8IP9

Wheat 40S ribosome in complex with a tRNAi


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Boric acid intercepts 80S ribosome migration from AUG-stop by stabilizing eRF1.

Tanaka, M.Yokoyama, T.Saito, H.Nishimoto, M.Tsuda, K.Sotta, N.Shigematsu, H.Shirouzu, M.Iwasaki, S.Ito, T.Fujiwara, T.

(2024) Nat Chem Biol 20: 605-614

  • DOI: https://doi.org/10.1038/s41589-023-01513-0
  • Primary Citation of Related Structures:  
    8IP8, 8IP9, 8IPA, 8IPB

  • PubMed Abstract: 

    In response to environmental changes, cells flexibly and rapidly alter gene expression through translational controls. In plants, the translation of NIP5;1, a boric acid diffusion facilitator, is downregulated in response to an excess amount of boric acid in the environment through upstream open reading frames (uORFs) that consist of only AUG and stop codons. However, the molecular details of how this minimum uORF controls translation of the downstream main ORF in a boric acid-dependent manner have remained unclear. Here, by combining ribosome profiling, translation complex profile sequencing, structural analysis with cryo-electron microscopy and biochemical assays, we show that the 80S ribosome assembled at AUG-stop migrates into the subsequent RNA segment, followed by downstream translation initiation, and that boric acid impedes this process by the stable confinement of eukaryotic release factor 1 on the 80S ribosome on AUG-stop. Our results provide molecular insight into translation regulation by a minimum and environment-responsive uORF.


  • Organizational Affiliation

    Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein eS24B [auth ba]137Triticum aestivumMutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein eS8C [auth ca]225Triticum aestivumMutation(s): 0 
UniProt
Find proteins for A0A3B6AYT7 (Triticum aestivum)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein eS10D [auth da]188Triticum aestivumMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23E [auth ga]142Triticum aestivumMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
RACK1F [auth ha]332Triticum aestivumMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein uS3G [auth ia]227Triticum aestivumMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein eS4H [auth ja]265Triticum aestivumMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein uS7I [auth ka]200Triticum aestivumMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein uS9J [auth la]149Triticum aestivumMutation(s): 0 
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Find proteins for A0A3B6HX49 (Triticum aestivum)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein uS10K [auth ma]127Triticum aestivumMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein uS11L [auth na]151Triticum aestivumMutation(s): 0 
UniProt
Find proteins for A0A3B6SS17 (Triticum aestivum)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein uS13M [auth oa]152Triticum aestivumMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein uS15N [auth pa]151Triticum aestivumMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein eS17O [auth qa]143Triticum aestivumMutation(s): 0 
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Find proteins for A0A3B5YWZ3 (Triticum aestivum)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein eS19P [auth ra]155Triticum aestivumMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein uS19Q [auth sa]154Triticum aestivumMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein eS25R [auth ta]108Triticum aestivumMutation(s): 0 
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Find proteins for W5EP45 (Triticum aestivum)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein eS28S [auth ua]86Triticum aestivumMutation(s): 0 
UniProt
Find proteins for Q7X9K4 (Triticum aestivum)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein uS8T [auth va]129Triticum aestivumMutation(s): 0 
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Find proteins for A0A077RZD1 (Triticum aestivum)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein uS14U [auth wa]56Triticum aestivumMutation(s): 0 
UniProt
Find proteins for A0A3B6LU46 (Triticum aestivum)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein eS27V [auth xa]86Triticum aestivumMutation(s): 0 
UniProt
Find proteins for W5HZ68 (Triticum aestivum)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein eS30W [auth ya]62Triticum aestivumMutation(s): 0 
UniProt
Find proteins for A0A3B6S9M7 (Triticum aestivum)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein uS2X [auth za]308Triticum aestivumMutation(s): 0 
UniProt
Find proteins for W5E2W7 (Triticum aestivum)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein eS1Y [auth bb]263Triticum aestivumMutation(s): 0 
UniProt
Find proteins for A0A3B6IU74 (Triticum aestivum)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein eS21Z [auth cb]82Triticum aestivumMutation(s): 0 
UniProt
Find proteins for W5EL62 (Triticum aestivum)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein eS26AA [auth db]156Triticum aestivumMutation(s): 0 
UniProt
Find proteins for A0A3B6LWE1 (Triticum aestivum)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein uS4BA [auth eb]195Triticum aestivumMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein uS5CA [auth fb]274Triticum aestivumMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein eS6DA [auth gb]250Triticum aestivumMutation(s): 0 
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Find proteins for A0A2X0SLI3 (Triticum aestivum)
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein eS7EA [auth hb]192Triticum aestivumMutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein uS17FA [auth ib]159Triticum aestivumMutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL41GA [auth IB]25Oryza sativaMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
18S ribosomal RNAA [auth aa]1,810Triticum aestivum
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Entity ID: 34
MoleculeChains LengthOrganismImage
mRNAHA [auth al]7Triticum aestivum
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Entity ID: 35
MoleculeChains LengthOrganismImage
tRNAiIA [auth cl]75Triticum aestivum
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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MD [auth wa],
ND [auth db]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth aa]
AC [auth aa]
AD [auth aa]
BB [auth aa]
BC [auth aa]
AB [auth aa],
AC [auth aa],
AD [auth aa],
BB [auth aa],
BC [auth aa],
BD [auth aa],
CB [auth aa],
CC [auth aa],
CD [auth aa],
DB [auth aa],
DC [auth aa],
DD [auth aa],
EB [auth aa],
EC [auth aa],
ED [auth aa],
FB [auth aa],
FC [auth aa],
FD [auth aa],
GB [auth aa],
GC [auth aa],
GD [auth aa],
HB [auth aa],
HC [auth aa],
HD [auth aa],
IB [auth aa],
IC [auth aa],
ID [auth aa],
JA [auth aa],
JB [auth aa],
JC [auth aa],
JD [auth aa],
KA [auth aa],
KB [auth aa],
KC [auth aa],
KD [auth aa],
LA [auth aa],
LB [auth aa],
LC [auth aa],
LD [auth ja],
MA [auth aa],
MB [auth aa],
MC [auth aa],
NA [auth aa],
NB [auth aa],
NC [auth aa],
OA [auth aa],
OB [auth aa],
OC [auth aa],
OD [auth al],
PA [auth aa],
PB [auth aa],
PC [auth aa],
PD [auth cl],
QA [auth aa],
QB [auth aa],
QC [auth aa],
QD [auth cl],
RA [auth aa],
RB [auth aa],
RC [auth aa],
SA [auth aa],
SB [auth aa],
SC [auth aa],
TA [auth aa],
TB [auth aa],
TC [auth aa],
UA [auth aa],
UB [auth aa],
UC [auth aa],
VA [auth aa],
VB [auth aa],
VC [auth aa],
WA [auth aa],
WB [auth aa],
WC [auth aa],
XA [auth aa],
XB [auth aa],
XC [auth aa],
YA [auth aa],
YB [auth aa],
YC [auth aa],
ZA [auth aa],
ZB [auth aa],
ZC [auth aa]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP19H05637

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-21
    Type: Initial release
  • Version 1.1: 2024-05-15
    Changes: Database references