Cuniculus
Organism_common: European Rabbit,Japanese White Rabbit,Dome Rabbit,Rabbits;
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S20
Chain: U

Organism_scientific: Oryctolagus Cuniculus
Organism_common: European Rabbit,Japanese White Rabbit,Dome Rabbit,Rabbits;
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S21
Chain: V

Organism_scientific: Oryctolagus Cuniculus
Organism_common: European Rabbit,Japanese White Rabbit,Dome Rabbit,Rabbits;
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S15a
Chain: W

Organism_scientific: Oryctolagus Cuniculus
Organism_common: European Rabbit,Japanese White Rabbit,Dome Rabbit,Rabbits;
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S23
Chain: X

Organism_scientific: Oryctolagus Cuniculus
Organism_common: European Rabbit,Japanese White Rabbit,Dome Rabbit,Rabbits;
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S24
Chain: Y

Organism_scientific: Oryctolagus Cuniculus
Organism_common: European Rabbit,Japanese White Rabbit,Dome Rabbit,Rabbits;
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S25
Chain: Z

Organism_scientific: Oryctolagus Cuniculus
Organism_common: European Rabbit,Japanese White Rabbit,Dome Rabbit,Rabbits;
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S26
Chain: a

Organism_scientific: Oryctolagus Cuniculus
Organism_common: European Rabbit,Japanese White Rabbit,Dome Rabbit,Rabbits;
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S27
Chain: b

Organism_scientific: Oryctolagus Cuniculus
Organism_common: European Rabbit,Japanese White Rabbit,Dome Rabbit,Rabbits;
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S28
Chain: c

Organism_scientific: Oryctolagus Cuniculus
Organism_common: European Rabbit,Japanese White Rabbit,Dome Rabbit,Rabbits;
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S29
Chain: d

Organism_scientific: Oryctolagus Cuniculus
Organism_common: European Rabbit,Japanese White Rabbit,Dome Rabbit,Rabbits;
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S30
Chain: e

Organism_scientific: Oryctolagus Cuniculus
Organism_common: European Rabbit,Japanese White Rabbit,Dome Rabbit,Rabbits;
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S27a
Chain: f

Organism_scientific: Oryctolagus Cuniculus
Organism_common: European Rabbit,Japanese White Rabbit,Dome Rabbit,Rabbits;
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein Rack1
Chain: g

Organism_scientific: Oryctolagus Cuniculus
Organism_common: European Rabbit,Japanese White Rabbit,Dome Rabbit,Rabbits;
Organism_taxid: 9986

Molecule: 18s Ribosomal Rna
Chain: I

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: Eukaryotic Translation Initiation Factor 1
Chain: l
Synonym: Eif1, A121, Protein Translation Factor Sui1 Homolo Sui1iso1;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Strain: K12
Gene: Eif1, Sui1
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Pet28a
Expression_system_plasmid: Pet28a-Heif1tev
symmetry Space Group: P 31 2 1
R_factor 0.347 R_Free 0.347
crystal
cell
length a length b length c angle alpha angle beta angle gamma
292.121 292.121 477.667 90.00 90.00 120.00
method X-Ray Diffractionresolution 7.81 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


a


b


c


d


e


f


l


Primary referenceThe initiation of mammalian protein synthesis and mRNA scanning mechanism., Lomakin IB, Steitz TA, Nature. 2013 Jul 21. doi: 10.1038/nature12355. PMID:23873042
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (3397 Kb) [Save to disk]
  • Biological Unit Coordinates (4kzx.pdb1.gz) 3379 Kb
  • CSU: Contacts of Structural Units for 4KZX
  • Structure Factors (222 Kb)
  • Retrieve 4KZX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4KZX from S2C, [Save to disk]
  • Re-refined 4kzx structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4KZX 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 4KZX
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4KZX, from MSDmotif at EBI
  • Fold representative 4kzx from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4kzx_Y] [4kzx_d] [4kzx_F] [4kzx] [4kzx_g] [4kzx_H] [4kzx_C] [4kzx_E] [4kzx_V] [4kzx_I] [4kzx_S] [4kzx_L] [4kzx_b] [4kzx_X] [4kzx_A] [4kzx_D] [4kzx_f] [4kzx_i] [4kzx_U] [4kzx_N] [4kzx_P] [4kzx_e] [4kzx_c] [4kzx_Z] [4kzx_G] [4kzx_J] [4kzx_B] [4kzx_Q] [4kzx_T] [4kzx_a] [4kzx_M] [4kzx_R] [4kzx_l] [4kzx_K] [4kzx_O] [4kzx_W]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4KZX: [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 4KZX
  • Community annotation for 4KZX at PDBWiki (http://pdbwiki.org)

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