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: 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 ...

    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 Center for integrated Protein Science Munich (CiPSM), University of Munich, Munich 81377, Germany wilson@lmb.uni-muenchen.de.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2 D273Escherichia coli K-12Mutation(s): 0 
Gene Names: rplBb3317JW3279
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Entity ID: 4
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50S ribosomal protein L3 E209Escherichia coli K-12Mutation(s): 0 
Gene Names: rplCb3320JW3282
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4 F201Escherichia coli K-12Mutation(s): 0 
Gene Names: rplDeryAb3319JW3281
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Entity ID: 6
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50S ribosomal protein L5 G179Escherichia coli K-12Mutation(s): 0 
Gene Names: rplEb3308JW3270
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Entity ID: 7
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50S ribosomal protein L6 H177Escherichia coli K-12Mutation(s): 0 
Gene Names: rplFb3305JW3267
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Entity ID: 8
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50S ribosomal protein L9 I149Escherichia coli K-12Mutation(s): 0 
Gene Names: rplIb4203JW4161
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Entity ID: 9
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50S ribosomal protein L13 N142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplMb3231JW3200
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Entity ID: 10
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50S ribosomal protein L14 O123Escherichia coli K-12Mutation(s): 0 
Gene Names: rplNb3310JW3272
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Entity ID: 11
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50S ribosomal protein L15 P144Escherichia coli K-12Mutation(s): 0 
Gene Names: rplOb3301JW3263
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Entity ID: 12
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50S ribosomal protein L16 Q136Escherichia coli K-12Mutation(s): 0 
Gene Names: rplPb3313JW3275
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Entity ID: 13
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50S ribosomal protein L17 R127Escherichia coli K-12Mutation(s): 0 
Gene Names: rplQb3294JW3256
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Entity ID: 14
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50S ribosomal protein L18 S117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplRb3304JW3266
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Entity ID: 15
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50S ribosomal protein L19 T115Escherichia coli K-12Mutation(s): 0 
Gene Names: rplSb2606JW2587
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Entity ID: 16
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50S ribosomal protein L20 U118Escherichia coli K-12Mutation(s): 0 
Gene Names: rplTpdzAb1716JW1706
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Entity ID: 17
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50S ribosomal protein L21 V103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplUb3186JW3153
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Entity ID: 18
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50S ribosomal protein L22 W110Escherichia coli K-12Mutation(s): 0 
Gene Names: rplVeryBb3315JW3277
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Entity ID: 19
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50S ribosomal protein L23 X100Escherichia coli K-12Mutation(s): 0 
Gene Names: rplWb3318JW3280
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Entity ID: 20
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50S ribosomal protein L24 Y104Escherichia coli K-12Mutation(s): 0 
Gene Names: rplXb3309JW3271
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Entity ID: 21
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50S ribosomal protein L25 Z94Escherichia coli K-12Mutation(s): 0 
Gene Names: rplYb2185JW2173
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Entity ID: 22
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50S ribosomal protein L27 085Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmAb3185JW3152
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Entity ID: 23
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50S ribosomal protein L28 178Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmBb3637JW3612
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Entity ID: 24
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50S ribosomal protein L29 263Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmCb3312JW3274
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Entity ID: 25
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50S ribosomal protein L30 359Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmDb3302JW3264
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Entity ID: 26
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50S ribosomal protein L31 470Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmEb3936JW3907
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Entity ID: 27
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50S ribosomal protein L32 557Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmFb1089JW1075
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Entity ID: 28
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50S ribosomal protein L33 655Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmGb3636JW3611
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Entity ID: 29
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50S ribosomal protein L34 746Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmHrimAssaFb3703JW3680
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Entity ID: 30
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50S ribosomal protein L35 865Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmIb1717JW1707
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Entity ID: 31
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50S ribosomal protein L36 938Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmJb3299JW3261
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Entity ID: 33
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30S ribosomal protein S2 b240Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsBb0169JW0164
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Entity ID: 34
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30S ribosomal protein S3 c233Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsCb3314JW3276
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Entity ID: 35
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30S ribosomal protein S4 d206Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsDramAb3296JW3258
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Entity ID: 36
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30S ribosomal protein S5 e167Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsEspcb3303JW3265
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Entity ID: 37
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30S ribosomal protein S6 f135Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsFb4200JW4158
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Entity ID: 38
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30S ribosomal protein S7 g179Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsGb3341JW3303
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Entity ID: 39
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30S ribosomal protein S8 h130Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsHb3306JW3268
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Entity ID: 40
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30S ribosomal protein S9 i130Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsIb3230JW3199
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Entity ID: 41
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30S ribosomal protein S10 j103Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsJnusEb3321JW3283
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Entity ID: 42
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30S ribosomal protein S11 k129Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsKb3297JW3259
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Entity ID: 43
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30S ribosomal protein S12 l124Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsLstrAb3342JW3304
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Entity ID: 44
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30S ribosomal protein S13 m118Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsMb3298JW3260
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Entity ID: 45
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30S ribosomal protein S15 o89Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsOsecCb3165JW3134
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Entity ID: 46
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30S ribosomal protein S16 p82Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsPb2609JW2590
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Entity ID: 47
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30S ribosomal protein S17 q84Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsQneaAb3311JW3273
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Entity ID: 48
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30S ribosomal protein S18 r75Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsRb4202JW4160
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Entity ID: 49
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30S ribosomal protein S20 t87Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsTb0023JW0022
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Entity ID: 50
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30S ribosomal protein S21 u71Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsUb3065JW3037
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Entity ID: 53
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50S ribosomal protein L10 J165Escherichia coli K-12Mutation(s): 0 
Gene Names: rplJb3985JW3948
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Entity ID: 54
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50S ribosomal protein L11 K142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplKrelCb3983JW3946
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Entity ID: 55
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30S ribosomal protein S14 n102Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsNb3307JW3269
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Entity ID: 56
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30S ribosomal protein S19 s92Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsSb3316JW3278
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Entity ID: 57
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GTP pyrophosphokinase,GTP pyrophosphokinase,GTP pyrophosphokinase z819Escherichia coliEscherichia coli O157:H7Mutation(s): 0 
Gene Names: relAZ4099ECs3644
EC: 2.7.6.5
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23S ribosomal RNAA2903Escherichia coli K-12
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5S ribosomal RNAB120Escherichia coli K-12
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Entity ID: 32
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16S ribosomal RNAa1539Escherichia coli K-12
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    mRNAv6Escherichia coli
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    Entity ID: 52
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    P-site tRNAx77Escherichia coli K-12
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    Entity ID: 58
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    deacylated A/R-tRNAy73Escherichia coli K-12
    Experimental Data & Validation

    Experimental Data

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

    Structure Validation

    View Full Validation Report



    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