1IBM Ribosome date Mar 28, 2001
title Structure Of The Thermus Thermophilus 30s Ribosomal Subunit In Complex With A Messenger Rna Fragment And Cognate Transfer Rna Anticodon Stem-Loop Bound At The A Site
authors J.M.Ogle, D.E.Brodersen, W.M.Clemons Jr., M.J.Tarry, A.P.Carter, V.Ramakrishnan
compound source
Molecule: 16s Ribosomal Rna
Chain: A
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: P-Site Messenger Rna Fragment
Chain: X
Engineered: Yes

Synthetic: Yes

Molecule: Anticodon Stem-Loop Of Phenylalanine Transfer Rna;
Chain: Y
Engineered: Yes

Synthetic: Yes

Molecule: A-Site Messenger Rna Fragment
Chain: Z
Engineered: Yes

Synthetic: Yes

Molecule: 30s Ribosomal Protein S2
Chain: B

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S3
Chain: C

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S4
Chain: D

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S5
Chain: E

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S6
Chain: F

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S7
Chain: G

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S8
Chain: H

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S9
Chain: I

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S10
Chain: J

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S11
Chain: K

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S12
Chain: L

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S13
Chain: M

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S14
Chain: N

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S15
Chain: O

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S16
Chain: P

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S17
Chain: Q

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S18
Chain: R

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S19
Chain: S

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S20
Chain: T

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein Thx
Chain: V

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274
symmetry Space Group: P 41 21 2
R_factor 0.231 R_Free 0.286
crystal
cell
length a length b length c angle alpha angle beta angle gamma
401.574 401.574 176.110 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.31 Å
ligand MG, ZN enzyme
note 1IBM (Molecule of the Month:pdb146)
Gene
Ontology
ChainFunctionProcessComponent
B


C


D


E


F


G


H


I


J


K


L


M


N


O


P


Q


R


S


T


V


Primary referenceRecognition of cognate transfer RNA by the 30S ribosomal subunit., Ogle JM, Brodersen DE, Clemons WM Jr, Tarry MJ, Carter AP, Ramakrishnan V, Science 2001 May 4;292(5518):897-902. PMID:11340196
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (960 Kb) [Save to disk]
  • Biological Unit Coordinates (1ibm.pdb1.gz) 942 Kb
  • LPC: Ligand-Protein Contacts for 1IBM
  • CSU: Contacts of Structural Units for 1IBM
  • Likely Quarternary Molecular Structure file(s) for 1IBM
  • Structure Factors (1701 Kb)
  • Retrieve 1IBM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1IBM from S2C, [Save to disk]
  • Re-refined 1ibm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1IBM 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 1IBM
  • 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 1IBM, from MSDmotif at EBI
  • Structure summary from SCOR (Structural Classification of RNA)
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ibma_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1ibmb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1ibmc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1ibmd_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1ibme_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1ibmf_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1ibmg_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1ibmh_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1ibmi_, region I [Jmol] [rasmolscript] [script source]
        - Domain d1ibmj_, region J [Jmol] [rasmolscript] [script source]
        - Domain d1ibmk_, region K [Jmol] [rasmolscript] [script source]
        - Domain d1ibml_, region L [Jmol] [rasmolscript] [script source]
        - Domain d1ibmm_, region M [Jmol] [rasmolscript] [script source]
        - Domain d1ibmn_, region N [Jmol] [rasmolscript] [script source]
        - Domain d1ibmo_, region O [Jmol] [rasmolscript] [script source]
        - Domain d1ibmp_, region P [Jmol] [rasmolscript] [script source]
        - Domain d1ibmq_, region Q [Jmol] [rasmolscript] [script source]
        - Domain d1ibmr_, region R [Jmol] [rasmolscript] [script source]
        - Domain d1ibms_, region S [Jmol] [rasmolscript] [script source]
        - Domain d1ibmt_, region T [Jmol] [rasmolscript] [script source]
        - Domain d1ibmv_, region V [Jmol] [rasmolscript] [script source]
  • Fold representative 1ibm from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1ibm_C] [1ibm_N] [1ibm_B] [1ibm_Z] [1ibm_O] [1ibm_K] [1ibm_L] [1ibm_F] [1ibm_M] [1ibm_E] [1ibm] [1ibm_J] [1ibm_R] [1ibm_Y] [1ibm_H] [1ibm_P] [1ibm_S] [1ibm_G] [1ibm_D] [1ibm_V] [1ibm_I] [1ibm_Q] [1ibm_X] [1ibm_A] [1ibm_T]
  • SWISS-PROT database: [Q5SHN7] [P80376] [Q5SHN3] [P80377] [Q5SHQ1] [Q5SJ76] [Q5SJH3] [Q5SHP7] [Q5SLQ0] [Q5SHP2] [P80380] [P80371] [P80372] [P80373] [Q5SHQ5] [Q5SLP8] [P17291] [Q5SHQ2] [P80374] [Q5SIH3]
  • Domain organization of [RS10_THET8] [RS11_THET8] [RS12_THET8] [RS13_THET8] [RS14Z_THET8] [RS15_THET8] [RS16_THET8] [RS17_THET8] [RS18_THET8] [RS19_THET8] [RS20_THET8] [RS2_THET8] [RS3_THET8] [RS4_THET8] [RS5_THET8] [RS6_THET8] [RS7_THET8] [RS8_THET8] [RS9_THET8] [RSHX_THET8] by SWISSPFAM
  • Domains found in 1IBM: [KH] [Ribosomal_S10] [Ribosomal_S15] [Ribosomal_S4] [S4 ] by SMART
  • Other resources with information on 1IBM
  • Community annotation for 1IBM at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Domain movements in 1IBM from the Database of Macromolecular Movements.
  • Images from IMB Jena Image Library of Biological Macromolecules.

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