7BL4

in vitro reconstituted 50S-ObgE-GMPPNP-RsfS particle


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Snapshots of native pre-50S ribosomes reveal a biogenesis factor network and evolutionary specialization.

Nikolay, R.Hilal, T.Schmidt, S.Qin, B.Schwefel, D.Vieira-Vieira, C.H.Mielke, T.Burger, J.Loerke, J.Amikura, K.Flugel, T.Ueda, T.Selbach, M.Deuerling, E.Spahn, C.M.T.

(2021) Mol Cell 81: 1200-1215.e9

  • DOI: 10.1016/j.molcel.2021.02.006
  • Primary Citation of Related Structures:  
    7BL3, 7BL4, 7BL2, 7BL5, 7BL6

  • PubMed Abstract: 
  • Ribosome biogenesis is a fundamental multi-step cellular process that culminates in the formation of ribosomal subunits, whose production and modification are regulated by numerous biogenesis factors. In this study, we analyze physiologic prokaryotic ribosome biogenesis by isolating bona fide pre-50S subunits from an Escherichia coli strain with the biogenesis factor ObgE, affinity tagged at its native gene locus ...

    Ribosome biogenesis is a fundamental multi-step cellular process that culminates in the formation of ribosomal subunits, whose production and modification are regulated by numerous biogenesis factors. In this study, we analyze physiologic prokaryotic ribosome biogenesis by isolating bona fide pre-50S subunits from an Escherichia coli strain with the biogenesis factor ObgE, affinity tagged at its native gene locus. Our integrative structural approach reveals a network of interacting biogenesis factors consisting of YjgA, RluD, RsfS, and ObgE on the immature pre-50S subunit. In addition, our study provides mechanistic insight into how the GTPase ObgE, in concert with other biogenesis factors, facilitates the maturation of the 50S functional core and reveals both conserved and divergent evolutionary features of ribosome biogenesis between prokaryotes and eukaryotes.


    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: 1
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L36A [auth g]38Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmJFAZ83_23215
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2B [auth C]273Escherichia coli K-12Mutation(s): 0 
Gene Names: rplBb3317JW3279
UniProt
Find proteins for P60422 (Escherichia coli (strain K12))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3C [auth D]209Escherichia coli K-12Mutation(s): 0 
Gene Names: rplCb3320JW3282
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4D [auth E]201Escherichia coli K-12Mutation(s): 0 
Gene Names: rplDeryAb3319JW3281
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5E [auth F]179Escherichia coli K-12Mutation(s): 0 
Gene Names: rplEb3308JW3270
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6F [auth G]177Escherichia coli K-12Mutation(s): 0 
Gene Names: rplFb3305JW3267
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13G [auth J]142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplMb3231JW3200
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15H [auth L]144Escherichia coli K-12Mutation(s): 0 
Gene Names: rplOb3301JW3263
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L17I [auth N]127Escherichia coli K-12Mutation(s): 0 
Gene Names: rplQb3294JW3256
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18J [auth O]117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplRb3304JW3266
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L20K [auth Q]118Escherichia coli K-12Mutation(s): 0 
Gene Names: rplTpdzAb1716JW1706
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21L [auth R]103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplUb3186JW3153
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L22M [auth S]110Escherichia coli K-12Mutation(s): 0 
Gene Names: rplVeryBb3315JW3277
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L23N [auth T]100Escherichia coli K-12Mutation(s): 0 
Gene Names: rplWb3318JW3280
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24O [auth U]104Escherichia coli K-12Mutation(s): 0 
Gene Names: rplXb3309JW3271
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L25P [auth V]94Escherichia coli K-12Mutation(s): 0 
Gene Names: rplYb2185JW2173
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Entity ID: 17
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50S ribosomal protein L27Q [auth W]85Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmAb3185JW3152
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Entity ID: 18
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50S ribosomal protein L28R [auth X]78Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmBb3637JW3612
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29S [auth Y]63Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmCb3312JW3274
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Entity ID: 20
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50S ribosomal protein L30T [auth Z]59Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmDb3302JW3264
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Entity ID: 21
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50S ribosomal protein L32U [auth 0]57Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmFb1089JW1075
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Entity ID: 22
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50S ribosomal protein L33V [auth 1]55Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmGb3636JW3611
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Entity ID: 23
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50S ribosomal protein L34W [auth 2]46Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmHrimAssaFb3703JW3680
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Entity ID: 24
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50S ribosomal protein L14X [auth K]123Escherichia coli K-12Mutation(s): 0 
Gene Names: rplNb3310JW3272
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Entity ID: 25
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50S ribosomal protein L19Y [auth P]115Escherichia coli K-12Mutation(s): 0 
Gene Names: rplSb2606JW2587
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L16Z [auth M]136Escherichia coli K-12Mutation(s): 0 
Gene Names: rplPb3313JW3275
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L9AA [auth H]149Escherichia coli K-12Mutation(s): 0 
Gene Names: rplIb4203JW4161
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Entity ID: 28
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50S ribosomal protein L31BA [auth d]70Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmEb3936JW3907
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal silencing factor RsfSEA [auth 6]105Escherichia coli K-12Mutation(s): 0 
Gene Names: rsfSrsfAslm3ybeBb0637JW5090
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
GTPase ObgE/CgtAFA [auth 9]390Escherichia coli K-12Mutation(s): 0 
Gene Names: obgEcgtAobgyhbZb3183JW3150
EC: 3.6.5
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L35GA [auth 3]65Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmIb1717JW1707
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Entity ID: 29
MoleculeChainsLengthOrganismImage
23S ribosomal RNACA [auth A]2904Escherichia coli K-12
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Entity ID: 30
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5S ribosomal RNADA [auth B]119Escherichia coli K-12
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 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 Foundation (DFG)GermanyFOR1805
German Research Foundation (DFG)GermanySFB740
Human Frontier Science Program (HFSP)GermanyRPG0008/2014

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-12
    Type: Initial release