4KZZ Ribosome date May 30, 2013
title Rabbit 40s Ribosomal Subunit In Complex With Mrna, Initiator Eif1a
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: Initiator Met-Rna-I
Chain: j
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: Mrna
Chain: k
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic
Organism_taxid: 32630
Other_details: Mrna

Molecule: Human Initiation Factor Eif1a
Chain: n
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Strain: K12
Gene: Eif1ax
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21de3
Expression_system_vector_type: Pet28a
Expression_system_plasmid: Pet28a-Heif1atev
symmetry Space Group: P 31 2 1
R_factor 0.345 R_Free 0.359
crystal
cell
length a length b length c angle alpha angle beta angle gamma
297.750 297.750 485.160 90.00 90.00 120.00
method X-Ray Diffractionresolution 7.03 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


n


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] (3461 Kb) [Save to disk]
  • Biological Unit Coordinates (4kzz.pdb1.gz) 3441 Kb
  • CSU: Contacts of Structural Units for 4KZZ
  • Structure Factors (574 Kb)
  • Retrieve 4KZZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4KZZ from S2C, [Save to disk]
  • Re-refined 4kzz structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4KZZ 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 4KZZ
  • 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 4KZZ, from MSDmotif at EBI
  • Fold representative 4kzz from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4kzz_U] [4kzz_E] [4kzz_c] [4kzz_N] [4kzz_i] [4kzz_L] [4kzz_A] [4kzz_D] [4kzz_W] [4kzz_B] [4kzz_b] [4kzz_Y] [4kzz] [4kzz_C] [4kzz_J] [4kzz_k] [4kzz_j] [4kzz_G] [4kzz_S] [4kzz_O] [4kzz_g] [4kzz_F] [4kzz_M] [4kzz_n] [4kzz_I] [4kzz_V] [4kzz_d] [4kzz_R] [4kzz_Z] [4kzz_P] [4kzz_Q] [4kzz_a] [4kzz_H] [4kzz_T] [4kzz_f] [4kzz_K] [4kzz_e] [4kzz_X]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4KZZ: [KH] [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 4KZZ
  • Community annotation for 4KZZ at PDBWiki (http://pdbwiki.org)

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