5L3P

Cryo-EM structure of stringent response factor RelA bound to ErmCL-stalled ribosome complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

The stringent factor RelA adopts an open conformation on the ribosome to stimulate ppGpp synthesis.

Arenz, S.Abdelshahid, M.Sohmen, D.Payoe, R.Starosta, A.L.Berninghausen, O.Hauryliuk, V.Beckmann, R.Wilson, D.N.

(2016) Nucleic Acids Res 44: 6471-6481

  • DOI: https://doi.org/10.1093/nar/gkw470
  • Primary Citation of Related Structures:  
    5L3P

  • PubMed Abstract: 

    Under stress conditions, such as nutrient starvation, deacylated tRNAs bound within the ribosomal A-site are recognized by the stringent factor RelA, which converts ATP and GTP/GDP to (p)ppGpp. The signaling molecules (p)ppGpp globally rewire the cellular transcriptional program and general metabolism, leading to stress adaptation. Despite the additional importance of the stringent response for regulation of bacterial virulence, antibiotic resistance and persistence, structural insight into how the ribosome and deacylated-tRNA stimulate RelA-mediated (p)ppGpp has been lacking. Here, we present a cryo-EM structure of RelA in complex with the Escherichia coli 70S ribosome with an average resolution of 3.7 Å and local resolution of 4 to >10 Å for RelA. The structure reveals that RelA adopts a unique 'open' conformation, where the C-terminal domain (CTD) is intertwined around an A/T-like tRNA within the intersubunit cavity of the ribosome and the N-terminal domain (NTD) extends into the solvent. We propose that the open conformation of RelA on the ribosome relieves the autoinhibitory effect of the CTD on the NTD, thus leading to stimulation of (p)ppGpp synthesis by RelA.


  • Organizational Affiliation

    Gene Center and Department for Biochemistry, University of Munich, Munich 81377, Germany.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2C [auth D]273Escherichia coli K-12Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3D [auth E]209Escherichia coli K-12Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4E [auth F]201Escherichia coli K-12Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5F [auth G]179Escherichia coli K-12Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6G [auth H]177Escherichia coli K-12Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9H [auth I]149Escherichia coli K-12Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13I [auth N]142Escherichia coli K-12Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14J [auth O]123Escherichia coli K-12Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15K [auth P]144Escherichia coli K-12Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16L [auth Q]136Escherichia coli K-12Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17M [auth R]127Escherichia coli K-12Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18N [auth S]117Escherichia coli K-12Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19O [auth T]115Escherichia coli K-12Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20P [auth U]118Escherichia coli K-12Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21Q [auth V]103Escherichia coli K-12Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22R [auth W]110Escherichia coli K-12Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23S [auth X]100Escherichia coli K-12Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24T [auth Y]104Escherichia coli K-12Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25U [auth Z]94Escherichia coli K-12Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27V [auth 0]85Escherichia coli K-12Mutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28W [auth 1]78Escherichia coli K-12Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29X [auth 2]63Escherichia coli K-12Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30Y [auth 3]59Escherichia coli K-12Mutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31Z [auth 4]70Escherichia coli K-12Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32AA [auth 5]57Escherichia coli K-12Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33BA [auth 6]55Escherichia coli K-12Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34CA [auth 7]46Escherichia coli K-12Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35DA [auth 8]65Escherichia coli K-12Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36EA [auth 9]38Escherichia coli K-12Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2GA [auth b]240Escherichia coli K-12Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3HA [auth c]233Escherichia coli K-12Mutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4IA [auth d]206Escherichia coli K-12Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5JA [auth e]167Escherichia coli K-12Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6KA [auth f]135Escherichia coli K-12Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7LA [auth g]179Escherichia coli K-12Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8MA [auth h]130Escherichia coli K-12Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9NA [auth i]130Escherichia coli K-12Mutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10OA [auth j]103Escherichia coli K-12Mutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11PA [auth k]129Escherichia coli K-12Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12QA [auth l]124Escherichia coli K-12Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13RA [auth m]118Escherichia coli K-12Mutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15SA [auth o]89Escherichia coli K-12Mutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16TA [auth p]82Escherichia coli K-12Mutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17UA [auth q]84Escherichia coli K-12Mutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18VA [auth r]75Escherichia coli K-12Mutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20WA [auth t]87Escherichia coli K-12Mutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21XA [auth u]71Escherichia coli K-12Mutation(s): 0 
UniProt
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L10AB [auth J]165Escherichia coli K-12Mutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11BB [auth K]142Escherichia coli K-12Mutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14CB [auth n]102Escherichia coli K-12Mutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19DB [auth s]92Escherichia coli K-12Mutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
GTP pyrophosphokinase,GTP pyrophosphokinase,GTP pyrophosphokinaseEB [auth z]819Escherichia coliEscherichia coli O157:H7Mutation(s): 0 
Gene Names: relAZ4099ECs3644
EC: 2.7.6.5
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Entity ID: 1
MoleculeChains LengthOrganismImage
23S ribosomal RNA2,903Escherichia coli K-12
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Entity ID: 2
MoleculeChains LengthOrganismImage
5S ribosomal RNA120Escherichia coli K-12
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Entity ID: 32
MoleculeChains LengthOrganismImage
16S ribosomal RNAFA [auth a]1,539Escherichia coli K-12
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Entity ID: 51
MoleculeChains LengthOrganismImage
mRNAYA [auth v]6Escherichia coli
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Entity ID: 52
MoleculeChains LengthOrganismImage
P-site tRNAZA [auth x]77Escherichia coli K-12
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Entity ID: 58
MoleculeChains LengthOrganismImage
deacylated A/R-tRNAFB [auth y]73Escherichia coli K-12
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONSPIDER
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyGRK1721
German Research FoundationGermanyFOR-1805
SPPGermany1879
SFBGermany464
Swedish Research CouncilSweden2013-4680

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-20
    Type: Initial release
  • Version 1.1: 2017-08-30
    Changes: Author supporting evidence, Data collection, Derived calculations, Experimental preparation
  • Version 1.2: 2017-09-13
    Changes: Author supporting evidence
  • Version 2.0: 2019-02-20
    Changes: Data collection, Derived calculations, Polymer sequence
  • Version 2.1: 2019-10-02
    Changes: Data collection, Other