5XYI Ribosome date Jul 08, 2017
title Small Subunit Of Trichomonas Vaginalis Ribosome
authors Z.Li, Q.Guo, L.Zheng, Y.Ji, Y.Xie, D.Lai, Z.Lun, X.Suo, N.Gao
compound source
Molecule: 18s
Chain: 2
 Organism_scientific: Trichomonas Vaginalis
Organism_taxid: 5722

Molecule: 40s Ribosomal Protein Sa
Chain: A
Synonym: Us2
Organism_scientific: Trichomonas Vaginalis
Organism_taxid: 5722

Molecule: Ribosomal Protein S3ae, Putative
Chain: B
Synonym: Es1
Organism_scientific: Trichomonas Vaginalis
Organism_taxid: 5722

Molecule: Uncharacterized Protein
Chain: C
Synonym: Us5
Organism_scientific: Trichomonas Vaginalis
Organism_taxid: 5722

Molecule: Ribosomal Protein S3, Putative
Chain: D
Synonym: Us3
Organism_scientific: Trichomonas Vaginalis
Organism_taxid: 5722

Molecule: 40s Ribosomal Protein S4
Chain: E
Synonym: Es4
Organism_scientific: Trichomonas Vaginalis
Organism_taxid: 5722

Molecule: 40s Ribosomal Protein S5-B, Putative
Chain: F
Synonym: Us7
Organism_scientific: Trichomonas Vaginalis
Organism_taxid: 5722

Molecule: 40s Ribosomal Protein S6
Chain: G
Synonym: Es6
Organism_scientific: Trichomonas Vaginalis
Organism_taxid: 5722

Molecule: 40s Ribosomal Protein S7, Putative
Chain: H
Synonym: Es7
Organism_scientific: Trichomonas Vaginalis
Organism_taxid: 5722

Molecule: 40s Ribosomal Protein S8
Chain: I
Synonym: Es8
Organism_scientific: Trichomonas Vaginalis
Organism_taxid: 5722

Molecule: Uncharacterized Protein
Chain: J
Synonym: Us4
Organism_scientific: Trichomonas Vaginalis
Organism_taxid: 5722

Molecule: Plectins10 Domain Containing Protein
Chain: K
Synonym: Es10
Organism_scientific: Trichomonas Vaginalis
Organism_taxid: 5722

Molecule: Uncharacterized Protein
Chain: L
Synonym: Us17
Organism_scientific: Trichomonas Vaginalis
Organism_taxid: 5722

Molecule: Ribosomal Protein L7ae, Putative
Chain: M
Synonym: Es12
Organism_scientific: Trichomonas Vaginalis
Organism_taxid: 5722

Molecule: 40s Ribosomal Protein S13, Putative
Chain: N
Synonym: Us15
Organism_scientific: Trichomonas Vaginalis
Organism_taxid: 5722

Molecule: Ribosomal Protein S14
Chain: O
Synonym: Us11
Organism_scientific: Trichomonas Vaginalis
Organism_taxid: 5722

Molecule: Ribosomal Protein S19, Putative
Chain: P
Synonym: Us19
Organism_scientific: Trichomonas Vaginalis
Organism_taxid: 5722

Molecule: 40s Ribosomal Protein S16, Putative
Chain: Q
Synonym: Us9
Organism_scientific: Trichomonas Vaginalis
Organism_taxid: 5722

Molecule: 40s Ribosomal Protein S17-B, Putative
Chain: R
Synonym: Es17
Organism_scientific: Trichomonas Vaginalis
Organism_taxid: 5722

Molecule: Ribosomal Protein S13ps18e, Putative
Chain: S
Synonym: Us13
Organism_scientific: Trichomonas Vaginalis
Organism_taxid: 5722

Molecule: Ribosomal Protein S19e, Putative
Chain: T
Synonym: Es19
Organism_scientific: Trichomonas Vaginalis
Organism_taxid: 5722

Molecule: Ribosomal Protein S10ps20e, Putative
Chain: U
Synonym: Us10
Organism_scientific: Trichomonas Vaginalis
Organism_taxid: 5722

Molecule: 40s Ribosomal Protein S21
Chain: V
Synonym: Es21
Organism_scientific: Trichomonas Vaginalis
Organism_taxid: 5722

Molecule: Ribosomal Protein S15a
Chain: W
Synonym: Us8
Organism_scientific: Trichomonas Vaginalis
Organism_taxid: 5722

Molecule: 40s Ribosomal Protein S23, Putative
Chain: X
Synonym: Us12
Organism_scientific: Trichomonas Vaginalis
Organism_taxid: 5722

Molecule: Ribosomal Protein S24e, Putative
Chain: Y
Synonym: Es24
Organism_scientific: Trichomonas Vaginalis
Organism_taxid: 5722

Molecule: Uncharacterized Protein
Chain: Z
Synonym: Es25
Organism_scientific: Trichomonas Vaginalis
Organism_taxid: 5722

Molecule: 40s Ribosomal Protein S26
Chain: a
Synonym: Es26
Organism_scientific: Trichomonas Vaginalis
Organism_taxid: 5722

Molecule: 40s Ribosomal Protein S27
Chain: b
Synonym: Es27
Organism_scientific: Trichomonas Vaginalis
Organism_taxid: 5722

Molecule: Uncharacterized Protein
Chain: c
Synonym: Es28
Organism_scientific: Trichomonas Vaginalis
Organism_taxid: 5722

Molecule: 40s Ribosomal Protein S29, Putative
Chain: d
Synonym: Us14
Organism_scientific: Trichomonas Vaginalis
Organism_taxid: 5722

Molecule: 40s Ribosomal Protein S30
Chain: e
Synonym: Es30
Organism_scientific: Trichomonas Vaginalis
Organism_taxid: 5722

Molecule: Guanine Nucleotide-Binding Protein Beta Subunit,
Chain: g
Synonym: Rack1
Organism_scientific: Trichomonas Vaginalis
Organism_taxid: 5722

Molecule: El41
Chain: n
Organism_scientific: Trichomonas Vaginalis
Organism_taxid: 5722
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 3.35 Å
Gene
Ontology
ChainFunctionProcessComponent
A


B


C


D


E


F


G


H


I


J


K


L


M


N


O


P


Q


R


S


T


U


V


W


X


Y


Z


a


b


c


d


e


g


n


Primary referenceCryo-EM structures of the 80S ribosomes from human parasites Trichomonas vaginalis and Toxoplasma gondii., Li Z, Guo Q, Zheng L, Ji Y, Xie YT, Lai DH, Lun ZR, Suo X, Gao N, Cell Res. 2017 Aug 15. doi: 10.1038/cr.2017.104. PMID:28809395
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1318 Kb) [Save to disk]
  • Biological Unit Coordinates (5xyi.pdb1.gz) 1307 Kb
  • CSU: Contacts of Structural Units for 5XYI
  • Retrieve 5XYI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5XYI from S2C, [Save to disk]
    • View 5XYI 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 5XYI
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5xyi_F] [5xyi_Q] [5xyi_T] [5xyi_S] [5xyi_2] [5xyi_b] [5xyi_G] [5xyi_X] [5xyi_I] [5xyi_K] [5xyi_a] [5xyi_C] [5xyi_O] [5xyi_L] [5xyi_d] [5xyi_e] [5xyi_D] [5xyi_B] [5xyi_P] [5xyi_H] [5xyi_g] [5xyi_N] [5xyi_J] [5xyi_n] [5xyi_V] [5xyi_Y] [5xyi_U] [5xyi_M] [5xyi_A] [5xyi_c] [5xyi_E] [5xyi_R] [5xyi_Z] [5xyi_W]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5XYI
  • Community annotation for 5XYI at PDBWiki (http://pdbwiki.org)

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