5ADY

Cryo-EM structures of the 50S ribosome subunit bound with HflX


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Hflx is a Ribosome Splitting Factor Rescuing Stalled Ribosomes Under Stress Conditions

Zhang, Y.Mandava, C.S.Cao, W.Li, X.Zhang, D.Li, N.Zhang, Y.Zhang, X.Qin, Y.Mi, K.Lei, J.Sanyal, S.Gao, N.

(2015) Nat Struct Mol Biol 22: 906

  • DOI: https://doi.org/10.1038/nsmb.3103
  • Primary Citation of Related Structures:  
    5ADY

  • PubMed Abstract: 

    Adverse cellular conditions often lead to nonproductive translational stalling and arrest of ribosomes on mRNAs. Here, we used fast kinetics and cryo-EM to characterize Escherichia coli HflX, a GTPase with unknown function. Our data reveal that HflX is a heat shock-induced ribosome-splitting factor capable of dissociating vacant as well as mRNA-associated ribosomes with deacylated tRNA in the peptidyl site. Structural data demonstrate that the N-terminal effector domain of HflX binds to the peptidyl transferase center in a strikingly similar manner as that of the class I release factors and induces dramatic conformational changes in central intersubunit bridges, thus promoting subunit dissociation. Accordingly, loss of HflX results in an increase in stalled ribosomes upon heat shock. These results suggest a primary role of HflX in rescuing translationally arrested ribosomes under stress conditions.


  • Organizational Affiliation

    Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L32A [auth 0]57Escherichia coli K-12Mutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L33B [auth 1]55Escherichia coli K-12Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L34C [auth 2]46Escherichia coli K-12Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L35D [auth 3]65Escherichia coli K-12Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L36E [auth 4]38Escherichia coli K-12Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L1F [auth 5]234Escherichia coli K-12Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
GTPASE HFLXG [auth 6]426Escherichia coli K-12Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L10H [auth 7]165Escherichia coli K-12Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L2K [auth C]273Escherichia coli K-12Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L3L [auth D]209Escherichia coli K-12Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L4M [auth E]201Escherichia coli K-12Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L5N [auth F]179Escherichia coli K-12Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L6O [auth G]177Escherichia coli K-12Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L9P [auth H]149Escherichia coli K-12Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L11Q [auth I]142Escherichia coli K-12Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L13R [auth J]142Escherichia coli K-12Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L14S [auth K]123Escherichia coli K-12Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L15T [auth L]144Escherichia coli K-12Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L16U [auth M]136Escherichia coli K-12Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L17V [auth N]127Escherichia coli K-12Mutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L18W [auth O]117Escherichia coli K-12Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L19X [auth P]115Escherichia coli K-12Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L20Y [auth Q]118Escherichia coli K-12Mutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L21Z [auth R]103Escherichia coli K-12Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L22AA [auth S]110Escherichia coli K-12Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L23BA [auth T]100Escherichia coli K-12Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L24CA [auth U]104Escherichia coli K-12Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L25DA [auth V]94Escherichia coli K-12Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L27EA [auth W]85Escherichia coli K-12Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L28FA [auth X]78Escherichia coli K-12Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L29GA [auth Y]63Escherichia coli K-12Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L30HA [auth Z]59Escherichia coli K-12Mutation(s): 0 
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Entity ID: 9
MoleculeChains LengthOrganismImage
5S RRNAI [auth A]120Escherichia coli K-12
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Entity ID: 10
MoleculeChains LengthOrganismImage
23S RRNAJ [auth B]2,903Escherichia coli K-12
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP

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IA [auth 6]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
MG
Query on MG

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JA [auth 6]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
RECONSTRUCTIONSPIDER

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-14
    Type: Initial release
  • Version 1.1: 2015-10-21
    Changes: Database references
  • Version 1.2: 2015-12-02
    Changes: Database references
  • Version 1.3: 2017-08-02
    Changes: Data collection, Derived calculations
  • Version 1.4: 2018-06-20
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.5: 2018-10-24
    Changes: Advisory, Data collection, Derived calculations