2YKR

30S ribosomal subunit with RsgA bound in the presence of GMPPNP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.80 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

Structural Basis for the Function of a Small Gtpase Rsga on the 30S Ribosomal Subunit Maturation Revealed by Cryoelectron Microscopy.

Guo, Q.Yuan, Y.Xu, Y.Feng, B.Liu, L.Chen, K.Sun, M.Yang, Z.Lei, J.Gao, N.

(2011) Proc Natl Acad Sci U S A 108: 13100

  • DOI: 10.1073/pnas.1104645108
  • Primary Citation of Related Structures:  
    2YKR

  • PubMed Abstract: 
  • The bacterial RsgA, a circularly permutated GTPase, whose GTPase activity is dependent on the 30S ribosomal subunit, is a late-stage ribosome biogenesis factor involved in the 30S subunit maturation. The role of RsgA is to release another 30S biogene ...

    The bacterial RsgA, a circularly permutated GTPase, whose GTPase activity is dependent on the 30S ribosomal subunit, is a late-stage ribosome biogenesis factor involved in the 30S subunit maturation. The role of RsgA is to release another 30S biogenesis factor, RbfA, from the mature 30S subunit in a GTP-dependent manner. Using cryoelectron microscopy, we have determined the structure of the 30S subunit bound with RsgA in the presence of GMPPNP at subnanometer resolution. In the structure, RsgA binds to the central part of the 30S subunit, close to the decoding center, in a position that is incompatible with multiple biogenesis factors, all three translation initiation factors, as well as A-, P-site tRNAs and the 50S subunit. Further structural analysis not only provides a structural model for the RsgA-dependent release of RbfA from the nascent 30S subunit, but also indicates RsgA's role in the ribosomal protein assembly, to promote some tertiary binding protein incorporation. Moreover, together with available biochemical and genetic data, our results suggest that RsgA might be a general checkpoint protein in the late stage of the 30S subunit biogenesis, whose function is not only to release biogenesis factors (e.g., RbfA) from the nascent 30S subunit, but also to block the association of initiation factors to the premature 30S subunit.


    Organizational Affiliation

    Ministry of Education Protein Science Laboratory, Center for Structural Biology, School of Life Sciences, and Department of Chemistry, Tsinghua University, Beijing 100084, China.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S2B218Escherichia coli DH5[alpha]Mutation(s): 0 
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Entity ID: 3
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30S RIBOSOMAL PROTEIN S3C206Escherichia coli DH5[alpha]Mutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S4D205Escherichia coli DH5[alpha]Mutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S5E150Escherichia coli DH5[alpha]Mutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S6F100Escherichia coli DH5[alpha]Mutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S7G151Escherichia coli DH5[alpha]Mutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S8H129Escherichia coli DH5[alpha]Mutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S9I127Escherichia coli DH5[alpha]Mutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S10J98Escherichia coli DH5[alpha]Mutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S11K117Escherichia coli DH5[alpha]Mutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S12L123Escherichia coli DH5[alpha]Mutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S13M114Escherichia coli DH5[alpha]Mutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S14N100Escherichia coli DH5[alpha]Mutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S15O88Escherichia coli DH5[alpha]Mutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S16P82Escherichia coli DH5[alpha]Mutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S17Q80Escherichia coli DH5[alpha]Mutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S18R55Escherichia coli DH5[alpha]Mutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S19S79Escherichia coli DH5[alpha]Mutation(s): 0 
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Entity ID: 20
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30S RIBOSOMAL PROTEIN S20T85Escherichia coli DH5[alpha]Mutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S21U51Escherichia coli DH5[alpha]Mutation(s): 0 
Find proteins for P68679 (Escherichia coli (strain K12))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
PUTATIVE RIBOSOME BIOGENESIS GTPASE RSGAW350Escherichia coli DH5[alpha]Mutation(s): 0 
EC: 3.6.1
Find proteins for P39286 (Escherichia coli (strain K12))
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S RRNAA1533Escherichia coli DH5[alpha]
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-08-24
    Type: Initial release
  • Version 1.1: 2013-03-20
    Changes: Other, Refinement description
  • Version 1.2: 2017-08-30
    Changes: Data collection, Derived calculations, Refinement description, Structure summary