4CSU

Cryo-EM structures of the 50S ribosome subunit bound with ObgE


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Literature

Structural and Functional Insights Into the Mode of Action of a Universally Conserved Obg Gtpase.

Feng, B.Mandava, C.S.Guo, Q.Wang, J.Cao, W.Li, N.Zhang, Y.Zhang, Y.Wang, Z.Wu, J.Sanyal, S.Lei, J.Gao, N.

(2014) PLoS Biol 12: 1866

  • DOI: 10.1371/journal.pbio.1001866
  • Primary Citation of Related Structures:  
    4CSU

  • PubMed Abstract: 
  • Obg proteins are a family of P-loop GTPases, conserved from bacteria to human. The Obg protein in Escherichia coli (ObgE) has been implicated in many diverse cellular functions, with proposed molecular roles in two global processes, ribosome assembly ...

    Obg proteins are a family of P-loop GTPases, conserved from bacteria to human. The Obg protein in Escherichia coli (ObgE) has been implicated in many diverse cellular functions, with proposed molecular roles in two global processes, ribosome assembly and stringent response. Here, using pre-steady state fast kinetics we demonstrate that ObgE is an anti-association factor, which prevents ribosomal subunit association and downstream steps in translation by binding to the 50S subunit. ObgE is a ribosome dependent GTPase; however, upon binding to guanosine tetraphosphate (ppGpp), the global regulator of stringent response, ObgE exhibits an enhanced interaction with the 50S subunit, resulting in increased equilibrium dissociation of the 70S ribosome into subunits. Furthermore, our cryo-electron microscopy (cryo-EM) structure of the 50S·ObgE·GMPPNP complex indicates that the evolutionarily conserved N-terminal domain (NTD) of ObgE is a tRNA structural mimic, with specific interactions with peptidyl-transferase center, displaying a marked resemblance to Class I release factors. These structural data might define ObgE as a specialized translation factor related to stress responses, and provide a framework towards future elucidation of functional interplay between ObgE and ribosome-associated (p)ppGpp regulators. Together with published data, our results suggest that ObgE might act as a checkpoint in final stages of the 50S subunit assembly under normal growth conditions. And more importantly, ObgE, as a (p)ppGpp effector, might also have a regulatory role in the production of the 50S subunit and its participation in translation under certain stressed conditions. Thus, our findings might have uncovered an under-recognized mechanism of translation control by environmental cues.


    Organizational Affiliation

    Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L28077Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmBb3637JW3612
Find proteins for P0A7M2 (Escherichia coli (strain K12))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L29163Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmCb3312JW3274
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L30258Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmDb3302JW3264
Find proteins for P0AG51 (Escherichia coli (strain K12))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L32356Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmFb1089JW1075
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L33454Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmGb3636JW3611
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L15234Escherichia coli K-12Mutation(s): 0 
Gene Names: rplAb3984JW3947
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L34646Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmHrimAssaFb3703JW3680
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L35764Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmIb1717JW1707
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Entity ID: 9
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50S RIBOSOMAL PROTEIN L36838Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmJb3299JW3261
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
GTPASE OBGE/CGTA9390Escherichia coli K-12Mutation(s): 0 
Gene Names: obgEcgtAobgyhbZb3183JW3150
EC: 3.6.5
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L2C272Escherichia coli K-12Mutation(s): 0 
Gene Names: rplBb3317JW3279
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L3D209Escherichia coli K-12Mutation(s): 0 
Gene Names: rplCb3320JW3282
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L4E201Escherichia coli K-12Mutation(s): 0 
Gene Names: rplDeryAb3319JW3281
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L5F178Escherichia coli K-12Mutation(s): 0 
Gene Names: rplEb3308JW3270
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L6G176Escherichia coli K-12Mutation(s): 0 
Gene Names: rplFb3305JW3267
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Entity ID: 18
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50S RIBOSOMAL PROTEIN L9H149Escherichia coli K-12Mutation(s): 0 
Gene Names: rplIb4203JW4161
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Entity ID: 19
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50S RIBOSOMAL PROTEIN L11I141Escherichia coli K-12Mutation(s): 0 
Gene Names: rplKrelCb3983JW3946
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Entity ID: 20
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50S RIBOSOMAL PROTEIN L13J142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplMb3231JW3200
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Entity ID: 21
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50S RIBOSOMAL PROTEIN L14K123Escherichia coli K-12Mutation(s): 0 
Gene Names: rplNb3310JW3272
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Entity ID: 22
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50S RIBOSOMAL PROTEIN L15L143Escherichia coli K-12Mutation(s): 0 
Gene Names: rplOb3301JW3263
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Entity ID: 23
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50S RIBOSOMAL PROTEIN L16M136Escherichia coli K-12Mutation(s): 0 
Gene Names: rplPb3313JW3275
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Entity ID: 24
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50S RIBOSOMAL PROTEIN L17N127Escherichia coli K-12Mutation(s): 0 
Gene Names: rplQb3294JW3256
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Entity ID: 25
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50S RIBOSOMAL PROTEIN L18O116Escherichia coli K-12Mutation(s): 0 
Gene Names: rplRb3304JW3266
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Entity ID: 26
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50S RIBOSOMAL PROTEIN L19P114Escherichia coli K-12Mutation(s): 0 
Gene Names: rplSb2606JW2587
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Entity ID: 27
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50S RIBOSOMAL PROTEIN L20Q117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplTpdzAb1716JW1706
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Entity ID: 28
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50S RIBOSOMAL PROTEIN L21R103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplUb3186JW3153
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Entity ID: 29
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50S RIBOSOMAL PROTEIN L22S110Escherichia coli K-12Mutation(s): 0 
Gene Names: rplVeryBb3315JW3277
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Entity ID: 30
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50S RIBOSOMAL PROTEIN L23T100Escherichia coli K-12Mutation(s): 0 
Gene Names: rplWb3318JW3280
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Entity ID: 31
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50S RIBOSOMAL PROTEIN L24U103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplXb3309JW3271
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L25W94Escherichia coli K-12Mutation(s): 0 
Gene Names: rplYb2185JW2173
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Entity ID: 33
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50S RIBOSOMAL PROTEIN L27Y84Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmAb3185JW3152
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Entity ID: 11
MoleculeChainsLengthOrganismImage
5S RRNAA118Escherichia coli K-12
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Entity ID: 12
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23S RRNAB2903Escherichia coli K-12
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-06-04
    Type: Initial release
  • Version 2.0: 2017-08-02
    Changes: Atomic model, Data collection, Derived calculations