6GC7

50S ribosomal subunit assembly intermediate state 1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 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 Visualization of the Formation and Activation of the 50S Ribosomal Subunit during In Vitro Reconstitution.

Nikolay, R.Hilal, T.Qin, B.Mielke, T.Burger, J.Loerke, J.Textoris-Taube, K.Nierhaus, K.H.Spahn, C.M.T.

(2018) Mol Cell 70: 881-893.e3

  • DOI: 10.1016/j.molcel.2018.05.003
  • Primary Citation of Related Structures:  
    6GC0, 6GBZ, 6GC4, 6GC7, 6GC6, 6GC8

  • PubMed Abstract: 
  • The assembly of ribosomal subunits is an essential prerequisite for protein biosynthesis in all domains of life. Although biochemical and biophysical approaches have advanced our understanding of ribosome assembly, our mechanistic comprehension of this process is still limited ...

    The assembly of ribosomal subunits is an essential prerequisite for protein biosynthesis in all domains of life. Although biochemical and biophysical approaches have advanced our understanding of ribosome assembly, our mechanistic comprehension of this process is still limited. Here, we perform an in vitro reconstitution of the Escherichia coli 50S ribosomal subunit. Late reconstitution products were subjected to high-resolution cryo-electron microscopy and multiparticle refinement analysis to reconstruct five distinct precursors of the 50S subunit with 4.3-3.8 Å resolution. These assembly intermediates define a progressive maturation pathway culminating in a late assembly particle, whose structure is more than 96% identical to a mature 50S subunit. Our structures monitor the formation and stabilization of structural elements in a nascent particle in unprecedented detail and identify the maturation of the rRNA-based peptidyl transferase center as the final critical step along the 50S assembly pathway.


    Organizational Affiliation

    Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany. Electronic address: christian.spahn@charite.de.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3B [auth D]209Escherichia coli K-12Mutation(s): 0 
Gene Names: rplCb3320JW3282
UniProt
Find proteins for P60438 (Escherichia coli (strain K12))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4C [auth E]201Escherichia coli K-12Mutation(s): 0 
Gene Names: rplDeryAb3319JW3281
UniProt
Find proteins for P60723 (Escherichia coli (strain K12))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13D [auth J]142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplMb3231JW3200
UniProt
Find proteins for P0AA10 (Escherichia coli (strain K12))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14E [auth K]122Escherichia coli K-12Mutation(s): 0 
Gene Names: rplNb3310JW3272
UniProt
Find proteins for P0ADY3 (Escherichia coli (strain K12))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15F [auth L]143Escherichia coli K-12Mutation(s): 0 
Gene Names: rplOb3301JW3263
UniProt
Find proteins for P02413 (Escherichia coli (strain K12))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L17G [auth N]120Escherichia coli K-12Mutation(s): 0 
Gene Names: rplQb3294JW3256
UniProt
Find proteins for P0AG44 (Escherichia coli (strain K12))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19H [auth P]114Escherichia coli K-12Mutation(s): 0 
Gene Names: rplSb2606JW2587
UniProt
Find proteins for P0A7K6 (Escherichia coli (strain K12))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L20I [auth Q]117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplTpdzAb1716JW1706
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21J [auth R]103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplUb3186JW3153
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Find proteins for P0AG48 (Escherichia coli (strain K12))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L22K [auth S]110Escherichia coli K-12Mutation(s): 0 
Gene Names: rplVeryBb3315JW3277
UniProt
Find proteins for P61175 (Escherichia coli (strain K12))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L23L [auth T]93Escherichia coli K-12Mutation(s): 0 
Gene Names: rplWb3318JW3280
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24M [auth U]102Escherichia coli K-12Mutation(s): 0 
Gene Names: rplXb3309JW3271
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Find proteins for P60624 (Escherichia coli (strain K12))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29N [auth Y]63Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmCb3312JW3274
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Find proteins for P0A7M6 (Escherichia coli (strain K12))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32O [auth 0]56Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmFb1089JW1075
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Find proteins for P0A7N4 (Escherichia coli (strain K12))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34P [auth 2]46Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmHrimAssaFb3703JW3680
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Find proteins for P0A7P5 (Escherichia coli (strain K12))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30Q [auth Z]58Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmDb3302JW3264
UniProt
Find proteins for P0AG51 (Escherichia coli (strain K12))
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Entity ID: 1
MoleculeChainsLengthOrganismImage
23S ribosomal RNAA2904Escherichia coli K-12
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyFOR1805
German Research FoundationGermanySFB740

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Other