3BBX

The Hsp15 protein fitted into the low resolution Cryo-EM map of the 50S.nc-tRNA.Hsp15 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 10.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Recycling of Aborted Ribosomal 50S Subunit-Nascent Chain-tRNA Complexes by the Heat Shock Protein Hsp15.

Jiang, L.Schaffitzel, C.Bingel-Erlenmeyer, R.Ban, N.Korber, P.Koning, R.I.de Geus, D.C.Plaisier, J.R.Abrahams, J.P.

(2009) J Mol Biol 386: 1357-1367

  • DOI: https://doi.org/10.1016/j.jmb.2008.10.079
  • Primary Citation of Related Structures:  
    3BBU, 3BBV, 3BBX

  • PubMed Abstract: 

    When heat shock prematurely dissociates a translating bacterial ribosome, its 50S subunit is prevented from reinitiating protein synthesis by tRNA covalently linked to the unfinished protein chain that remains threaded through the exit tunnel. Hsp15, a highly upregulated bacterial heat shock protein, reactivates such dead-end complexes. Here, we show with cryo-electron microscopy reconstructions and functional assays that Hsp15 translocates the tRNA moiety from the A site to the P site of stalled 50S subunits. By stabilizing the tRNA in the P site, Hsp15 indirectly frees up the A site, allowing a release factor to land there and cleave off the tRNA. Such a release factor must be stop codon independent, suggesting a possible role for a poorly characterized class of putative release factors that are upregulated by cellular stress, lack a codon recognition domain and are conserved in eukaryotes.


  • Organizational Affiliation

    Department of Biophysical Structural Chemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25C [auth V]94Escherichia coliMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2D [auth C]273Escherichia coliMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3E [auth D]209Escherichia coliMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4F [auth E]201Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5G [auth F]178Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6H [auth G]176Escherichia coliMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9I [auth H]149Escherichia coliMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13142Escherichia coliMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14123Escherichia coliMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15144Escherichia coliMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16136Escherichia coliMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17127Escherichia coliMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18117Escherichia coliMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19114Escherichia coliMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20117Escherichia coliMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21103Escherichia coliMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22110Escherichia coliMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23100Escherichia coliMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24103Escherichia coliMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27V [auth W]84Escherichia coliMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29W [auth X]63Escherichia coliMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30X [auth Y]58Escherichia coliMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31Y [auth Z]70Escherichia coliMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32Z [auth 0]56Escherichia coliMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33AA [auth 1]54Escherichia coliMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34BA [auth 2]46Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35CA [auth 3]64Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36DA [auth 4]38Escherichia coliMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
5S ribosomal RNA120Escherichia coli
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Entity ID: 2
MoleculeChains LengthOrganismImage
23S ribosomal RNA2,904Escherichia coli
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth B]
AC [auth B]
AD [auth B]
AE [auth Q]
BB [auth B]
AB [auth B],
AC [auth B],
AD [auth B],
AE [auth Q],
BB [auth B],
BC [auth B],
BD [auth B],
BE [auth Q],
CB [auth B],
CC [auth B],
CD [auth B],
CE [auth S],
DB [auth B],
DC [auth B],
DD [auth B],
DE [auth S],
EA [auth B],
EB [auth B],
EC [auth B],
ED [auth B],
EE [auth T],
FA [auth B],
FB [auth B],
FC [auth B],
FD [auth B],
FE [auth T],
GA [auth B],
GB [auth B],
GC [auth B],
GD [auth B],
GE [auth U],
HA [auth B],
HB [auth B],
HC [auth B],
HD [auth B],
HE [auth 2],
IA [auth B],
IB [auth B],
IC [auth B],
ID [auth B],
IE [auth 2],
JA [auth B],
JB [auth B],
JC [auth B],
JD [auth B],
JE [auth 2],
KA [auth B],
KB [auth B],
KC [auth B],
KD [auth B],
LA [auth B],
LB [auth B],
LC [auth B],
LD [auth B],
MA [auth B],
MB [auth B],
MC [auth B],
MD [auth B],
NA [auth B],
NB [auth B],
NC [auth B],
ND [auth B],
OA [auth B],
OB [auth B],
OC [auth B],
OD [auth B],
PA [auth B],
PB [auth B],
PC [auth B],
PD [auth B],
QA [auth B],
QB [auth B],
QC [auth B],
QD [auth B],
RA [auth B],
RB [auth B],
RC [auth B],
RD [auth B],
SA [auth B],
SB [auth B],
SC [auth B],
SD [auth C],
TA [auth B],
TB [auth B],
TC [auth B],
TD [auth E],
UA [auth B],
UB [auth B],
UC [auth B],
UD [auth E],
VA [auth B],
VB [auth B],
VC [auth B],
VD [auth E],
WA [auth B],
WB [auth B],
WC [auth B],
WD [auth L],
XA [auth B],
XB [auth B],
XC [auth B],
XD [auth L],
YA [auth B],
YB [auth B],
YC [auth B],
YD [auth L],
ZA [auth B],
ZB [auth B],
ZC [auth B],
ZD [auth L]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 10.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONEMAN

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-10-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-07-18
    Changes: Data collection
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations, Refinement description