6OM6

Structure of trans-translation inhibitor bound to E. coli 70S ribosome with P site tRNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structure of trans-translation inhibitor bound to E. coli 70S ribosome with P site tRNA

Hoffer, E.D.Mehrani, A.Keiler, K.C.Stagg, S.M.Dunham, C.M.

(2021) Nat Commun 


Macromolecules

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2 B273Escherichia coliMutation(s): 0 
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Entity ID: 7
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50S ribosomal protein L3 C209Escherichia coliMutation(s): 0 
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Entity ID: 8
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50S ribosomal protein L4 D201Escherichia coliMutation(s): 0 
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Entity ID: 9
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50S ribosomal protein L5 E179Escherichia coliMutation(s): 0 
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Entity ID: 10
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50S ribosomal protein L6 F177Escherichia coliMutation(s): 0 
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Entity ID: 11
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50S ribosomal protein L9 G149Escherichia coliMutation(s): 0 
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Entity ID: 12
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50S ribosomal protein L13 J142Escherichia coliMutation(s): 0 
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Entity ID: 13
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50S ribosomal protein L14 K123Escherichia coliMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15 L144Escherichia coliMutation(s): 0 
Gene Names: 
rplOA8C65_19395A9R57_24660ACU57_21045AM464_09135AUQ13_22145BANRA_01932BANRA_03684BHS87_18545BJJ90_02210BMA87_18510BON75_18850BON98_13310BUE81_25610BvCms2454_01416BvCmsHHP001_00334BvCmsHHP019_04131BvCmsHHP056_02703BvCmsKSP026_02554BvCmsSINP011_02480BW690_10710BZL31_22885C5F72_02595C5F73_02860C5N07_23575C9E25_20065C9Z39_20710CA593_09735CG692_20270CI693_13520CI694_01990CIG45_22410D0X26_24495D2185_22985D3821_17755D3O91_20305D3Y67_24390D4638_19455D4718_17880D9C99_17930D9D20_21995D9D44_22490D9G29_15635D9G69_20945D9H68_17710D9J52_19090D9Z28_15390DAH37_14685DBQ99_03415DJ503_19770DL326_22310DNC98_19095DT034_22410DTL43_21000E2119_19640E2134_21880E2135_06185E4A44_21305E4K51_21490E4K55_21420E4K60_18985E4K61_20025E5P22_10480E5P28_20875EA213_19860EAI42_04990EAI52_16365EC1094V2_354EC3234A_55c00230EC3426_04459ECTO6_00449ED307_17010EEP23_17135EG808_17075EI021_21030EI028_20740EI032_18995EI041_20035EIZ93_12470EL75_0396EL79_0415EL80_0407ELT20_19170EPT01_19765ERS085365_03907ERS085416_03881ERS139211_03685ERS150873_04051EXX71_21335EYD11_02080F1E19_19655F9040_18095FRV13_20015FV293_22465FWK02_06270G5632_17770G5688_20025GHR40_07050GKF39_20550GKF74_18130GKF86_20070GKF89_18470GP671_20580GP689_20785GP954_00945GP979_02005GQE33_22230GQE34_14255GQE64_20420GQM17_19915GRW05_09060GRW27_21285GRW42_19350GRW57_03540GRW80_20585GRW81_21150NCTC10963_00456NCTC11022_03475NCTC11126_02772NCTC12650_00710NCTC13216_01351NCTC9045_00567NCTC9062_02686NCTC9117_00757NCTC9706_02738PGD_00585RK56_021420SAMEA3472047_03862SAMEA3472080_04748SAMEA3484427_04887SAMEA3484429_04875SAMEA3752559_00346SAMEA3753300_02227

Find proteins for A0A037Y8L6 (Escherichia coli)
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Entity ID: 15
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50S ribosomal protein L16 M136Escherichia coliMutation(s): 0 
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Entity ID: 16
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50S ribosomal protein L17 N127Escherichia coliMutation(s): 0 
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Entity ID: 17
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50S ribosomal protein L18 O117Escherichia coliMutation(s): 0 
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Entity ID: 18
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50S ribosomal protein L19 P115Escherichia coliMutation(s): 0 
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Entity ID: 19
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50S ribosomal protein L20 Q118Escherichia coliMutation(s): 0 
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Entity ID: 20
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50S ribosomal protein L21 R103Escherichia coliMutation(s): 0 
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Entity ID: 21
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50S ribosomal protein L22 S110Escherichia coliMutation(s): 0 
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Entity ID: 22
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50S ribosomal protein L23 T100Escherichia coliMutation(s): 0 
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Entity ID: 23
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50S ribosomal protein L24 U104Escherichia coliMutation(s): 0 
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Entity ID: 24
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50S ribosomal protein L25 V94Escherichia coliMutation(s): 0 
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Entity ID: 25
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50S ribosomal protein L28 X78Escherichia coliMutation(s): 0 
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Entity ID: 26
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50S ribosomal protein L29 Y63Escherichia coliMutation(s): 0 
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Entity ID: 27
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50S ribosomal protein L30 Z59Escherichia coliMutation(s): 0 
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Entity ID: 28
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50S ribosomal protein L31 a70Escherichia coliMutation(s): 0 
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Entity ID: 29
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50S ribosomal protein L32 b57Escherichia coliMutation(s): 0 
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Entity ID: 30
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50S ribosomal protein L33 c55Escherichia coliMutation(s): 0 
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Entity ID: 31
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50S ribosomal protein L34 d46Escherichia coliMutation(s): 0 
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Entity ID: 32
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50S ribosomal protein L35 e65Escherichia coliMutation(s): 0 
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Entity ID: 33
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50S ribosomal protein L36 f38Escherichia coliMutation(s): 0 
Find proteins for A0A0E2L017 (Escherichia coli (strain UMEA 3162-1))
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Entity ID: 34
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30S ribosomal protein S2 g241Escherichia coliMutation(s): 0 
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Entity ID: 35
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30S ribosomal protein S3 h233Escherichia coliMutation(s): 0 
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Entity ID: 36
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30S ribosomal protein S4 i206Escherichia coliMutation(s): 0 
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Entity ID: 37
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30S ribosomal protein S5 j167Escherichia coliMutation(s): 0 
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Entity ID: 38
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30S ribosomal protein S6 k135Escherichia coliMutation(s): 0 
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Entity ID: 39
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30S ribosomal protein S7 l179Escherichia coliMutation(s): 0 
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Entity ID: 40
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30S ribosomal protein S8 m130Escherichia coliMutation(s): 0 
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Entity ID: 41
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30S ribosomal protein S9 n130Escherichia coliMutation(s): 0 
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Entity ID: 42
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30S ribosomal protein S10 o103Escherichia coliMutation(s): 0 
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Entity ID: 43
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30S ribosomal protein S11 p129Escherichia coliMutation(s): 0 
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Entity ID: 44
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30S ribosomal protein S12 q124Escherichia coliMutation(s): 0 
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Entity ID: 45
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30S ribosomal protein S13 r118Escherichia coliMutation(s): 0 
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Entity ID: 46
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30S ribosomal protein S14 s101Escherichia coliMutation(s): 0 
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Entity ID: 47
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30S ribosomal protein S15 t89Escherichia coliMutation(s): 0 
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Entity ID: 48
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30S ribosomal protein S16 u82Escherichia coliMutation(s): 0 
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Entity ID: 49
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30S ribosomal protein S17 v84Escherichia coliMutation(s): 0 
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Entity ID: 50
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30S ribosomal protein S18 w75Escherichia coliMutation(s): 0 
Find proteins for A0A0E2KXL3 (Escherichia coli (strain UMEA 3162-1))
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Entity ID: 51
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30S ribosomal protein S19 x92Escherichia coliMutation(s): 0 
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Entity ID: 52
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30S ribosomal protein S20 y87Escherichia coliMutation(s): 0 
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Entity ID: 53
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30S ribosomal protein S21 z71Escherichia coliMutation(s): 0 
Find proteins for A0A0E2L2J1 (Escherichia coli (strain UMEA 3162-1))
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Entity ID: 54
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50S ribosomal protein L27 W85Escherichia coliMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
23S ribosomal RNA12904Escherichia coli
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16S ribosomal RNA21534Escherichia coli
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5S ribosomal RNA3120Escherichia coli
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  • Entity ID: 4
    MoleculeChainsLengthOrganismImage
    mRNA45Escherichia coli
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    Entity ID: 5
    MoleculeChainsLengthOrganismImage
    tRNA(gly)576Escherichia coli
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    KKL
    Query on KKL

    Download Ideal Coordinates CCD File 
    1
    4-amino-N-[5-(4-ethynylphenyl)-1,3,4-oxadiazol-2-yl]benzamide
    C17 H12 N4 O2
    FIEDYLNUYGEAJG-UHFFFAOYSA-N
     Ligand Interaction
    Modified Residues  1 Unique
    IDChainsTypeFormula2D DiagramParent
    0TD
    Query on 0TD
    qL-PEPTIDE LINKINGC5 H9 N O4 SASP
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.10 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM093278
    National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM121650

    Revision History  (Full details and data files)

    • Version 1.0: 2021-02-10
      Type: Initial release