5GAG Ribosome date Nov 26, 2015
title Rnc In Complex With Srp-Sr In The Closed State
authors A.Jomaa, D.Boehringer, M.Leibundgut, N.Ban
compound source
Molecule: Srp 4.5s Rna
Chain: 1
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Trna Ccaend
Chain: 2

Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 23s Rrna
Chain: A

Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 5s Rrna
Chain: B

Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L2
Chain: C
Synonym: Ribosomal Protein Ul2

Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L3
Chain: D
Synonym: Ribosomal Protein Ul3

Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L4
Chain: E
Synonym: Ribosomal Protein Ul4

Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L5
Chain: F
Synonym: Ribosomal Protein Ul5

Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L6
Chain: G
Synonym: Ribosomal Protein Ul6

Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L9
Chain: H
Synonym: Ribosomal Protein Bl9

Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L10
Chain: I
Synonym: 50s Ribosomal Protein L8, Ribosomal Protein Ul10

Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L11
Chain: J
Synonym: Ribosomal Protein Ul11

Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L13
Chain: K
Synonym: Ribosomal Protein Ul13

Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L14
Chain: L
Synonym: Ribosomal Protein Ul14

Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L15
Chain: M
Synonym: Ribosomal Protein Ul15

Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L16
Chain: N
Synonym: Ribosomal Protein Ul16

Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L17
Chain: O
Synonym: Ribosomal Protein Ul17

Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L18
Chain: P
Synonym: Ribosomal Protein Ul18

Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L19
Chain: Q
Synonym: Ribosomal Protein Bl19

Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L20
Chain: R
Synonym: Ribosomal Protein Bl20

Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L21
Chain: S
Synonym: Ribosomal Protein Bl21

Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L22
Chain: T
Synonym: Ribosomal Protein Ul22

Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L23
Chain: U

Organism_scientific: Escherichia Coli (Strain K12)
Organism_taxid: 83333
Strain: K12

Molecule: 50s Ribosomal Protein L24
Chain: V
Synonym: Ribosomal Protein Ul24

Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L25
Chain: W
Synonym: Ribosomal Protein Bl25

Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L27
Chain: X
Synonym: Ribosomal Protein Bl27

Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L28
Chain: Y
Synonym: Ribosomal Protein Bl28

Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L29
Chain: Z
Synonym: Ribosomal Protein Ul29

Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L30
Chain: a
Synonym: Ribosomal Protein Ul30

Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L32
Chain: b
Synonym: Ribosomal Protein Bl32

Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L33
Chain: c
Synonym: Ribosomal Protein Bl33

Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L34
Chain: d
Synonym: Ribosomal Protein Bl34

Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L35
Chain: e
Synonym: Ribosomal Protein A,Ribosomal Protein Bl35

Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L36
Chain: f
Synonym: Ribosomal Protein B,Ribosomal Protein Bl36

Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: Signal Recognition Particle Protein Ffh
Chain: I
Engineered: Yes
Other_details: Notes: Less Defined Regions Were Replac
Unk Residues. Full Sequence Is Below: Mfdnltdrlsrtlrnisgrgrltednvkdtlrevrmalleadvalpvvrefinrvkeka Pgqefvkivrnelvaamgeenqtlnlaaqppavvlmaglqgagkttsvgklgkflrekh Vyrpaaikqletlaeqvgvdffpsdvgqkpvdivnaalkeaklkfydvllvdtagrlhv Vhasinpvetlfvvdamtgqdaantakafnealpltgvvltkvdgdarggaalsirhit Ektealepfhpdriasrilgmgdvlsliedieskvdraqaeklasklkkgdgfdlndfl Gmaslmgklpgmgqipdnvksqmddkvlvrmeaiinsmtmkerakpeiikgsrkrriaa Rllkqfddmqrmmkkmkkggmakmmrsmkgmmppgfpgr;

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: 1a9l Ss
Chain: k
Engineered: Yes

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Expression_system: Escherichia Coli
Expression_system_taxid: 562
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 3.80 Å
ligand MG, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
C


D


E


F


G


H


I


J


K


L


M


N


O


P


Q


R
  • translation repressor activi...


  • S


    T


    U


    V


    W


    X


    Y


    Z


    a


    b


    c


    d


    e


    f


    i


    Primary referenceStructures of the E. coli translating ribosome with SRP and its receptor and with the translocon., Jomaa A, Boehringer D, Leibundgut M, Ban N, Nat Commun. 2016 Jan 25;7:10471. doi: 10.1038/ncomms10471. PMID:26804923
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1899 Kb) [Save to disk]
  • Biological Unit Coordinates (5gag.pdb1.gz) 1878 Kb
  • LPC: Ligand-Protein Contacts for 5GAG
  • CSU: Contacts of Structural Units for 5GAG
  • Retrieve 5GAG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5GAG from S2C, [Save to disk]
  • View 5GAG 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 5GAG
  • 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 5gag from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5gag_f] [5gag_N] [5gag_D] [5gag_2] [5gag_d] [5gag_C] [5gag_J] [5gag_e] [5gag_Z] [5gag_G] [5gag_a] [5gag_Q] [5gag_L] [5gag_b] [5gag_X] [5gag_k] [5gag_U] [5gag_A] [5gag_c] [5gag_B] [5gag_S] [5gag_R] [5gag_W] [5gag_T] [5gag_i] [5gag_P] [5gag_F] [5gag] [5gag_E] [5gag_K] [5gag_O] [5gag_1] [5gag_I] [5gag_Y] [5gag_M] [5gag_V] [5gag_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5GAG: [AAA] [KOW] [RL11] [Ribosomal_L14] [Ribosomal_L2] [Ribosomal_L2_C] [SRP54] [SRP54_N ] by SMART
  • Other resources with information on 5GAG
  • Community annotation for 5GAG at PDBWiki (http://pdbwiki.org)

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