1KQS

The Haloarcula marismortui 50S Complexed with a Pretranslocational Intermediate in Protein Synthesis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A pre-translocational intermediate in protein synthesis observed in crystals of enzymatically active 50S subunits.

Schmeing, T.M.Seila, A.C.Hansen, J.L.Freeborn, B.Soukup, J.K.Scaringe, S.A.Strobel, S.A.Moore, P.B.Steitz, T.A.

(2002) Nat Struct Biol 9: 225-230

  • DOI: 10.1038/nsb758
  • Primary Citation of Related Structures:  
    1KQS

  • PubMed Abstract: 
  • The large ribosomal subunit catalyzes peptide bond formation during protein synthesis. Its peptidyl transferase activity has often been studied using a 'fragment assay' that depends on high concentrations of methanol or ethanol. Here we describe a ve ...

    The large ribosomal subunit catalyzes peptide bond formation during protein synthesis. Its peptidyl transferase activity has often been studied using a 'fragment assay' that depends on high concentrations of methanol or ethanol. Here we describe a version of this assay that does not require alcohol and use it to show, both crystallographically and biochemically, that crystals of the large ribosomal subunits from Haloarcula marismortui are enzymatically active. Addition of these crystals to solutions containing substrates results in formation of products, which ceases when crystals are removed. When substrates are diffused into large subunit crystals, the subsequent structure shows that products have formed. The CC-puromycin-peptide product is found bound to the A-site and the deacylated CCA is bound to the P-site, with its 3prime prime or minute OH near N3 A2486 (Escherichia coli A2451). Thus, this structure represents a state that occurs after peptide bond formation but before the hybrid state of protein synthesis.


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, USA.



Macromolecules

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L2A239Haloarcula marismortuiMutation(s): 0 
Find proteins for P20276 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L3B337Haloarcula marismortuiMutation(s): 0 
Find proteins for P20279 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L4C246Haloarcula marismortuiMutation(s): 0 
Find proteins for P12735 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L5D176Haloarcula marismortuiMutation(s): 0 
Find proteins for P14124 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L6E177Haloarcula marismortuiMutation(s): 0 
Find proteins for P14135 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L7AEF119Haloarcula marismortuiMutation(s): 0 
Find proteins for P12743 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L10G348Haloarcula marismortuiMutation(s): 0 
Find proteins for P15825 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L10EH167Haloarcula marismortuiMutation(s): 0 
Find proteins for P60617 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L13I145Haloarcula marismortuiMutation(s): 0 
Find proteins for P29198 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L14J132Haloarcula marismortuiMutation(s): 0 
Find proteins for P22450 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L15K164Haloarcula marismortuiMutation(s): 0 
Find proteins for P12737 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 16
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RIBOSOMAL PROTEIN L15EL194Haloarcula marismortuiMutation(s): 0 
Find proteins for P60618 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L18M186Haloarcula marismortuiMutation(s): 0 
Find proteins for P14123 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L18EN115Haloarcula marismortuiMutation(s): 0 
Find proteins for P12733 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L19EO148Haloarcula marismortuiMutation(s): 0 
Find proteins for P14119 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L21EP95Haloarcula marismortuiMutation(s): 0 
Find proteins for P12734 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L22Q154Haloarcula marismortuiMutation(s): 0 
Find proteins for P10970 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L23R84Haloarcula marismortuiMutation(s): 0 
Find proteins for P12732 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L24S119Haloarcula marismortuiMutation(s): 0 
Find proteins for P10972 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L24ET66Haloarcula marismortuiMutation(s): 0 
Find proteins for P14116 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L29U70Haloarcula marismortuiMutation(s): 0 
Find proteins for P10971 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L30V154Haloarcula marismortuiMutation(s): 0 
Find proteins for P14121 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L31EW91Haloarcula marismortuiMutation(s): 0 
Find proteins for P18138 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L32EX240Haloarcula marismortuiMutation(s): 0 
Find proteins for P12736 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L37AeY73Haloarcula marismortuiMutation(s): 0 
Find proteins for P60619 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L37EZ56Haloarcula marismortuiMutation(s): 0 
Find proteins for P32410 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L39E148Haloarcula marismortuiMutation(s): 0 
Find proteins for P22452 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L44E292Haloarcula marismortuiMutation(s): 0 
Find proteins for P32411 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
23S RRNA02922Haloarcula marismortui
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5S RRNA9122Haloarcula marismortui
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  • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    CCA33N/A
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    • Entity ID: 4
      MoleculeChainsLengthOrganismImage
      CC-Pmn-pcb42N/A
      Small Molecules
      Ligands 9 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      PPU
      Query on PPU

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      4
      PUROMYCIN-5'-MONOPHOSPHATE
      C22 H30 N7 O8 P
      NYICMZBLMICLBS-NVWDDTSBSA-N
       Ligand Interaction
      BTN
      Query on BTN

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      4
      BIOTIN
      C10 H16 N2 O3 S
      YBJHBAHKTGYVGT-ZKWXMUAHSA-N
       Ligand Interaction
      PHA
      Query on PHA

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      4
      PHENYLALANINAL
      C9 H11 N O
      CQIUZHAQYHXKRY-VIFPVBQESA-N
       Ligand Interaction
      ACA
      Query on ACA

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      4
      6-AMINOHEXANOIC ACID
      C6 H13 N O2
      SLXKOJJOQWFEFD-UHFFFAOYSA-N
       Ligand Interaction
      CD
      Query on CD

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      2, N, T, Y, Z
      CADMIUM ION
      Cd
      WLZRMCYVCSSEQC-UHFFFAOYSA-N
       Ligand Interaction
      K
      Query on K

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      0
      POTASSIUM ION
      K
      NPYPAHLBTDXSSS-UHFFFAOYSA-N
       Ligand Interaction
      CL
      Query on CL

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      0, 2, A, B, I, K, L, M, N, Q, X
      CHLORIDE ION
      Cl
      VEXZGXHMUGYJMC-UHFFFAOYSA-M
       Ligand Interaction
      MG
      Query on MG

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      0, 2, 9, A, J, S, X, Y
      MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      NA
      Query on NA

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      0, 9, A, C, H, I, K, L, P, Q, R
      SODIUM ION
      Na
      FKNQFGJONOIPTF-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.10 Å
      • R-Value Free: 0.220 
      • R-Value Work: 0.173 
      • R-Value Observed: 0.173 
      • Space Group: C 2 2 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 212.784α = 90
      b = 300.349β = 90
      c = 574.961γ = 90
      Software Package:
      Software NamePurpose
      CNSrefinement
      DENZOdata reduction
      SCALEPACKdata scaling
      CNSphasing

      Structure Validation

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      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2002-02-22
        Type: Initial release
      • Version 1.1: 2008-04-27
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance