RCSB PDB - 4V95: Crystal structure of YAEJ bound to the 70S ribosome

 4V95

Crystal structure of YAEJ bound to the 70S ribosome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural basis for the rescue of stalled ribosomes: structure of YaeJ bound to the ribosome.

Gagnon, M.G.Seetharaman, S.V.Bulkley, D.Steitz, T.A.

(2012) Science 335: 1370-1372

  • DOI: https://doi.org/10.1126/science.1217443
  • Primary Citation of Related Structures:  
    4V95

  • PubMed Abstract: 

    In bacteria, the hybrid transfer-messenger RNA (tmRNA) rescues ribosomes stalled on defective messenger RNAs (mRNAs). However, certain gram-negative bacteria have evolved proteins that are capable of rescuing stalled ribosomes in a tmRNA-independent manner. Here, we report a 3.2 angstrom-resolution crystal structure of the rescue factor YaeJ bound to the Thermus thermophilus 70S ribosome in complex with the initiator tRNA(i)(fMet) and a short mRNA. The structure reveals that the C-terminal tail of YaeJ functions as a sensor to discriminate between stalled and actively translating ribosomes by binding in the mRNA entry channel downstream of the A site between the head and shoulder of the 30S subunit. This allows the N-terminal globular domain to sample different conformations, so that its conserved GGQ motif is optimally positioned to catalyze the hydrolysis of peptidyl-tRNA. This structure gives insights into the mechanism of YaeJ function and provides a basis for understanding how it rescues stalled ribosomes.


  • Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal Protein S2B [auth AB],
EB [auth CB]
256Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal Protein S3C [auth AC],
FB [auth CC]
239Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal Protein S4D [auth AD],
GB [auth CD]
209Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal Protein S5E [auth AE],
HB [auth CE]
162Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal Protein S6F [auth AF],
IB [auth CF]
101Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal Protein S7G [auth AG],
JB [auth CG]
156Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal Protein S8H [auth AH],
KB [auth CH]
138Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal Protein S9I [auth AI],
LB [auth CI]
128Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal Protein S10J [auth AJ],
MB [auth CJ]
105Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal Protein S11K [auth AK],
NB [auth CK]
129Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal Protein S12L [auth AL],
OB [auth CL]
132Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal Protein S13M [auth AM],
PB [auth CM]
126Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal Protein S14N [auth AN],
QB [auth CN]
61Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal Protein S15O [auth AO],
RB [auth CO]
89Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal Protein S16P [auth AP],
SB [auth CP]
88Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal Protein S17Q [auth AQ],
TB [auth CQ]
105Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal Protein S18R [auth AR],
UB [auth CR]
88Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal Protein S19S [auth AS],
VB [auth CS]
93Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal Protein S20T [auth AT],
WB [auth CT]
106Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal Protein THXU [auth AU],
XB [auth CU]
27Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
YAEJV [auth AY]140Escherichia coli K-12Mutation(s): 0 
Gene Names: yaeJ
EC: 3.1.1.29
UniProt
Find proteins for P40711 (Escherichia coli (strain K12))
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L2AA [auth BD],
CC [auth DD]
276Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L3BA [auth BE],
DC [auth DE]
206Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L4CA [auth BF],
EC [auth DF]
210Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L5DA [auth BG],
FC [auth DG]
182Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L6EA [auth BH],
GC [auth DH]
180Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L9FA [auth BI],
HC [auth DI]
148Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L13GA [auth BN],
IC [auth DN]
140Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L14HA [auth BO],
JC [auth DO]
122Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L15IA [auth BP],
KC [auth DP]
150Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L16JA [auth BQ],
LC [auth DQ]
141Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L17KA [auth BR],
MC [auth DR]
118Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q9Z9H5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L18LA [auth BS],
NC [auth DS]
112Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L19MA [auth BT],
OC [auth DT]
146Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L20NA [auth BU],
PC [auth DU]
118Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L21OA [auth BV],
QC [auth DV]
101Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L22PA [auth BW],
RC [auth DW]
113Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L23QA [auth BX],
SC [auth DX]
96Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L24RA [auth BY],
TC [auth DY]
110Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L25SA [auth BZ],
UC [auth DZ]
206Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L27TA [auth B0],
VC [auth D0]
85Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L28UA [auth B1],
WC [auth D1]
98Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P60494 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L29VA [auth B2],
XC [auth D2]
72Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SHP6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L30WA [auth B3],
YC [auth D3]
60Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L31XA [auth B4],
ZC [auth D4]
71Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SJE1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L32AD [auth D5],
YA [auth B5]
60Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P80339 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L33BD [auth D6],
ZA [auth B6]
54Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P35871 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L34AB [auth B7],
CD [auth D7]
49Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L35BB [auth B8],
DD [auth D8]
65Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SKU1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L36CB [auth B9],
ED [auth D9]
37Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SHR2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
APC [auth DY]
EMB [auth CD]
GMB [auth CN]
GPC [auth D4]
HDB [auth B4]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AAA [auth BA]
AAB [auth BA]
AAC [auth DA]
ABA [auth BA]
ABB [auth BB]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 209.96α = 90
b = 448.86β = 90
c = 624.2γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
PHENIXmodel building
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 1.2: 2018-06-27
    Changes: Data collection, Database references, Derived calculations, Source and taxonomy
  • Version 1.3: 2018-07-11
    Changes: Data collection, Source and taxonomy
  • Version 1.4: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Structure summary