7D6Z

Molecular model of the cryo-EM structure of 70S ribosome in complex with peptide deformylase and trigger factor


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 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

Structural insights into the interplay of protein biogenesis factors with the 70S ribosome.

Akbar, S.Bhakta, S.Sengupta, J.

(2021) Structure 

  • DOI: 10.1016/j.str.2021.03.005
  • Primary Citation of Related Structures:  
    7D6Z, 7D80

  • PubMed Abstract: 
  • Bacterial co-translational N-terminal methionine excision, an early event of nascent polypeptide chain processing, is mediated by two enzymes: peptide deformylase (PDF) and methionine aminopeptidase (MetAP). Trigger factor (TF), the only ribosome-associated bacterial chaperone, offers co-translational chaperoning assistance ...

    Bacterial co-translational N-terminal methionine excision, an early event of nascent polypeptide chain processing, is mediated by two enzymes: peptide deformylase (PDF) and methionine aminopeptidase (MetAP). Trigger factor (TF), the only ribosome-associated bacterial chaperone, offers co-translational chaperoning assistance. Here, we present two high-resolution cryoelectron microscopy structures of tRNA-bound E. coli ribosome complexes showing simultaneous binding of PDF and TF, in the absence (3.4 Å) and presence of MetAP (4.1 Å). These structures establish molecular details of the interactions of the factors with the ribosome, and thereby reveal the structural basis of nascent chain processing. Our results suggest that simultaneous binding of all three factors is not a functionally favorable mechanism of nascent chain processing. Strikingly, an unusual structural distortion of the 70S ribosome, potentially driven by binding of multiple copies of MetAP, is observed when MetAP is incubated with a pre-formed PDF-TF-bound ribosome complex.


    Organizational Affiliation

    Structural Biology & Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India. Electronic address: jayati@iicb.res.in.



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30S ribosomal protein S20A [auth 0]87Escherichia coliMutation(s): 0 
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30S ribosomal protein S21B [auth 1]71Escherichia coliMutation(s): 0 
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50S ribosomal protein L31F [auth 6]70Escherichia coliMutation(s): 0 
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50S ribosomal protein L2I [auth C]273Escherichia coliMutation(s): 0 
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50S ribosomal protein L3J [auth D]209Escherichia coliMutation(s): 0 
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50S ribosomal protein L4K [auth E]201Escherichia coliMutation(s): 0 
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50S ribosomal protein L5L [auth F]179Escherichia coliMutation(s): 0 
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50S ribosomal protein L6M [auth G]177Escherichia coliMutation(s): 0 
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50S ribosomal protein L9N [auth H]149Escherichia coliMutation(s): 0 
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50S ribosomal protein L11O [auth I]142Escherichia coliMutation(s): 0 
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50S ribosomal protein L13P [auth J]142Escherichia coliMutation(s): 0 
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50S ribosomal protein L14Q [auth K]123Escherichia coliMutation(s): 0 
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50S ribosomal protein L15R [auth L]144Escherichia coliMutation(s): 0 
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50S ribosomal protein L16S [auth M]136Escherichia coliMutation(s): 0 
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50S ribosomal protein L17T [auth N]127Escherichia coliMutation(s): 0 
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50S ribosomal protein L18U [auth O]117Escherichia coliMutation(s): 0 
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50S ribosomal protein L19V [auth P]115Escherichia coliMutation(s): 0 
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50S ribosomal protein L20W [auth Q]118Escherichia coliMutation(s): 0 
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50S ribosomal protein L21X [auth R]103Escherichia coliMutation(s): 0 
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50S ribosomal protein L22Y [auth S]110Escherichia coliMutation(s): 0 
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50S ribosomal protein L30Z [auth T]59Escherichia coliMutation(s): 0 
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50S ribosomal protein L24AA [auth U]104Escherichia coliMutation(s): 0 
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50S ribosomal protein L25BA [auth V]94Escherichia coliMutation(s): 0 
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50S ribosomal protein L27CA [auth W]85Escherichia coliMutation(s): 0 
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50S ribosomal protein L28DA [auth X]78Escherichia coliMutation(s): 0 
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50S ribosomal protein L29EA [auth Y]63Escherichia coliMutation(s): 0 
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50S ribosomal protein L23FA [auth Z]100Escherichia coliMutation(s): 0 
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50S ribosomal protein L32GA [auth a]57Escherichia coliMutation(s): 0 
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50S ribosomal protein L33HA [auth b]55Escherichia coliMutation(s): 0 
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50S ribosomal protein L34IA [auth c]46Escherichia coliMutation(s): 0 
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50S ribosomal protein L35JA [auth d]65Escherichia coliMutation(s): 0 
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50S ribosomal protein L36KA [auth e]38Escherichia coliMutation(s): 0 
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Peptide deformylaseMA [auth g]169Escherichia coli K-12Mutation(s): 0 
Gene Names: deffmsb3287JW3248
EC: 3.5.1.88
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Trigger factorNA [auth h]118Escherichia coli K-12Mutation(s): 0 
Gene Names: tigb0436JW0426
EC: 5.2.1.8
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30S ribosomal protein S2OA [auth i]241Escherichia coliMutation(s): 0 
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30S ribosomal protein S3PA [auth j]233Escherichia coliMutation(s): 0 
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30S ribosomal protein S4QA [auth k]206Escherichia coliMutation(s): 0 
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30S ribosomal protein S5RA [auth l]167Escherichia coliMutation(s): 0 
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30S ribosomal protein S6, fully modified isoformSA [auth m]135Escherichia coliMutation(s): 0 
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30S ribosomal protein S7TA [auth n]179Escherichia coliMutation(s): 0 
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30S ribosomal protein S8UA [auth o]130Escherichia coliMutation(s): 0 
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30S ribosomal protein S9VA [auth p]130Escherichia coliMutation(s): 0 
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30S ribosomal protein S10WA [auth q]103Escherichia coliMutation(s): 0 
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30S ribosomal protein S11XA [auth r]129Escherichia coliMutation(s): 0 
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30S ribosomal protein S12YA [auth s]124Escherichia coliMutation(s): 0 
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30S ribosomal protein S13ZA [auth t]118Escherichia coliMutation(s): 0 
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30S ribosomal protein S14AB [auth u]101Escherichia coliMutation(s): 0 
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30S ribosomal protein S15BB [auth v]89Escherichia coliMutation(s): 0 
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30S ribosomal protein S16CB [auth w]82Escherichia coliMutation(s): 0 
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30S ribosomal protein S17DB [auth x]84Escherichia coliMutation(s): 0 
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30S ribosomal protein S18EB [auth y]75Escherichia coliMutation(s): 0 
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30S ribosomal protein S19FB [auth z]92Escherichia coliMutation(s): 0 
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E-site tRNAC [auth 2]73Escherichia coli
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P-site tRNAD [auth 3]77Escherichia coli
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A-site tRNAE [auth 4]76Escherichia coli
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Entity ID: 7
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23S ribosomal rRNAG [auth A]2903Escherichia coli
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Entity ID: 8
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5S ribosomal rRNAH [auth B]118Escherichia coli
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16S ribosomal rRNALA [auth f]1539Escherichia coli
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Science and Engineering Research Board (SERB)IndiaSB/SO/BB- 0025/2014
Science and Engineering Research Board (SERB)IndiaCRG/2019/001788
Council of Scientific & Industrial Research (CSIR)India--

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-07
    Type: Initial release