7BV8

Mature 50S ribosomal subunit from RrmJ knock out E.coli strain


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.14 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Loss of a single methylation in 23S rRNA delays 50S assembly at multiple late stages and impairs translation initiation and elongation.

Wang, W.Li, W.Ge, X.Yan, K.Mandava, C.S.Sanyal, S.Gao, N.

(2020) Proc Natl Acad Sci U S A 117: 15609-15619

  • DOI: 10.1073/pnas.1914323117
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Ribosome biogenesis is a complex process, and dozens of factors are required to facilitate and regulate the subunit assembly in bacteria. The 2'-O-methylation of U2552 in 23S rRNA by methyltransferase RrmJ is a crucial step in late-stage assembly of ...

    Ribosome biogenesis is a complex process, and dozens of factors are required to facilitate and regulate the subunit assembly in bacteria. The 2'-O-methylation of U2552 in 23S rRNA by methyltransferase RrmJ is a crucial step in late-stage assembly of the 50S subunit. Its absence results in severe growth defect and marked accumulation of pre50S assembly intermediates. In the present work, we employed cryoelectron microscopy to characterize a set of late-stage pre50S particles isolated from an Escherichia coli Δ rrmJ strain. These assembly intermediates (solved at 3.2 to 3.8 Å resolution) define a collection of late-stage particles on a progressive assembly pathway. Apart from the absence of L16, L35, and L36, major structural differences between these intermediates and the mature 50S subunit are clustered near the peptidyl transferase center, such as H38, H68-71, and H89-93. In addition, the ribosomal A-loop of the mature 50S subunit from Δ rrmJ strain displays large local flexibility on nucleotides next to unmethylated U2552. Fast kinetics-based biochemical assays demonstrate that the Δ rrmJ 50S subunit is only 50% active and two times slower than the WT 50S subunit in rapid subunit association. While the Δ rrmJ 70S ribosomes show no defect in peptide bond formation, peptide release, and ribosome recycling, they translocate with 20% slower rate than the WT ribosomes in each round of elongation. These defects amplify during synthesis of the full-length proteins and cause overall defect in protein synthesis. In conclusion, our data reveal the molecular roles of U2552 methylation in both ribosome biogenesis and protein translation.


    Organizational Affiliation

    State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, 100871 Beijing, China; suparna.sanyal@icm.uu.se gaon@pku.edu.cn.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2C273Escherichia coli K-12Mutation(s): 0 
Gene Names: rplBb3317JW3279
Find proteins for P60422 (Escherichia coli (strain K12))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6G177Escherichia coli K-12Mutation(s): 0 
Gene Names: rplFb3305JW3267
Find proteins for P0AG55 (Escherichia coli (strain K12))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10I165Escherichia coli K-12Mutation(s): 0 
Gene Names: rplJb3985JW3948
Find proteins for P0A7J3 (Escherichia coli (strain K12))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11J142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplKrelCb3983JW3946
Find proteins for P0A7J7 (Escherichia coli (strain K12))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14L123Escherichia coli K-12Mutation(s): 0 
Gene Names: rplNb3310JW3272
Find proteins for P0ADY3 (Escherichia coli (strain K12))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15M144Escherichia coli K-12Mutation(s): 0 
Gene Names: rplOb3301JW3263
Find proteins for P02413 (Escherichia coli (strain K12))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19Q115Escherichia coli K-12Mutation(s): 0 
Gene Names: rplSb2606JW2587
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20R118Escherichia coli K-12Mutation(s): 0 
Gene Names: rplTpdzAb1716JW1706
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22T110Escherichia coli K-12Mutation(s): 0 
Gene Names: rplVeryBb3315JW3277
Find proteins for P61175 (Escherichia coli (strain K12))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34d46Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmHrimAssaFb3703JW3680
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13K142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplMb3231JW3200
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16N136Escherichia coli K-12Mutation(s): 0 
Gene Names: rplPb3313JW3275
Find proteins for P0ADY7 (Escherichia coli (strain K12))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17O127Escherichia coli K-12Mutation(s): 0 
Gene Names: rplQb3294JW3256
Find proteins for P0AG44 (Escherichia coli (strain K12))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18P117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplRb3304JW3266
Find proteins for P0C018 (Escherichia coli (strain K12))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21S103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplUb3186JW3153
Find proteins for P0AG48 (Escherichia coli (strain K12))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23U100Escherichia coli K-12Mutation(s): 0 
Gene Names: rplWb3318JW3280
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24V104Escherichia coli K-12Mutation(s): 0 
Gene Names: rplXb3309JW3271
Find proteins for P60624 (Escherichia coli (strain K12))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25W94Escherichia coli K-12Mutation(s): 0 
Gene Names: rplYb2185JW2173
Find proteins for P68919 (Escherichia coli (strain K12))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27X85Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmAb3185JW3152
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28Y78Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmBb3637JW3612
Find proteins for P0A7M2 (Escherichia coli (strain K12))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29Z63Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmCb3312JW3274
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30a59Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmDb3302JW3264
Find proteins for P0AG51 (Escherichia coli (strain K12))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32b57Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmFb1089JW1075
Find proteins for P0A7N4 (Escherichia coli (strain K12))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33c55Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmGb3636JW3611
Find proteins for P0A7N9 (Escherichia coli (strain K12))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35e65Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmIb1717JW1707
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36f38Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmJb3299JW3261
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3D209Escherichia coli K-12Mutation(s): 0 
Gene Names: rplCb3320JW3282
Find proteins for P60438 (Escherichia coli (strain K12))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4E201Escherichia coli K-12Mutation(s): 0 
Gene Names: rplDeryAb3319JW3281
Find proteins for P60723 (Escherichia coli (strain K12))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5F179Escherichia coli K-12Mutation(s): 0 
Gene Names: rplEb3308JW3270
Find proteins for P62399 (Escherichia coli (strain K12))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9H149Escherichia coli K-12Mutation(s): 0 
Gene Names: rplIb4203JW4161
Find proteins for P0A7R1 (Escherichia coli (strain K12))
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Entity ID: 1
MoleculeChainsLengthOrganism
23S rRNAA2903Escherichia coli K-12

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Entity ID: 2
MoleculeChainsLengthOrganism
5S rRNAB120Escherichia coli K-12
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.14 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31630087
Ministry of Science and Technology (MoST, China)China2016YFA0500700
Other governmentChinaChina Postdoctoral Science Foundation 1131000065
Other governmentChinaShenzhen Science and Technology Innovation Committee (JCYJ20180302174213122)

Revision History 

  • Version 1.0: 2020-07-01
    Type: Initial release
  • Version 1.1: 2020-07-08
    Changes: Database references
  • Version 1.2: 2020-07-22
    Changes: Database references