5LMS Ribosome date Aug 01, 2016
title Structure Of Bacterial 30s-If1-If3-Mrna-Trna Translation Pre Initiation Complex(State-2c)
authors T.Hussain, J.L.Llacer, B.T.Wimberly, V.Ramakrishnan
compound source
Molecule: 16s Rrna
Chain: A
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: 30s Ribosomal Protein S2
Chain: B

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S3
Chain: C

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S4
Chain: D

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S5
Chain: E

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S6
Chain: F
Synonym: Ts9

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S7
Chain: G

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S8
Chain: H

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S9
Chain: I

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S10
Chain: J

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S11
Chain: K

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S12
Chain: L

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S13
Chain: M

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S14 Type Z
Chain: N

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S15
Chain: O

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S16
Chain: P

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S17
Chain: Q

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S18
Chain: R

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S19
Chain: S

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S20
Chain: T

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein Thx
Chain: V
Synonym: S31

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: Translation Initiation Factor If-1
Chain: W
Engineered: Yes

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Gene: Infa, Ttha1669
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_plasmid: Pet13a

Molecule: Translation Initiation Factor If-3
Chain: X
Engineered: Yes

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Gene: Infc, Ttha0551
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_plasmid: Pet13a

Molecule: Mrna
Chain: Y
Engineered: Yes

Synthetic: Yes
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: Trnai
Chain: Z

Organism_scientific: Escherichia Coli
Organism_taxid: 562
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 5.10 Å
ligand 4SU, 5MU, G7M, MG, OMC, PSU, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
B


C


D


E


F


G


H


I


J


K


L


M


N


O


P


Q


R


S


T


V


W


X


Primary referenceLarge-Scale Movements of IF3 and tRNA during Bacterial Translation Initiation., Hussain T, Llacer JL, Wimberly BT, Kieft JS, Ramakrishnan V, Cell. 2016 Sep 22;167(1):133-144.e13. doi: 10.1016/j.cell.2016.08.074. PMID:27662086
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (948 Kb) [Save to disk]
  • Biological Unit Coordinates (5lms.pdb1.gz) 940 Kb
  • LPC: Ligand-Protein Contacts for 5LMS
  • CSU: Contacts of Structural Units for 5LMS
  • Retrieve 5LMS in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5LMS from S2C, [Save to disk]
  • View 5LMS 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 5LMS
  • 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 5lms from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5lms_V] [5lms_Y] [5lms_W] [5lms_F] [5lms_Z] [5lms_X] [5lms_P] [5lms_H] [5lms_R] [5lms_T] [5lms_E] [5lms_Q] [5lms_D] [5lms_B] [5lms_K] [5lms_M] [5lms_C] [5lms_S] [5lms_A] [5lms_O] [5lms_J] [5lms_G] [5lms_I] [5lms] [5lms_N] [5lms_L]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5LMS: [KH] [Ribosomal_S10] [Ribosomal_S15] [Ribosomal_S4] [S1] [S4 ] by SMART
  • Other resources with information on 5LMS
  • Community annotation for 5LMS at PDBWiki (http://pdbwiki.org)

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