3J8G

Electron cryo-microscopy structure of EngA bound with the 50S ribosomal subunit


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.00 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

Structural insights into the function of a unique tandem GTPase EngA in bacterial ribosome assembly

Zhang, X.Yan, K.Zhang, Y.Li, N.Ma, C.Li, Z.Zhang, Y.Feng, B.Liu, J.Sun, Y.Xu, Y.Lei, J.Gao, N.

(2014) Nucleic Acids Res 

  • DOI: 10.1093/nar/gku1135
  • Primary Citation of Related Structures:  
    3J8G

  • PubMed Abstract: 
  • Many ribosome-interacting GTPases, with proposed functions in ribosome biogenesis, are also implicated in the cellular regulatory coupling between ribosome assembly process and various growth control pathways. EngA is an essential GTPase in bacteria, ...

    Many ribosome-interacting GTPases, with proposed functions in ribosome biogenesis, are also implicated in the cellular regulatory coupling between ribosome assembly process and various growth control pathways. EngA is an essential GTPase in bacteria, and intriguingly, it contains two consecutive GTPase domains (GD), being one-of-a-kind among all known GTPases. EngA is required for the 50S subunit maturation. However, its molecular role remains elusive. Here, we present the structure of EngA bound to the 50S subunit. Our data show that EngA binds to the peptidyl transferase center (PTC) and induces dramatic conformational changes on the 50S subunit, which virtually returns the 50S subunit to a state similar to that of the late-stage 50S assembly intermediates. Very interestingly, our data show that the two GDs exhibit a pseudo-two-fold symmetry in the 50S-bound conformation. Our results indicate that EngA recognizes certain forms of the 50S assembly intermediates, and likely facilitates the conformational maturation of the PTC of the 23S rRNA in a direct manner. Furthermore, in a broad context, our data also suggest that EngA might be a sensor of the cellular GTP/GDP ratio, endowed with multiple conformational states, in response to fluctuations in cellular nucleotide pool, to facilitate and regulate ribosome assembly.


    Organizational Affiliation

    Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China ninggao@tsinghua.edu.cn.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L28078Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmBb3637JW3612
Find proteins for P0A7M2 (Escherichia coli (strain K12))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14K123Escherichia coli K-12Mutation(s): 0 
Gene Names: rplNb3310JW3272
Find proteins for P0ADY3 (Escherichia coli (strain K12))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15L144Escherichia coli K-12Mutation(s): 0 
Gene Names: rplOb3301JW3263
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29163Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmCb3312JW3274
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L16M136Escherichia coli K-12Mutation(s): 0 
Gene Names: rplPb3313JW3275
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L17N127Escherichia coli K-12Mutation(s): 0 
Gene Names: rplQb3294JW3256
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18O117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplRb3304JW3266
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Entity ID: 10
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50S ribosomal protein L19P115Escherichia coli K-12Mutation(s): 0 
Gene Names: rplSb2606JW2587
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Entity ID: 11
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50S ribosomal protein L20Q118Escherichia coli K-12Mutation(s): 0 
Gene Names: rplTpdzAb1716JW1706
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Entity ID: 12
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50S ribosomal protein L21R103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplUb3186JW3153
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Entity ID: 13
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50S ribosomal protein L22S110Escherichia coli K-12Mutation(s): 0 
Gene Names: rplVeryBb3315JW3277
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Entity ID: 14
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50S ribosomal protein L3D209Escherichia coli K-12Mutation(s): 0 
Gene Names: rplCb3320JW3282
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L23T100Escherichia coli K-12Mutation(s): 0 
Gene Names: rplWb3318JW3280
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30259Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmDb3302JW3264
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Entity ID: 17
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50S ribosomal protein L24U104Escherichia coli K-12Mutation(s): 0 
Gene Names: rplXb3309JW3271
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Entity ID: 18
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50S ribosomal protein L25W94Escherichia coli K-12Mutation(s): 0 
Gene Names: rplYb2185JW2173
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
GTPase DerX490Escherichia coli K-12Mutation(s): 0 
Gene Names: derengAyfgKb2511JW5403
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Entity ID: 20
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50S ribosomal protein L4E201Escherichia coli K-12Mutation(s): 0 
Gene Names: rplDeryAb3319JW3281
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Entity ID: 21
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50S ribosomal protein L27Y85Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmAb3185JW3152
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Entity ID: 22
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50S ribosomal protein L32357Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmFb1089JW1075
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Entity ID: 23
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50S ribosomal protein L15234Escherichia coli K-12Mutation(s): 0 
Gene Names: rplAb3984JW3947
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Entity ID: 24
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50S ribosomal protein L34646Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmHrimAssaFb3703JW3680
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Entity ID: 25
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50S ribosomal protein L35765Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmIb1717JW1707
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Entity ID: 26
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50S ribosomal protein L36838Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmJb3299JW3261
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Entity ID: 27
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50S ribosomal protein L2C273Escherichia coli K-12Mutation(s): 0 
Gene Names: rplBb3317JW3279
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Entity ID: 28
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50S ribosomal protein L5F179Escherichia coli K-12Mutation(s): 0 
Gene Names: rplEb3308JW3270
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Entity ID: 29
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50S ribosomal protein L6G177Escherichia coli K-12Mutation(s): 0 
Gene Names: rplFb3305JW3267
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L9H149Escherichia coli K-12Mutation(s): 0 
Gene Names: rplIb4203JW4161
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L11I142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplKrelCb3983JW3946
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Entity ID: 32
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50S ribosomal protein L13J142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplMb3231JW3200
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Entity ID: 1
MoleculeChainsLengthOrganismImage
5S rRNAA117Escherichia coli K-12
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Entity ID: 2
MoleculeChainsLengthOrganismImage
23S rRNAB2903Escherichia coli K-12
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-26
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Data collection, Database references, Structure summary