7BL5

pre-50S-ObgE particle


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 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:  
    7BL2, 7BL3, 7BL4, 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 L2A [auth C]273Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 2
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50S ribosomal protein L3B [auth D]209Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 3
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50S ribosomal protein L4C [auth E]201Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6D [auth G]177Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13E [auth J]142Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 6
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50S ribosomal protein L15F [auth L]144Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 7
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50S ribosomal protein L17G [auth N]127Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 8
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50S ribosomal protein L18H [auth O]117Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 9
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50S ribosomal protein L20I [auth Q]118Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 10
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50S ribosomal protein L21J [auth R]103Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 11
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50S ribosomal protein L22K [auth S]110Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 12
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50S ribosomal protein L23L [auth T]100Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 13
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50S ribosomal protein L24M [auth U]104Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 14
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50S ribosomal protein L25N [auth V]94Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 15
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50S ribosomal protein L27O [auth W]85Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 16
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50S ribosomal protein L28P [auth X]78Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 17
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50S ribosomal protein L29Q [auth Y]63Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 18
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50S ribosomal protein L30R [auth Z]59Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 19
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50S ribosomal protein L32S [auth 0]57Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 20
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50S ribosomal protein L33T [auth 1]55Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 21
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50S ribosomal protein L34U [auth 2]46Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 23
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50S ribosomal protein L11W [auth I]142Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 24
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50S ribosomal protein L14X [auth K]123Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 25
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50S ribosomal protein L19Y [auth P]115Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal silencing factor RsfSZ [auth 6]105Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal large subunit pseudouridine synthase DAA [auth 7]326Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
EC: 5.4.99.23
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
UPF0307 protein YjgABA [auth 8]183Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
GTPase ObgE/CgtACA [auth 9]390Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
EC: 3.6.5
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L16DA [auth M]136Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L9FA [auth H]149Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L10GA [auth e]165Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5HA [auth F]179Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 35
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50S ribosomal protein L31IA [auth b]70Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 22
MoleculeChainsLengthOrganismImage
5S ribosomal RNAV [auth B]120Escherichia coli str. K-12 substr. MG1655
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Entity ID: 31
MoleculeChainsLengthOrganismImage
23S ribosomal RNAEA [auth A]2,919Escherichia coli str. K-12 substr. MG1655
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

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JA [auth 9]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
ZN
Query on ZN

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MA [auth b]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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KA [auth 9],
LA [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 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 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