5JB3 Translation date Apr 13, 2016
title Cryo-Em Structure Of A Full Archaeal Ribosomal Translation I Complex In The P-Remote Conformation
authors P.D.Coureux, E.Schmitt, Y.Mechulam
compound source
Molecule: 16s Ribosomal Rna
Chain: 2
Other_details: 16s Model From Pyrococcus Furiosus (Pdb Code Used For Fitting;
 Organism_scientific: Pyrococcus Abyssi Ge5
Organism_taxid: 272844

Molecule: 30s Ribosomal Protein S11
Chain: M
Other_details: 30s Ribosomal Protein Us11 Model From Pyroco Furiosus (Pdb Code 4v6u) Used For Fitting;
Organism_scientific: Pyrococcus Abyssi Ge5
Organism_taxid: 272844

Molecule: 30s Ribosomal Protein S12
Chain: N
Other_details: 30s Ribosomal Protein Us12 Model From Pyroco Furiosus (Pdb Code 4v6u) Used For Fitting;
Organism_scientific: Pyrococcus Abyssi Ge5
Organism_taxid: 272844

Molecule: 30s Ribosomal Protein S15
Chain: Q
Other_details: 30s Ribosomal Protein Us15 Model From Pyroco Furiosus (Pdb Code 4v6u) Used For Fitting;
Organism_scientific: Pyrococcus Abyssi Ge5
Organism_taxid: 272844

Molecule: 30s Ribosomal Protein S17p
Chain: R
Other_details: 30s Ribosomal Protein Us17 Model From Pyroco Furiosus (Pdb Code 4v6u) Used For Fitting;
Organism_scientific: Pyrococcus Abyssi Ge5
Organism_taxid: 272844

Molecule: 30s Ribosomal Protein S3ae
Chain: A
Synonym: Ribosomal Protein S1e
Other_details: 30s Ribosomal Protein Us3 Model From Pyrococ Furiosus (Pdb Code 4v6u) Used For Fitting;
Organism_scientific: Pyrococcus Abyssi Ge5
Organism_taxid: 272844

Molecule: 30s Ribosomal Protein S2
Chain: B
Other_details: 30s Ribosomal Protein Us2 Model From Pyrococ Furiosus (Pdb Code 4v6u) Used For Fitting;
Organism_scientific: Pyrococcus Abyssi Ge5
Organism_taxid: 272844

Molecule: 30s Ribosomal Protein S24e
Chain: V
Other_details: 30s Ribosomal Protein Es24 Model From Pyroco Furiosus (Pdb Code 4v6u) Used For Fitting;
Organism_scientific: Pyrococcus Abyssi Ge5
Organism_taxid: 272844

Molecule: 30s Ribosomal Protein S27e
Chain: W
Other_details: 30s Ribosomal Protein Es27 Model From Pyroco Furiosus (Pdb Code 4v6u) Used For Fitting;
Organism_scientific: Pyrococcus Abyssi Ge5
Organism_taxid: 272844

Molecule: 30s Ribosomal Protein S3
Chain: Z
Other_details: 30s Ribosomal Protein Us3 Model From Pyrococ Furiosus (Pdb Code 4v6u) Used For Fitting;
Organism_scientific: Pyrococcus Abyssi Ge5
Organism_taxid: 272844

Molecule: 30s Ribosomal Protein S4
Chain: D
Other_details: 30s Ribosomal Protein Us4 Model From Pyrococ Furiosus (Pdb Code 4v6u) Used For Fitting;
Organism_scientific: Pyrococcus Abyssi Ge5
Organism_taxid: 272844

Molecule: 30s Ribosomal Protein S4e
Chain: E
Other_details: 30s Ribosomal Protein Es4 Model From Pyrococ Furiosus (Pdb Code 4v6u) Used For Fitting;
Organism_scientific: Pyrococcus Abyssi Ge5
Organism_taxid: 272844

Molecule: 30s Ribosomal Protein S5
Chain: F
Other_details: 30s Ribosomal Protein Us5 Model From Pyrococ Furiosus (Pdb Code 4v6u) Used For Fitting;
Organism_scientific: Pyrococcus Abyssi Ge5
Organism_taxid: 272844

Molecule: 30s Ribosomal Protein S6e
Chain: G
Other_details: 30s Ribosomal Protein Es6 Model From Pyrococ Furiosus (Pdb Code 4v6u) Used For Fitting;
Organism_scientific: Pyrococcus Abyssi Ge5
Organism_taxid: 272844

Molecule: 30s Ribosomal Protein S8
Chain: I
Other_details: 30s Ribosomal Protein Us8 Model From Pyrococ Furiosus (Pdb Code 4v6u) Used For Fitting;
Organism_scientific: Pyrococcus Abyssi Ge5
Organism_taxid: 272844

Molecule: 30s Ribosomal Protein S8e
Chain: J
Other_details: 30s Ribosomal Protein Es8 Model From Pyrococ Furiosus (Pdb Code 4v6u) Used For Fitting;
Organism_scientific: Pyrococcus Abyssi Ge5
Organism_taxid: 272844

Molecule: 30s Ribosomal Protein Sx
Chain: C
Other_details: 30s Ribosomal Protein Sx Model From Pyrococc Furiosus (Pdb Code 4v6u) Used For Fitting;
Organism_scientific: Pyrococcus Abyssi Ge5
Organism_taxid: 272844

Molecule: 50s Ribosomal Protein L7ae
Chain: 3
Synonym: Ribosomal Protein L8e
Other_details: 50s Ribosomal Protein L7ae Model From Pyroco Furiosus (Pdb Code 4v6u) Used For Fitting;
Organism_scientific: Pyrococcus Abyssi Ge5
Organism_taxid: 272844

Molecule: 30s Ribosomal Protein S10
Chain: L
Other_details: 30s Ribosomal Protein Us10 Model From Pyroco Furiosus (Pdb Code 4v6u) Used For Fitting;
Organism_scientific: Pyrococcus Abyssi Ge5
Organism_taxid: 272844

Molecule: 30s Ribosomal Protein S13
Chain: O
Other_details: 30s Ribosomal Protein Us13 Model From Pyroco Furiosus (Pdb Code 4v6u) Used For Fitting;
Organism_scientific: Pyrococcus Abyssi Ge5
Organism_taxid: 272844

Molecule: 30s Ribosomal Protein S14 Type Z
Chain: P
Other_details: 30s Ribosomal Protein Us14 Model From Pyroco Furiosus (Pdb Code 4v6u) Used For Fitting;
Organism_scientific: Pyrococcus Abyssi Ge5
Organism_taxid: 272844

Molecule: 30s Ribosomal Protein S17e
Chain: S
Other_details: 30s Ribosomal Protein Es17 Model From Pyroco Furiosus (Pdb Code 4v6u) Used For Fitting;
Organism_scientific: Pyrococcus Abyssi Ge5
Organism_taxid: 272844

Molecule: 30s Ribosomal Protein S19
Chain: T
Other_details: 30s Ribosomal Protein Us19 Model From Pyroco Furiosus (Pdb Code 4v6u) Used For Fitting;
Organism_scientific: Pyrococcus Abyssi Ge5
Organism_taxid: 272844

Molecule: 30s Ribosomal Protein S19e
Chain: U
Other_details: 30s Ribosomal Protein Es19 Model From Pyroco Furiosus (Pdb Code 4v6u) Used For Fitting;
Organism_scientific: Pyrococcus Abyssi Ge5
Organism_taxid: 272844

Molecule: 30s Ribosomal Protein S28e
Chain: X
Other_details: 30s Ribosomal Protein Es28 Model From Pyroco Furiosus (Pdb Code 4v6u) Used For Fitting;
Organism_scientific: Pyrococcus Abyssi Ge5
Organism_taxid: 272844

Molecule: 30s Ribosomal Protein S27ae
Chain: Y
Other_details: 30s Ribosomal Protein Es27 Model From Pyroco Furiosus (Pdb Code 4v6u) Used For Fitting;
Organism_scientific: Pyrococcus Abyssi Ge5
Organism_taxid: 272844

Molecule: 30s Ribosomal Protein S7
Chain: H
Other_details: 30s Ribosomal Protein Us5 Model From Pyrococ Furiosus (Pdb Code 4v6u) Used For Fitting;
Organism_scientific: Pyrococcus Abyssi Ge5
Organism_taxid: 272844

Molecule: 30s Ribosomal Protein S9
Chain: K
Other_details: 30s Ribosomal Protein Us9 Model From Pyrococ Furiosus (Pdb Code 4v6u) Used For Fitting;
Organism_scientific: Pyrococcus Abyssi Ge5
Organism_taxid: 272844

Molecule: 30s Ribosomal Protein El41
Chain
Other_details: 30s Ribosomal Protein El41 Model From Pyroco Furiosus (Pdb Code 4v6u) Used For Fitting;
Organism_scientific: Pyrococcus Abyssi Ge5
Organism_taxid: 272844

Molecule: Initiator Met-Trna Fmet From E. Coli (A1u72 Varia
Chain: 4
Engineered: Yes
Other_details: Trna Model From Sulfolobus Solfataricus (Pdb 3v11) Used For Fitting;
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Variant: A1u72
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Mrna
Chain: 5
Engineered: Yes
Synthetic: Yes
Organism_scientific: Pyrococcus Abyssi Ge5
Organism_taxid: 272844

Molecule: Protein Translation Factor Sui1 Homolog
Chain: 1
Engineered: Yes
Organism_scientific: Pyrococcus Abyssi Ge5
Organism_taxid: 272844
Gene: Mj0463
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Translation Initiation Factor 1a
Chain: 6
Synonym: Aif-1a
Engineered: Yes
Organism_scientific: Pyrococcus Abyssi Ge5
Organism_taxid: 272844
Gene: Eif1a, Aif1a, Pyrab05910, Pab2441
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Translation Initiation Factor 2 Subunit Gamma
Chain: 7
Synonym: Aif2-Gamma,Eif-2-Gamma
Engineered: Yes
Other_details: Aif2-Gamma Model From Sulfolobus Solfataricu Code 3v11) Used For Fitting;
Organism_scientific: Pyrococcus Abyssi Ge5
Organism_taxid: 272844
Gene: Eif2g, Sso0412
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Translation Initiation Factor 2 Subunit Beta
Chain: 8
Synonym: Aif2-Beta,Eif-2-Beta
Engineered: Yes
Other_details: Aif2-Beta Model From Sulfolobus Solfataricus 3v11) Used For Fitting;
Organism_scientific: Pyrococcus Abyssi Ge5
Organism_taxid: 272844
Gene: Eif2b, Aif2b, Sso2381
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Translation Initiation Factor 2 Subunit Alpha
Chain: 9
Synonym: Aif2-Alpha,Eif-2-Alpha
Engineered: Yes
Other_details: Aif2-Alpha Model From Sulfolobus Solfataricu Code 3v11) Used For Fitting
Organism_scientific: Pyrococcus Abyssi Ge5
Organism_taxid: 272844
Gene: Eif2a, Aif2a, Sso1050
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 5.34 Å
ligand 5MU, GNP, H2U, MET, MG, OMC, PSU, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
1


3
  • ribonuclease P activity


    • 6


    7
  • translation elongation facto...


    • 8


    9


    A


    B


    D


    E


    F


    G


    H


    I


    J


    K


    L


    M


    N


    O


    P


    Q


    R


    S


    T


    U


    V


    W


    X


    Y


    Z


    Primary referenceCryo-EM study of start codon selection during archaeal translation initiation., Coureux PD, Lazennec-Schurdevin C, Monestier A, Larquet E, Cladiere L, Klaholz BP, Schmitt E, Mechulam Y, Nat Commun. 2016 Nov 7;7:13366. doi: 10.1038/ncomms13366. PMID:27819266
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1209 Kb) [Save to disk]
  • Biological Unit Coordinates (5jb3.pdb1.gz) 1197 Kb
  • LPC: Ligand-Protein Contacts for 5JB3
  • CSU: Contacts of Structural Units for 5JB3
  • Retrieve 5JB3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5JB3 from S2C, [Save to disk]
    • View 5JB3 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 5JB3
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1l5jb3, region B:373-862 [Jmol] [rasmolscript] [script source]
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5jb3] [5jb3_2] [5jb3_U] [5jb3_X] [5jb3_4] [5jb3_R] [5jb3_H] [5jb3_O] [5jb3_D] [5jb3_S] [5jb3_B] [5jb3_3] [5jb3_E] [5jb3_C] [5jb3_M] [5jb3_Y] [5jb3_W] [5jb3_Q] [5jb3_P] [5jb3_J] [5jb3_I] [5jb3_V] [5jb3_6] [5jb3_N] [5jb3_G] [5jb3_0] [5jb3_Z] [5jb3_8] [5jb3_T] [5jb3_A] [5jb3_F] [5jb3_K] [5jb3_7] [5jb3_9] [5jb3_5] [5jb3_L] [5jb3_1]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5JB3: [KH] [KOW] [Ribosomal_S10] [Ribosomal_S13_N] [Ribosomal_S15] [Ribosomal_S19e] [Ribosomal_S27] [Ribosomal_S3Ae] [Ribosomal_S4] [Ribosomal_S6e] [S1] [S4] [eIF1a] [eIF2B_5 ] by SMART
    • Other resources with information on 5JB3
  • Community annotation for 5JB3 at PDBWiki (http://pdbwiki.org)

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