6WD0

Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure I-A)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cryo-EM of elongating ribosome with EF-Tu•GTP elucidates tRNA proofreading.

Loveland, A.B.Demo, G.Korostelev, A.A.

(2020) Nature 

  • DOI: 10.1038/s41586-020-2447-x
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Ribosomes accurately decode mRNA by proofreading each aminoacyl-tRNA that is delivered by the elongation factor EF-Tu 1 . To understand the molecular mechanism of this proofreading step it is necessary to visualize GTP-catalysed elongation ...

    Ribosomes accurately decode mRNA by proofreading each aminoacyl-tRNA that is delivered by the elongation factor EF-Tu 1 . To understand the molecular mechanism of this proofreading step it is necessary to visualize GTP-catalysed elongation, which has remained a challenge 2-4 . Here we use time-resolved cryogenic electron microscopy to reveal 33 ribosomal states after the delivery of aminoacyl-tRNA by EF-Tu•GTP. Instead of locking cognate tRNA upon initial recognition, the ribosomal decoding centre dynamically monitors codon-anticodon interactions before and after GTP hydrolysis. GTP hydrolysis enables the GTPase domain of EF-Tu to extend away, releasing EF-Tu from tRNA. The 30S subunit then locks cognate tRNA in the decoding centre and rotates, enabling the tRNA to bypass 50S protrusions during accommodation into the peptidyl transferase centre. By contrast, the decoding centre fails to lock near-cognate tRNA, enabling the dissociation of near-cognate tRNA both during initial selection (before GTP hydrolysis) and proofreading (after GTP hydrolysis). These findings reveal structural similarity between ribosomes in initial selection states 5,6 and in proofreading states, which together govern the efficient rejection of incorrect tRNA.


    Organizational Affiliation

    RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA. andrei.korostelev@umassmed.edu.



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50S ribosomal protein L4d201Escherichia coliMutation(s): 0 
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50S ribosomal protein L9g149Escherichia coliMutation(s): 0 
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50S ribosomal protein L22s110Escherichia coliMutation(s): 0 
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50S ribosomal protein L15l143Escherichia coliMutation(s): 0 
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rplOA8C65_19395A9R57_24660ACU57_21045AM464_09135AUQ13_22145BANRA_01932BANRA_03684BHS87_18545BJJ90_02210BMA87_18510BON75_18850BUE81_25610BvCms2454_01416BvCmsHHP001_00334BvCmsHHP019_04131BvCmsHHP056_02703BvCmsKSP026_02554BvCmsSINP011_02480BW690_10710BZL31_22885C5N07_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_06185E4K55_21420E4K60_18985E4K61_20025E5P22_10480E5P28_20875EA213_19860EAI42_04990EAI52_16365EC1094V2_354EC3234A_55c00230EC3426_04459ECTO6_00449ED307_17010EEP23_17135EG808_17075EI021_21030EI028_20740EI032_18995EI041_20035EIZ86_16985EIZ93_12470EL75_0396EL79_0415EL80_0407ELT20_19170EPT01_19765ERS085365_03907ERS085416_03881ERS139211_03685ERS150873_04051EXX71_21335EYD11_02080F1E19_19655FRV13_20015FV293_22465FWK02_06270GHR40_07050GKF74_18130GKF86_20070GKF89_18470GP689_20785GQE34_14255GQE64_20420GQM17_19915GRW42_19350GRW80_20585NCTC10963_00456NCTC11022_03475NCTC11126_02772NCTC12650_00710NCTC13216_01351NCTC9045_00567NCTC9062_02686NCTC9117_00757NCTC9706_02738PGD_00585RK56_021420SAMEA3472047_03862SAMEA3472080_04748SAMEA3484427_04887SAMEA3484429_04875SAMEA3752559_00346SAMEA3753300_02227

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30S ribosomal protein S2G225Escherichia coliMutation(s): 0 
Gene Names: 
rpsBA6581_19565A6592_02990A8C65_17850A9819_00790A9P13_21180A9R57_04400AC067_04635AJ318_03080AM446_22760AM464_17645AM465_25885AML35_22875APT94_19995APU18_02555ARC77_20180AU473_25970AUQ13_07500AW059_09840AWE53_010740AWF59_003780AWG78_007095AWG90_002345AWP75_13480AZZ83_003980B6V57_00930B7C53_01360B9M99_16250B9N33_22515B9T59_07520BANRA_00547BANRA_02273BANRA_03339BE963_14830BEN53_03085BER14_07785BFD68_21815BHF03_16550BHF46_07885BHS87_00800BIQ87_00790BIU72_13410BIZ41_19080BJJ90_21360BK248_07255BK334_15020BK373_09595BK375_04645BK383_20240BMA87_12300BMT49_02175BMT91_01365BON65_09430BON66_02955BON75_17145BON83_24855BON86_04410BON87_26695BON91_06960BON92_02750BON96_17215BTQ04_14405BUE81_01710BvCms12BK_00034BvCms2454_04107BvCms35BK_02145BvCmsC61A_04364BvCmsHHP001_04838BvCmsHHP019_00044BvCmsHHP056_04094BvCmsKKP036_03788BvCmsKSNP120_00104BvCmsKSP026_04711BvCmsKSP058_03767BvCmsKSP076_03014BvCmsNSP007_03764BvCmsSINP022_00326BW690_02470BWI89_14055BWP17_11915BXT93_00705BZL31_14940BZL69_20205C2M16_10795C2U48_09610C4K41_20910C4M78_19960C5715_17350C5N07_08575C5P44_18010C6669_04250C6B13_04325C7B06_05860C7B07_04280C7B08_09695C7B18_05305C9E25_15390C9E67_25210C9Z23_08405C9Z29_10375C9Z39_04990C9Z43_09525C9Z68_04785C9Z70_08115C9Z78_00165C9Z78_02775CA593_02870CCZ14_20505CCZ17_20470CDC27_24690CDL37_07245CG692_09500CI693_15090CI694_28160CIG45_06990CQP61_22090CR539_04935CRE06_00170CRJUMX01_610033CRT43_00990CRX46_05020CSB64_09595CT146_12115CUB99_08015CVH05_24475CWM24_05035D0X26_09420D1912_13690D2185_20130D2188_12785D3821_06210D3822_17335D3M98_08935D3O91_03185D3P01_06970D3P02_17575D3Y67_16405D4011_00170D4023_14650D4074_16625D4638_01785D4660_00170D4718_00170D4L91_00170D4M06_01450D4U49_05950D4U85_02335D4V08_16070D5I97_00170D6C36_00175D6D43_00170D6T60_04050D6X63_10625D6X76_09800D7K33_03410D7K63_00165D7K66_11610D7Y10_00165D8Y65_01905D9C99_12680D9D20_18630D9D31_08885D9D33_03385D9D43_02305D9D44_06780D9D94_08705D9E13_16330D9E34_01105D9E35_14530D9E49_02145D9E73_02485D9F17_00165D9F32_01785D9G11_19100D9G29_09875D9G42_07585D9G48_08785D9G69_05830D9H10_00165D9H36_21790D9H53_14245D9H68_13775D9H70_04355D9I20_08115D9I37_13510D9I87_01640D9I88_06435D9I97_03805D9J03_00165D9J11_16825D9J52_04560D9J58_13455D9J60_02075D9J78_12380D9K02_06620D9K54_16750D9L89_00165D9L99_05940D9X77_14905D9X97_00165D9Z28_03940DAH26_11215DAH34_04190DAH37_16335DAH43_04025DBQ99_21360DD762_01090DEN86_04070DJ487_06020DJ492_12760DJ503_00895DK132_00130DL251_18750DL257_01645DL292_03085DL326_07525DL455_01615DL979_07560DLT82_10665DLW88_03755DLX38_05600DLX40_11060DLY44_08780DM102_18365DM129_14540DM272_00165DM280_04680DM962_03245DM973_00130DMC44_08865DMI04_00170DMI53_01515DMO02_00170DMZ50_04115DN627_10245DN703_10125DNB37_01435DNC98_14250DND16_04815DNJ62_00170DNK12_00170DNR35_01445DNR41_13200DNX30_02270DOE35_00170DOM23_00165DOS18_01655DOT81_00170DOU81_00170DOY22_00170DOY56_00170DP258_09355DQE83_10255DQE91_03230DQG35_00170DRP48_00170DS721_00170DS966_12905DT034_05340DTL43_05925DTL90_09735DTM10_02780DTM45_12630DTZ20_16560DU309_06140DU321_03650DU333_05950DW236_10615DWB25_20305DXT73_18920DXX80_017135E0L04_16465E0L12_05055E2112_01240E2114_18160E2115_17375E2119_15580E2127_15010E2128_01350E2129_02860E2134_11975E2135_11635E2148_14070E4K55_06965E4K60_12610E4K61_17665E5P22_04090E5P28_13975E5P37_21190E5S46_19535E5S58_05605E5S61_20145EA159_18560EA167_19605EA189_12745EA191_19905EA198_08655EA200_20625EA203_17930EA213_17805EA214_17045EA218_05095EA222_15560EA225_05600EA231_02020EA232_17985EA233_03700EA242_20415EA245_19675EA250_20395EA410_04885EA429_13730EA434_02545EA435_20380EA834_19145EAI42_08300EAI52_11005EB509_04560EB510_04565EB515_00165EBA84_00165EBJ06_10275EC3234A_2c01500EC3426_00920EC382_02955ECONIH1_00890ECs0171ECTO124_04042ECTO6_03894ED225_10455ED307_13035ED607_02625ED611_09635ED648_00165ED903_08485ED944_00165EEA45_04510EEP23_00165EF082_10775EF173_00165EG808_13600EGC26_04060EGT48_20250EGU87_00165EHD45_00165EHD63_00165EHJ66_10080EHV81_01735EHV90_15890EHW09_06780EHX09_00165EI021_19845EI028_17525EI032_14690EI041_03160EIA08_06325EIA21_00165EIZ86_11710EIZ93_07925EL75_3596EL79_3705EL80_3652ELT20_04470ELT23_12175ELT33_15870ELT34_19890ELT48_12180ELT49_18475ELT58_11815ELU82_16775ELU85_21270ELU96_20275ELV05_06475ELV13_13145ELV15_10275ELV24_19200ELV28_04185ELX79_12490ELX83_20605ELY23_06765ELY24_11290ELY50_16140EO241_11800EPS76_09885EPS91_15145EPS94_12740EPT01_02595EPU41_00950EQ820_08895EQ823_16635EQ825_22910EQ830_01905ERL57_05895ERS085365_03087ERS085366_02719ERS085383_01177ERS085386_01543ERS085404_00708ERS085406_00569ERS085411_00031ERS085416_03650ERS139211_02987ERS150873_01111EST51_20100EVY14_15615EWK56_14885EXM29_15760ExPECSC019_03545ExPECSC038_03990ExPECSC065_04179EXX06_08815EXX13_05315EXX23_14665EXX53_06965EXX55_08280EXX71_19560EXX87_03335EYD11_18540EYX82_24365EYX99_20960EYY27_25445EYY34_22885F7F11_02075F7G01_02645F7G03_01455F9059_17980F9Z74_08200FAF34_018075FE846_19735FKO60_12340FNJ67_21465FNJ69_22375FNJ83_02345FORC82_3871FQU83_21885FRV13_02390FV293_02895FV295_13970FV438_03735FY127_02945GFU40_18985GFU45_18860GFU47_13780GHR40_00590GII91_13045GIY13_04535GIY19_11140GJ11_00885GJ638_08085GJD97_22995GKE15_05200GKE22_02185GKE24_06260GKE26_05200GKE29_08795GKE31_05160GKE39_03930GKE46_02210GKE58_05115GKE60_05170GKE64_02210GKE77_05545GKE87_12060GKE92_14180GKE93_04110GKF03_12930GKF28_16145GKF34_15440GKF47_15415GKF74_13200GKF86_01190GKF89_14780GKG08_11265GKG09_11865GKG11_12455GKG12_02120GKG22_11875GKG29_11915GN312_14025GNZ00_06515GNZ02_07900GP664_18015GP689_18795GP700_07630GP712_03555GP720_09585GP727_05960GP912_05760GQA06_13075GQE22_02625GQE34_08855GQE42_12800GQE47_19150GQE58_21125GQE64_01395GQE68_05070GQE88_09270GQM13_12620GQM17_05190GQN33_07395GQS26_13490GRW42_18985GRW80_16650HmCms169_00360HmCms184_03911HmCmsJML074_03001HmCmsJML146_01754HmCmsJML204_00825HMPREF3040_02610MJ49_06195MS6198_01840MS8345_00167NCTC10082_01383NCTC10089_04076NCTC10090_02160NCTC10767_03962NCTC10963_04191NCTC10974_04616NCTC11126_03634NCTC12650_04328NCTC12950_04424NCTC13127_05455NCTC13148_05196NCTC13846_03878NCTC7922_05813NCTC7927_04507NCTC7928_04613NCTC8450_01117NCTC8500_04546NCTC8621_04202NCTC8959_04843NCTC9007_00459NCTC9044_03184NCTC9045_04711NCTC9050_02026NCTC9058_02797NCTC9062_04214NCTC9117_05053NCTC9119_04267NCTC9434_02610NCTC9701_04378NCTC9702_04760NCTC9706_01337NCTC9777_00472NCTC9969_04265PGD_03810RK56_028000SAMEA3472044_04157SAMEA3472047_02498SAMEA3472056_00973SAMEA3472080_03752SAMEA3472090_04487SAMEA3472108_03201SAMEA3472110_04513SAMEA3472112_04653SAMEA3472147_00380SAMEA3484427_01375SAMEA3484429_01106SAMEA3484434_01147SAMEA3485113_00840SAMEA3752372_04458SAMEA3752557_00874SAMEA3752559_03712SAMEA3752620_02090SAMEA3753097_03905SAMEA3753164_02433SAMEA3753300_01863SK85_00168SY51_00965U12A_00178U14A_00177UC41_07420UN91_10580WQ89_09555YDC107_3394

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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3H206Escherichia coliMutation(s): 0 
Gene Names: rpsCNCTC9094_00425
Find proteins for A0A376HTV6 (Escherichia coli)
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5J157Escherichia coliMutation(s): 0 
Find proteins for F4TL26 (Escherichia coli M718)
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6K100Escherichia coliMutation(s): 0 
Find proteins for S1CG62 (Escherichia coli KTE64)
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7L151Escherichia coliMutation(s): 0 
Find proteins for S1D5F0 (Escherichia coli KTE64)
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9N127Escherichia coliMutation(s): 0 
Find proteins for T9TH92 (Escherichia coli UMEA 3718-1)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5e177Escherichia coliMutation(s): 0 
Find proteins for S1EUW9 (Escherichia coli KTE73)
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11P116Escherichia coliMutation(s): 0 
Find proteins for I2UH22 (Escherichia coli 4.0522)
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12Q123Escherichia coliMutation(s): 0 
Find proteins for V6FZ95 (Escherichia coli 99.0741)
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13R114Escherichia coliMutation(s): 0 
Find proteins for A0A1X3KX08 (Escherichia coli H420)
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14S100Escherichia coliMutation(s): 0 
Find proteins for I2X0X3 (Escherichia coli 4.0967)
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16U82Escherichia coliMutation(s): 0 
Find proteins for B7MIU7 (Escherichia coli O45:K1 (strain S88 / ExPEC))
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19X79Escherichia coliMutation(s): 0 
Find proteins for F4SQ43 (Escherichia coli H736)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6f176Escherichia coliMutation(s): 0 
Find proteins for A0A5B7PA13 (Escherichia coli O26:H11)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10h131Escherichia coliMutation(s): 0 
Find proteins for A0A073FNB4 (Escherichia coli 2-427-07_S4_C3)
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Entity ID: 53
MoleculeChainsLengthOrganism
23S ribosomal RNA12903Escherichia coli

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Entity ID: 52
MoleculeChainsLengthOrganism
16S ribosomal RNA31539Escherichia coli

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Entity ID: 54
MoleculeChainsLengthOrganism
5S ribosomal RNA2120Escherichia coli

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Entity ID: 55
MoleculeChainsLengthOrganism
tRNAfMet5, 677Escherichia coli
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Entity ID: 56
MoleculeChainsLengthOrganism
mRNA418Escherichia coli
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FME
Query on FME

Download CCD File 
5
N-FORMYLMETHIONINE
C6 H11 N O3 S
PYUSHNKNPOHWEZ-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 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 StatesR01 GM106105
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM107465
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM127094

Revision History 

  • Version 1.0: 2020-07-01
    Type: Initial release
  • Version 1.1: 2020-07-15
    Changes: Database references