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
MoleculeChainsSequence LengthOrganismDetailsImage
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: 
rplO, A8C65_19395, A9R57_24660, ACU57_21045, AM464_09135, AUQ13_22145, BANRA_01932, BANRA_03684, BHS87_18545, BJJ90_02210, BMA87_18510, BON75_18850, BON98_13310, BUE81_25610, BvCms2454_01416, BvCmsHHP001_00334, BvCmsHHP019_04131, BvCmsHHP056_02703, BvCmsKSP026_02554, BvCmsSINP011_02480, BW690_10710, BZL31_22885, C5F72_02595, C5F73_02860, C5N07_23575, C9E25_20065, C9Z39_20710, CA593_09735, CG692_20270, CI693_13520, CI694_01990, CIG45_22410, D0X26_24495, D2185_22985, D3821_17755, D3O91_20305, D3Y67_24390, D4638_19455, D4718_17880, D9C99_17930, D9D20_21995, D9D44_22490, D9G29_15635, D9G69_20945, D9H68_17710, D9J52_19090, D9Z28_15390, DAH37_14685, DBQ99_03415, DJ503_19770, DL326_22310, DNC98_19095, DT034_22410, DTL43_21000, E2119_19640, E2134_21880, E2135_06185, E4A44_21305, E4K51_21490, E4K55_21420, E4K60_18985, E4K61_20025, E5P22_10480, E5P28_20875, EA213_19860, EAI42_04990, EAI52_16365, EC1094V2_354, EC3234A_55c00230, EC3426_04459, ECTO6_00449, ED307_17010, EEP23_17135, EG808_17075, EI021_21030, EI028_20740, EI032_18995, EI041_20035, EIZ93_12470, EL75_0396, EL79_0415, EL80_0407, ELT20_19170, EPT01_19765, ERS085365_03907, ERS085416_03881, ERS139211_03685, ERS150873_04051, EXX71_21335, EYD11_02080, F1E19_19655, F9040_18095, FRV13_20015, FV293_22465, FWK02_06270, G5632_17770, G5688_20025, GHR40_07050, GKF39_20550, GKF74_18130, GKF86_20070, GKF89_18470, GP671_20580, GP689_20785, GP954_00945, GP979_02005, GQE33_22230, GQE34_14255, GQE64_20420, GQM17_19915, GRW05_09060, GRW27_21285, GRW42_19350, GRW57_03540, GRW80_20585, GRW81_21150, NCTC10963_00456, NCTC11022_03475, NCTC11126_02772, NCTC12650_00710, NCTC13216_01351, NCTC9045_00567, NCTC9062_02686, NCTC9117_00757, NCTC9706_02738, PGD_00585, RK56_021420, SAMEA3472047_03862, SAMEA3472080_04748, SAMEA3484427_04887, SAMEA3484429_04875, SAMEA3752559_00346, SAMEA3753300_02227

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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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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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50S ribosomal protein L21 R103Escherichia coliMutation(s): 0 
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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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50S ribosomal protein L24 U104Escherichia coliMutation(s): 0 
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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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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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Entity ID: 2
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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


    View more in-depth experimental data

    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