3I1T Ribosome date Jun 27, 2009
title Crystal Structure Of The E. Coli 70s Ribosome In An Intermed Of Ratcheting
authors W.Zhang, J.A.Dunkle, J.H.D.Cate
compound source
Molecule: 50s Ribosomal Protein L2
Chain: C
Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333

Molecule: 50s Ribosomal Protein L3
Chain: D

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333

Molecule: 50s Ribosomal Protein L4
Chain: E

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333

Molecule: 50s Ribosomal Protein L5
Chain: F

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333

Molecule: 50s Ribosomal Protein L6
Chain: G

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333

Molecule: 50s Ribosomal Protein L9
Chain: H

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333

Molecule: 50s Ribosomal Protein L11
Chain: I

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333

Molecule: 50s Ribosomal Protein L13
Chain: J

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333

Molecule: 50s Ribosomal Protein L14
Chain: K

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333

Molecule: 50s Ribosomal Protein L15
Chain: L

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333

Molecule: 50s Ribosomal Protein L16
Chain: M

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333

Molecule: 50s Ribosomal Protein L17
Chain: N

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333

Molecule: 50s Ribosomal Protein L18
Chain: O

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333

Molecule: 50s Ribosomal Protein L19
Chain: P

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333

Molecule: 50s Ribosomal Protein L20
Chain: Q

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333

Molecule: 50s Ribosomal Protein L21
Chain: R

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333

Molecule: 50s Ribosomal Protein L22
Chain: S

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333

Molecule: 50s Ribosomal Protein L23
Chain: T

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333

Molecule: 50s Ribosomal Protein L24
Chain: U

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333

Molecule: 50s Ribosomal Protein L25
Chain: V

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333

Molecule: 50s Ribosomal Protein L27
Chain: W

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333

Molecule: 50s Ribosomal Protein L28
Chain: X

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333

Molecule: 50s Ribosomal Protein L29
Chain: Y

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333

Molecule: 50s Ribosomal Protein L30
Chain: Z

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333

Molecule: 50s Ribosomal Protein L32
Chain

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333

Molecule: 50s Ribosomal Protein L33
Chain: 1

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333

Molecule: 50s Ribosomal Protein L34
Chain: 2

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333

Molecule: 50s Ribosomal Protein L35
Chain: 3
Synonym: Ribosomal Protein A

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333

Molecule: 50s Ribosomal Protein L36
Chain: 4
Synonym: Ribosomal Protein B

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333

Molecule: 23s Rrna
Chain: A

Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 5s Rrna
Chain: B

Organism_scientific: Escherichia Coli
Organism_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.207 R_Free 0.253
crystal
cell
length a length b length c angle alpha angle beta angle gamma
210.720 435.070 628.730 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.81 Å
ligand MG, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
0


1


2


3


4


C


D


E


F


G


H


I


J


K


L


M


N


O


P


Q


R


S


T


U


V


W


X


Y


Z


Primary referenceStructures of the ribosome in intermediate states of ratcheting., Zhang W, Dunkle JA, Cate JH, Science. 2009 Aug 21;325(5943):1014-7. PMID:19696352
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (3919 Kb) [Save to disk]
  • Biological Unit Coordinates (3i1t.pdb1.gz) 3886 Kb
  • LPC: Ligand-Protein Contacts for 3I1T
  • CSU: Contacts of Structural Units for 3I1T
  • Structure Factors (4072 Kb)
  • Retrieve 3I1T in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3I1T from S2C, [Save to disk]
  • View 3I1T 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 3I1T
  • 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 3I1T, from MSDmotif at EBI
  • Fold representative 3i1t from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3i1t_U] [3i1t_R] [3i1t_V] [3i1t_S] [3i1t_0] [3i1t_L] [3i1t_T] [3i1t_X] [3i1t_D] [3i1t_A] [3i1t_C] [3i1t_E] [3i1t_B] [3i1t_H] [3i1t_W] [3i1t_I] [3i1t_2] [3i1t_Y] [3i1t_1] [3i1t_O] [3i1t_N] [3i1t_Z] [3i1t_Q] [3i1t_G] [3i1t_P] [3i1t_J] [3i1t_F] [3i1t_M] [3i1t_4] [3i1t_3] [3i1t] [3i1t_K]
  • SWISS-PROT database: [P0A7J7] [P0AA10] [P0ADY3] [P02413] [P0ADY7] [P0AG44] [P0C018] [P0A7K6] [P0A7L3] [P0AG48] [P61175] [P0ADZ0] [P60624] [P68919] [P0A7L8] [P0A7M2] [P0A7M6] [P60422] [P0AG51] [P0A7N4] [P0A7N9] [P0A7P5] [P0A7Q1] [P0A7Q6] [P60438] [P60723] [P62399] [P0AG55] [P0A7R1]
  • Domain organization of [RL11_ECOLI] [RL13_ECOLI] [RL14_ECOLI] [RL15_ECOLI] [RL16_ECOLI] [RL17_ECOLI] [RL18_ECOLI] [RL19_ECOLI] [RL20_ECOLI] [RL21_ECOLI] [RL22_ECOLI] [RL23_ECOLI] [RL24_ECOLI] [RL25_ECOLI] [RL27_ECOLI] [RL28_ECOLI] [RL29_ECOLI] [RL2_ECOLI] [RL30_ECOLI] [RL32_ECOLI] [RL33_ECOLI] [RL34_ECOLI] [RL35_ECOLI] [RL36_ECOLI] [RL3_ECOLI] [RL4_ECOLI] [RL5_ECOLI] [RL6_ECOLI] [RL9_ECOLI] by SWISSPFAM
  • Domains found in 3I1T: [KOW] [RL11 ] by SMART
  • Alignments of the sequence of 3I1T with the sequences similar proteins can be viewed for 3I1T's classification [RL11_ECOLI] [RL13_ECOLI] [RL14_ECOLI] [RL15_ECOLI] [RL16_ECOLI] [RL17_ECOLI] [RL18_ECOLI] [RL19_ECOLI] [RL20_ECOLI] [RL21_ECOLI] [RL22_ECOLI] [RL23_ECOLI] [RL24_ECOLI] [RL25_ECOLI] [RL27_ECOLI] [RL28_ECOLI] [RL29_ECOLI] [RL2_ECOLI] [RL30_ECOLI] [RL32_ECOLI] [RL33_ECOLI] [RL34_ECOLI] [RL35_ECOLI] [RL36_ECOLI] [RL3_ECOLI] [RL4_ECOLI] [RL5_ECOLI] [RL6_ECOLI] [RL9_ECOLI] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [RL11_ECOLI] [RL13_ECOLI] [RL14_ECOLI] [RL15_ECOLI] [RL16_ECOLI] [RL17_ECOLI] [RL18_ECOLI] [RL19_ECOLI] [RL20_ECOLI] [RL21_ECOLI] [RL22_ECOLI] [RL23_ECOLI] [RL24_ECOLI] [RL25_ECOLI] [RL27_ECOLI] [RL28_ECOLI] [RL29_ECOLI] [RL2_ECOLI] [RL30_ECOLI] [RL32_ECOLI] [RL33_ECOLI] [RL34_ECOLI] [RL35_ECOLI] [RL36_ECOLI] [RL3_ECOLI] [RL4_ECOLI] [RL5_ECOLI] [RL6_ECOLI] [RL9_ECOLI] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3I1T
  • Community annotation for 3I1T at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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