4V19 Ribosome date Sep 25, 2014
title Structure Of The Large Subunit Of The Mammalian Mitoribosome Of 2
authors B.J.Greber, D.Boehringer, M.Leibundgut, P.Bieri, A.Leitner, N.Sch R.Aebersold, N.Ban
compound source
Molecule: Mitoribosomal Protein Bl27m, Mrpl27
Chain
Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Liver

Molecule: Mitoribosomal Protein Bl28m, Mrpl28
Chain: 1

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Liver

Molecule: Mitoribosomal Protein Ul29m, Mrpl47
Chain: 2

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Liver

Molecule: Mitoribosomal Protein Ul30m, Mrpl30
Chain: 3

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Liver

Molecule: Mitoribosomal Protein Bl31m, Mrpl55
Chain: 4

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Liver

Molecule: Mitoribosomal Protein Bl32m, Mrpl32
Chain: 5

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Liver

Molecule: Mitoribosomal Protein Bl33m, Mrpl33
Chain: 6

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Liver

Molecule: Mitoribosomal Protein Bl34m, Mrpl34
Chain: 7

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Liver

Molecule: Mitoribosomal Protein Bl35m, Mrpl35
Chain: 8

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Liver

Molecule: Mitoribosomal Protein Bl36m, Mrpl36
Chain: 9

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Liver

Molecule: Mitoribosomal 16s Rrna
Chain: A

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Liver

Molecule: Mitoribosomal Cp Trna
Chain: B

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Liver

Molecule: Trna
Chain: C, Z
Fragment: Cca-3' End
Other_details: Chain C Is P-Site Trna And Chain Z Is A-Site

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Liver

Molecule: Mitoribosomal Protein Ul2m, Mrpl2
Chain: D

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Liver

Molecule: Mitoribosomal Protein Ul3m, Mrpl3
Chain: E

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Liver

Molecule: Mitoribosomal Protein Ul4m, Mrpl4
Chain: F

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Liver

Molecule: Mitoribosomal Protein Bl9m, Mrpl9
Chain: I

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Liver

Molecule: Mitoribosomal Protein Ul10m, Mrpl10
Chain: J

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Liver

Molecule: Mitoribosomal Protein Ul11m, Mrpl11
Chain: K

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Liver

Molecule: Mitoribosomal Protein Ul13m, Mrpl13
Chain: N

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Liver

Molecule: Mitoribosomal Protein Ul14m, Mrpl14
Chain: O

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Liver

Molecule: Mitoribosomal Protein Ul15m, Mrpl15
Chain: P

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Liver

Molecule: Mitoribosomal Protein Ul16m, Mrpl16
Chain: Q

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Liver

Molecule: Mitoribosomal Protein Bl17m, Mrpl17
Chain: R

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Liver

Molecule: Mitoribosomal Protein Ul18m, Mrpl18
Chain: S

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Liver

Molecule: Mitoribosomal Protein Bl19m, Mrpl19
Chain: T

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Liver

Molecule: Mitoribosomal Protein Bl20m, Mrpl20
Chain: U

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Liver

Molecule: Mitoribosomal Protein Bl21m, Mrpl21
Chain: V

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Liver

Molecule: Mitoribosomal Protein Ul22m, Mrpl22
Chain: W

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Liver

Molecule: Mitoribosomal Protein Ul23m, Mrpl23
Chain: X

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Liver

Molecule: Mitoribosomal Protein Ul24m, Mrpl24
Chain: Y

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Liver
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 3.40 Å
ligand MG, P5P, Y5P, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
0


1


2


3


4


5


6


7


8


9


D


E


F


I


J


K


N


O


P


Q


R


S


T


U


V


W


X


Y


Primary referenceThe complete structure of the large subunit of the mammalian mitochondrial ribosome., Greber BJ, Boehringer D, Leibundgut M, Bieri P, Leitner A, Schmitz N, Aebersold R, Ban N, Nature. 2014 Oct 1. doi: 10.1038/nature13895. PMID:25271403
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1431 Kb) [Save to disk]
  • Biological Unit Coordinates (4v19.pdb1.gz) 1398 Kb
  • LPC: Ligand-Protein Contacts for 4V19
  • CSU: Contacts of Structural Units for 4V19
  • Retrieve 4V19 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4V19 from S2C, [Save to disk]
  • View 4V19 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 4V19
  • 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
  • 3D motif for 4V19, from MSDmotif at EBI
  • Fold representative 4v19 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4v19_6] [4v19_X] [4v19_1] [4v19_I] [4v19_K] [4v19_S] [4v19_P] [4v19_T] [4v19_Y] [4v19_J] [4v19_9] [4v19_4] [4v19] [4v19_Q] [4v19_C] [4v19_U] [4v19_D] [4v19_Z] [4v19_7] [4v19_R] [4v19_F] [4v19_0] [4v19_8] [4v19_N] [4v19_3] [4v19_V] [4v19_5] [4v19_E] [4v19_2] [4v19_A] [4v19_W] [4v19_B] [4v19_O]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4V19: [KOW] [RL11] [Ribosomal_L14] [Ribosomal_L2] [Ribosomal_L2_C ] by SMART
  • Other resources with information on 4V19
  • Community annotation for 4V19 at PDBWiki (http://pdbwiki.org)

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