2UXC Ribosome date Mar 28, 2007
title Crystal Structure Of An Extended Trna Anticodon Stem Loop In With Its Cognate Mrna Ucgu In The Context Of The Thermus Th 30s Subunit.
authors C.M.Dunham, M.Selmer, S.S.Phelps, A.C.Kelley, T.Suzuki, S.Joseph, V.Ramakrishnan
compound source
Molecule: 16s Ribosomal Rna
Chain: A
Other_details: Chain A (16s Rna) Has E. Coli Numbering
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Atcc: 27634

Molecule: Ribosomal Protein S2
Chain: B

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Atcc: 27634

Molecule: Ribosomal Protein S3
Chain: C

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Atcc: 27634

Molecule: Ribosomal Protein S4
Chain: D

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Atcc: 27634

Molecule: Ribosomal Protein S5
Chain: E

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Atcc: 27634

Molecule: Ribosomal Protein S6
Chain: F

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Atcc: 27634

Molecule: Ribosomal Protein S7
Chain: G

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Atcc: 27634

Molecule: Ribosomal Protein S8
Chain: H

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Atcc: 27634

Molecule: Ribosomal Protein S9
Chain: I

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Atcc: 27634

Molecule: Ribosomal Protein S10
Chain: J

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Atcc: 27634

Molecule: Ribosomal Protein S11
Chain: K

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Atcc: 27634

Molecule: Ribosomal Protein S12
Chain: L

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Atcc: 27634

Molecule: Ribosomal Protein S13
Chain: M

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Atcc: 27634

Molecule: Ribosomal Protein S14
Chain: N

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Atcc: 27634

Molecule: Ribosomal Protein S15
Chain: O

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Atcc: 27634

Molecule: Ribosomal Protein S16
Chain: P

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Atcc: 27634

Molecule: Ribosomal Protein S17
Chain: Q

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Atcc: 27634

Molecule: Ribosomal Protein S18
Chain: R

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Atcc: 27634

Molecule: Ribosomal Protein S19
Chain: S

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Atcc: 27634

Molecule: Ribosomal Protein S20
Chain: T

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Atcc: 27634

Molecule: Ribosomal Protein Thx
Chain: U

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Atcc: 27634

Molecule: A-Site Messenger Rna Fragment Cggg
Chain: X
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Anticodon Stem-Loop Of Transfer Rna With Anticodo
Chain: Y
Engineered: Yes
Other_details: Sequence Based On E.Coli Trnaphe With Extend Anticodon

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 41 21 2
R_factor 0.217 R_Free 0.255
crystal
cell
length a length b length c angle alpha angle beta angle gamma
401.822 401.822 175.104 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.90 Å
ligand K, MG, PAR, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
B


C


D


E


F


G


H


I


J


K


L


M


N


O


P


Q


R


S


T


U


Primary referenceStructures of tRNAs with an expanded anticodon loop in the decoding center of the 30S ribosomal subunit., Dunham CM, Selmer M, Phelps SS, Kelley AC, Suzuki T, Joseph S, Ramakrishnan V, RNA. 2007 Jun;13(6):817-23. Epub 2007 Apr 6. PMID:17416634
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (963 Kb) [Save to disk]
  • Biological Unit Coordinates (2uxc.pdb1.gz) 945 Kb
  • LPC: Ligand-Protein Contacts for 2UXC
  • CSU: Contacts of Structural Units for 2UXC
  • Likely Quarternary Molecular Structure file(s) for 2UXC
  • Structure Factors (3014 Kb)
  • Retrieve 2UXC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2UXC from S2C, [Save to disk]
  • Re-refined 2uxc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2UXC 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 2UXC
  • 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 2UXC, from MSDmotif at EBI
  • Fold representative 2uxc from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2uxc_S] [2uxc_I] [2uxc_M] [2uxc_O] [2uxc_X] [2uxc_T] [2uxc_B] [2uxc_A] [2uxc_Y] [2uxc_D] [2uxc_H] [2uxc_N] [2uxc] [2uxc_R] [2uxc_P] [2uxc_G] [2uxc_L] [2uxc_E] [2uxc_C] [2uxc_Q] [2uxc_U] [2uxc_F] [2uxc_K] [2uxc_J]
  • SWISS-PROT database: [Q5SHN7] [P80376] [Q5SHN3] [P80377] [Q5SHQ1] [Q5SJ76] [Q5SJH3] [Q5SHP7] [Q5SLQ0] [Q5SHP2] [P62661] [P80371] [P80372] [P80373] [Q5SHQ5] [Q5SLP8] [P17291] [Q5SHQ2] [P62669] [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_THET2] [RS2_THET8] [RS3_THET8] [RS4_THET8] [RS5_THET8] [RS6_THET8] [RS7_THET8] [RS8_THET8] [RS9_THET2] [RSHX_THET8] by SWISSPFAM
  • Domains found in 2UXC: [KH] [Ribosomal_S10] [Ribosomal_S15] [Ribosomal_S4] [S4 ] by SMART
  • Other resources with information on 2UXC
  • Community annotation for 2UXC 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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