4XEJ

IRES bound to bacterial Ribosome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.246 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

Initiation of translation in bacteria by a structured eukaryotic IRES RNA.

Colussi, T.M.Costantino, D.A.Zhu, J.Donohue, J.P.Korostelev, A.A.Jaafar, Z.A.Plank, T.D.Noller, H.F.Kieft, J.S.

(2015) Nature 519: 110-113

  • DOI: https://doi.org/10.1038/nature14219
  • Primary Citation of Related Structures:  
    4XEJ

  • PubMed Abstract: 

    The central dogma of gene expression (DNA to RNA to protein) is universal, but in different domains of life there are fundamental mechanistic differences within this pathway. For example, the canonical molecular signals used to initiate protein synthesis in bacteria and eukaryotes are mutually exclusive. However, the core structures and conformational dynamics of ribosomes that are responsible for the translation steps that take place after initiation are ancient and conserved across the domains of life. We wanted to explore whether an undiscovered RNA-based signal might be able to use these conserved features, bypassing mechanisms specific to each domain of life, and initiate protein synthesis in both bacteria and eukaryotes. Although structured internal ribosome entry site (IRES) RNAs can manipulate ribosomes to initiate translation in eukaryotic cells, an analogous RNA structure-based mechanism has not been observed in bacteria. Here we report our discovery that a eukaryotic viral IRES can initiate translation in live bacteria. We solved the crystal structure of this IRES bound to a bacterial ribosome to 3.8 Å resolution, revealing that despite differences between bacterial and eukaryotic ribosomes this IRES binds directly to both and occupies the space normally used by transfer RNAs. Initiation in both bacteria and eukaryotes depends on the structure of the IRES RNA, but in bacteria this RNA uses a different mechanism that includes a form of ribosome repositioning after initial recruitment. This IRES RNA bridges billions of years of evolutionary divergence and provides an example of an RNA structure-based translation initiation signal capable of operating in two domains of life.


  • Organizational Affiliation

    1] Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA [2] Howard Hughes Medical Institute, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2A [auth AL02],
WA [auth BL02]
271Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3B [auth AL03],
XA [auth BL03]
204Thermus thermophilus HB27Mutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4C [auth AL04],
YA [auth BL04]
202Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5D [auth AL05],
ZA [auth BL05]
181Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6AB [auth BL06],
E [auth AL06]
159Thermus thermophilus HB27Mutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9BB [auth BL09],
F [auth AL09]
145Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11CB [auth BL11],
G [auth AL11]
147Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13DB [auth BL13],
H [auth AL13]
137Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14EB [auth BL14],
I [auth AL14]
122Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15FB [auth BL15],
J [auth AL15]
146Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16GB [auth BL16],
K [auth AL16]
134Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17HB [auth BL17],
L [auth AL17]
117Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18IB [auth BL18],
M [auth AL18]
98Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19JB [auth BL19],
N [auth AL19]
137Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20KB [auth BL20],
O [auth AL20]
117Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21LB [auth BL21],
P [auth AL21]
101Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22MB [auth BL22],
Q [auth AL22]
112Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23NB [auth BL23],
R [auth AL23]
92Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24OB [auth BL24],
S [auth AL24]
100Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25PB [auth BL25],
T [auth AL25]
187Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27QB [auth BL27],
U [auth AL27]
76Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28RB [auth BL28],
V [auth AL28]
88Thermus thermophilus HB27Mutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29SB [auth BL29],
W [auth AL29]
62Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30TB [auth BL30],
X [auth AL30]
59Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32UB [auth BL32],
Y [auth AL32]
52Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33VB [auth BL33],
Z [auth AL33]
44Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34AA [auth AL34],
WB [auth BL34]
48Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35BA [auth AL35],
XB [auth BL35]
63Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2CA [auth AS02],
YB [auth BS02]
234Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3DA [auth AS03],
ZB [auth BS03]
206Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4AC [auth BS04],
EA [auth AS04]
208Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5BC [auth BS05],
FA [auth AS05]
151Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6CC [auth BS06],
GA [auth AS06]
101Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7DC [auth BS07],
HA [auth AS07]
155Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8EC [auth BS08],
IA [auth AS08]
138Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9FC [auth BS09],
JA [auth AS09]
127Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10GC [auth BS10],
KA [auth AS10]
98Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11HC [auth BS11],
LA [auth AS11]
114Thermus thermophilus HB27Mutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12IC [auth BS12],
MA [auth AS12]
122Thermus thermophilus HB27Mutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13JC [auth BS13],
NA [auth AS13]
117Thermus thermophilus HB27Mutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14KC [auth BS14],
OA [auth AS14]
60Thermus thermophilus HB27Mutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15LC [auth BS15],
PA [auth AS15]
88Thermus thermophilus HB27Mutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16MC [auth BS16],
QA [auth AS16]
83Thermus thermophilus HB27Mutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17NC [auth BS17],
RA [auth AS17]
99Thermus thermophilus HB27Mutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18OC [auth BS18],
SA [auth AS18]
70Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19PC [auth BS19],
TA [auth AS19]
78Thermus thermophilus HB27Mutation(s): 0 
UniProt
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20QC [auth BS20],
UA [auth AS20]
99Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein ThxRC [auth BTHX],
VA [auth ATHX]
24Thermus thermophilus HB27Mutation(s): 0 
UniProt
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31SC [auth AL31],
TC [auth BL31]
30Thermus thermophilus HB27Mutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains LengthOrganismImage
16S ribosomal RNAUC [auth A16S],
XC [auth B16S]
1,506Thermus thermophilus HB27
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Entity ID: 51
MoleculeChains LengthOrganismImage
23S ribosomal RNAVC [auth A23S],
YC [auth B23S]
2,879Thermus thermophilus HB27
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Entity ID: 52
MoleculeChains LengthOrganismImage
5S ribosomal RNAWC [auth A5S],
ZC [auth B5S]
119Thermus thermophilus HB27
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Entity ID: 53
MoleculeChains LengthOrganismImage
IRES RNAAD [auth AIRE],
BD [auth BIRE]
196Plautia stali intestine virus
Sequence Annotations
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.246 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 209.05α = 90
b = 447.22β = 90
c = 608.96γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-25
    Type: Initial release
  • Version 1.1: 2015-03-18
    Changes: Database references
  • Version 1.2: 2015-08-26
    Changes: Data collection
  • Version 1.3: 2016-07-06
    Changes: Data collection
  • Version 1.4: 2016-09-28
    Changes: Data collection
  • Version 1.5: 2017-09-27
    Changes: Author supporting evidence, Derived calculations, Structure summary
  • Version 1.6: 2023-09-27
    Changes: Data collection, Database references, Refinement description