5A2Q Ribosome date May 21, 2015
title Structure Of The Hcv Ires Bound To The Human Ribosome
authors N.Quade, M.Leiundgut, D.Boehringer, J.V.D.Heuvel, N.Ban
compound source
Molecule: 18s Rrna
Chain: 2
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hek293-6e
Organ: Kidney

Molecule: Hcv Ires
Chain: 3

Synthetic: Yes
Organism_scientific: Hepatitis C Virus
Organism_taxid: 11103

Molecule: Ribosomal Protein Us2
Chain: A

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hek293-6e
Organ: Kidney

Molecule: Ribosomal Protein Es1
Chain: B

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hek293-6e
Organ: Kidney

Molecule: Ribosomal Protein Us5
Chain: C

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hek293-6e
Organ: Kidney

Molecule: Ribosomal Protein Us3
Chain: D

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hek293-6e
Organ: Kidney

Molecule: Ribosomal Protein Es4
Chain: E

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hek293-6e
Organ: Kidney

Molecule: Ribosomal Protein Us7
Chain: F

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hek293-6e
Organ: Kidney

Molecule: Ribosomal Protein Es6
Chain: G

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hek293-6e
Organ: Kidney

Molecule: Ribosomal Protein Es7
Chain: H

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hek293-6e
Organ: Kidney

Molecule: Ribosomal Protein Es8
Chain: I

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hek293-6e
Organ: Kidney

Molecule: Ribosomal Protein Us4
Chain: J

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hek293-6e
Organ: Kidney

Molecule: Ribosomal Protein Es10
Chain: K

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hek293-6e
Organ: Kidney

Molecule: Ribosomal Protein Us17
Chain: L

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hek293-6e
Organ: Kidney

Molecule: Ribosomal Protein Es12
Chain: M

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hek293-6e
Organ: Kidney

Molecule: Ribosomal Protein Us15
Chain: N

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hek293-6e
Organ: Kidney

Molecule: Ribosomal Protein Us11
Chain: O

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hek293-6e
Organ: Kidney

Molecule: Ribosomal Protein Us19
Chain: P

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hek293-6e
Organ: Kidney

Molecule: Ribosomal Protein Us9
Chain: Q

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hek293-6e
Organ: Kidney

Molecule: Ribosomal Protein Es17
Chain: R

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hek293-6e
Organ: Kidney

Molecule: Ribosomal Protein Us13
Chain: S

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hek293-6e
Organ: Kidney

Molecule: Ribosomal Protein Es19
Chain: T

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hek293-6e
Organ: Kidney

Molecule: Ribosomal Protein Us10
Chain: U

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hek293-6e
Organ: Kidney

Molecule: Ribosomal Protein Es21
Chain: V

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hek293-6e
Organ: Kidney

Molecule: Ribosomal Protein Us8
Chain: W

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hek293-6e
Organ: Kidney

Molecule: Ribosomal Protein Us12
Chain: X

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hek293-6e
Organ: Kidney

Molecule: Ribosomal Protein Es24
Chain: Y

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hek293-6e
Organ: Kidney

Molecule: Ribosomal Protein Es25
Chain: Z

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hek293-6e
Organ: Kidney

Molecule: Ribosomal Protein Es26
Chain: a

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hek293-6e
Organ: Kidney

Molecule: Ribosomal Protein Es27
Chain: b

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hek293-6e
Organ: Kidney

Molecule: Ribosomal Protein Es28
Chain: c

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hek293-6e
Organ: Kidney

Molecule: Ribosomal Protein Us14
Chain: d

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hek293-6e
Organ: Kidney

Molecule: Ribosomal Protein Es30
Chain: e

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hek293-6e
Organ: Kidney

Molecule: Ribosomal Protein Es31
Chain: f

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hek293-6e
Organ: Kidney

Molecule: Ribosomal Protein Rack1
Chain: g

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hek293-6e
Organ: Kidney

Molecule: Ribosomal Protein El41
Chain: h

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hek293-6e
Organ: Kidney

Molecule: Ribosomal Protein El19
Chain: r

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hek293-6e
Organ: Kidney

Molecule: Ribosomal Protein El24
Chain: w

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hek293-6e
Organ: Kidney
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 3.90 Å
ligand MG, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A

  • cytosolic small ribosomal su...
  • B


    C

  • cytosolic small ribosomal su...
  • D

  • cytosolic small ribosomal su...
  • E

  • ribosome
  • cytosolic small ribosomal su...
  • F

  • cytosolic small ribosomal su...
  • G

  • cytosolic small ribosomal su...
  • H

  • cytosolic small ribosomal su...
  • I

  • cytosolic small ribosomal su...
  • J

  • cytosolic small ribosomal su...
  • K

  • cytosolic small ribosomal su...
  • L

  • cytosolic small ribosomal su...
  • M

  • cytosolic small ribosomal su...
  • N

  • cytosolic small ribosomal su...
  • O

  • cytosolic small ribosomal su...
  • P

  • cytosolic small ribosomal su...
  • Q

  • cytosolic small ribosomal su...
  • R

  • cytosolic small ribosomal su...
  • S

  • small ribosomal subunit
  • cytosolic small ribosomal su...
  • T

  • cytosolic small ribosomal su...
  • U

  • cytosolic small ribosomal su...
  • V

  • cytosolic small ribosomal su...
  • W

  • cytosolic small ribosomal su...
  • X

  • cytosolic small ribosomal su...
  • Y

  • small ribosomal subunit
  • cytosolic small ribosomal su...
  • Z

  • small ribosomal subunit
  • cytosolic small ribosomal su...
  • b

  • cytosolic small ribosomal su...
  • d

  • small ribosomal subunit
  • cytosolic small ribosomal su...
  • e

  • small ribosomal subunit
  • cytosolic small ribosomal su...
  • g


    h


    Primary referenceCryo-EM structure of Hepatitis C virus IRES bound to the human ribosome at 3.9-A resolution., Quade N, Boehringer D, Leibundgut M, van den Heuvel J, Ban N, Nat Commun. 2015 Jul 8;6:7646. doi: 10.1038/ncomms8646. PMID:26155016
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1472 Kb) [Save to disk]
  • Biological Unit Coordinates (5a2q.pdb1.gz) 1454 Kb
  • LPC: Ligand-Protein Contacts for 5A2Q
  • CSU: Contacts of Structural Units for 5A2Q
  • Retrieve 5A2Q in mmCIF format [Save to disk]
  • View 5A2Q 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 5A2Q
  • 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 5a2q from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5a2q_J] [5a2q_C] [5a2q] [5a2q_H] [5a2q_f] [5a2q_P] [5a2q_Y] [5a2q_K] [5a2q_G] [5a2q_Q] [5a2q_3] [5a2q_E] [5a2q_S] [5a2q_Z] [5a2q_X] [5a2q_T] [5a2q_d] [5a2q_r] [5a2q_D] [5a2q_b] [5a2q_L] [5a2q_g] [5a2q_N] [5a2q_W] [5a2q_A] [5a2q_R] [5a2q_F] [5a2q_M] [5a2q_V] [5a2q_I] [5a2q_w] [5a2q_h] [5a2q_e] [5a2q_B] [5a2q_a] [5a2q_c] [5a2q_2] [5a2q_O] [5a2q_U]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5A2Q: [KH] [Ribosomal_S10] [Ribosomal_S13_N] [Ribosomal_S15] [Ribosomal_S19e] [Ribosomal_S27] [Ribosomal_S3Ae] [Ribosomal_S4] [Ribosomal_S6e] [S4] [WD40 ] by SMART
  • Other resources with information on 5A2Q
  • Community annotation for 5A2Q at PDBWiki (http://pdbwiki.org)

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