8JIW

Atomic structure of wheat ribosome reveals unique features of the plant ribosomes


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.88 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Cryo-EM structure of wheat ribosome reveals unique features of the plant ribosomes.

Mishra, R.K.Sharma, P.Khaja, F.T.Uday, A.B.Hussain, T.

(2024) Structure 

  • DOI: https://doi.org/10.1016/j.str.2024.02.006
  • Primary Citation of Related Structures:  
    8JIV, 8JIW

  • PubMed Abstract: 

    Plants being sessile organisms exhibit unique features in ribosomes, which might aid in rapid gene expression and regulation in response to varying environmental conditions. Here, we present high-resolution structures of the 60S and 80S ribosomes from wheat, a monocot staple crop plant (Triticum aestivum). While plant ribosomes have unique plant-specific rRNA modification (Cm1847) in the peptide exit tunnel (PET), the zinc-finger motif in eL34 is absent, and uL4 is extended, making an exclusive interaction network. We note differences in the eL15-helix 11 (25S) interaction, eL6-ES7 assembly, and certain rRNA chemical modifications between monocot and dicot ribosomes. In eukaryotes, we observe highly conserved rRNA modification (Gm75) in 5.8S rRNA and a flipped base (G1506) in PET. These features are likely involved in sensing or stabilizing nascent chain. Finally, we discuss the importance of the universal conservation of three consecutive rRNA modifications in all ribosomes for their interaction with A-site aminoacyl-tRNA.


  • Organizational Affiliation

    Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru PIN-560012, India.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein SAB [auth BA]304Triticum aestivumMutation(s): 0 
UniProt
Find proteins for A0A3B6AV88 (Triticum aestivum)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aC [auth BB]263Triticum aestivumMutation(s): 0 
UniProt
Find proteins for A0A3B6IU74 (Triticum aestivum)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
S5 DRBM domain-containing proteinD [auth BC]279Triticum aestivumMutation(s): 0 
UniProt
Find proteins for A0A3B6N0N5 (Triticum aestivum)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4E [auth BE]265Triticum aestivumMutation(s): 0 
UniProt
Find proteins for A0A1D5SLI4 (Triticum aestivum)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6F [auth BG]250Triticum aestivumMutation(s): 0 
UniProt
Find proteins for W5C8N6 (Triticum aestivum)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7G [auth BH]192Triticum aestivumMutation(s): 0 
UniProt
Find proteins for Q5I7K2 (Triticum aestivum)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8H [auth BI]224Triticum aestivumMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4, chloroplasticI [auth BJ]195Triticum aestivumMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11 N-terminal domain-containing proteinJ [auth BL]161Triticum aestivumMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S13/S15 N-terminal domain-containing proteinK [auth BN]151Triticum aestivumMutation(s): 0 
UniProt
Find proteins for W5I035 (Triticum aestivum)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14L [auth BO]151Triticum aestivumMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17M [auth BR]143Triticum aestivumMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21N [auth BV]82Triticum aestivumMutation(s): 0 
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Find proteins for W5EL62 (Triticum aestivum)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8, chloroplasticO [auth BW]130Triticum aestivumMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23P [auth BX]142Triticum aestivumMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24Q [auth BY]137Triticum aestivumMutation(s): 0 
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Find proteins for A0A3B6PK86 (Triticum aestivum)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26R [auth Ba]139Triticum aestivumMutation(s): 0 
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Find proteins for A0A3B6KQB8 (Triticum aestivum)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27S [auth Bb]86Triticum aestivumMutation(s): 0 
UniProt
Find proteins for W5HZ68 (Triticum aestivum)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30T [auth Be]62Triticum aestivumMutation(s): 0 
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Find proteins for A0A3B6S9M7 (Triticum aestivum)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41U [auth Cn]25Triticum aestivumMutation(s): 0 
UniProt
Find proteins for P62124 (Hordeum vulgare)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
KH type-2 domain-containing proteinV [auth BD]227Triticum aestivumMutation(s): 0 
UniProt
Find proteins for W5I1R7 (Triticum aestivum)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S7 domain-containing proteinW [auth BF]200Triticum aestivumMutation(s): 0 
UniProt
Find proteins for W5D067 (Triticum aestivum)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Plectin/S10 N-terminal domain-containing proteinX [auth BK]188Triticum aestivumMutation(s): 0 
UniProt
Find proteins for W5AUH7 (Triticum aestivum)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15Y [auth BP]153Triticum aestivumMutation(s): 0 
UniProt
Find proteins for A0A3B6LV48 (Triticum aestivum)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16Z [auth BQ]149Triticum aestivumMutation(s): 0 
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Find proteins for A0A3B6HX49 (Triticum aestivum)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18AA [auth BS]152Triticum aestivumMutation(s): 0 
UniProt
Find proteins for A0A3B6TWW5 (Triticum aestivum)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19BA [auth BT]155Triticum aestivumMutation(s): 0 
UniProt
Find proteins for W5FWF5 (Triticum aestivum)
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S10 domain-containing proteinCA [auth BU]117Triticum aestivumMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28DA [auth Bc]65Triticum aestivumMutation(s): 0 
UniProt
Find proteins for W5E8X2 (Triticum aestivum)
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29EA [auth Bd]56Triticum aestivumMutation(s): 0 
UniProt
Find proteins for A0A1D5ZKM9 (Triticum aestivum)
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinaseFA [auth Bg]335Triticum aestivumMutation(s): 0 
UniProt
Find proteins for A0A3B5Z4Q0 (Triticum aestivum)
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25GA [auth BZ]98Triticum aestivumMutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
18S rRNAA [auth Ad]1,811Triticum aestivum
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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PD [auth Bd]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

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GD [auth Ad]
HA [auth Ad]
HD [auth Ad]
ID [auth Ad]
JA [auth Ad]
GD [auth Ad],
HA [auth Ad],
HD [auth Ad],
ID [auth Ad],
JA [auth Ad],
JD [auth Ad],
KA [auth Ad],
KD [auth Ad],
LA [auth Ad],
LD [auth Ad],
MA [auth Ad],
NA [auth Ad],
ND [auth BT],
OA [auth Ad],
OD [auth Bd],
PA [auth Ad]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth Ad]
AC [auth Ad]
AD [auth Ad]
BB [auth Ad]
BC [auth Ad]
AB [auth Ad],
AC [auth Ad],
AD [auth Ad],
BB [auth Ad],
BC [auth Ad],
BD [auth Ad],
CB [auth Ad],
CC [auth Ad],
CD [auth Ad],
DB [auth Ad],
DC [auth Ad],
DD [auth Ad],
EB [auth Ad],
EC [auth Ad],
ED [auth Ad],
FB [auth Ad],
FC [auth Ad],
FD [auth Ad],
GB [auth Ad],
GC [auth Ad],
HB [auth Ad],
HC [auth Ad],
IA [auth Ad],
IB [auth Ad],
IC [auth Ad],
JB [auth Ad],
JC [auth Ad],
KB [auth Ad],
KC [auth Ad],
LB [auth Ad],
LC [auth Ad],
MB [auth Ad],
MC [auth Ad],
MD [auth BS],
NB [auth Ad],
NC [auth Ad],
OB [auth Ad],
OC [auth Ad],
PB [auth Ad],
PC [auth Ad],
QA [auth Ad],
QB [auth Ad],
QC [auth Ad],
RA [auth Ad],
RB [auth Ad],
RC [auth Ad],
SA [auth Ad],
SB [auth Ad],
SC [auth Ad],
TA [auth Ad],
TB [auth Ad],
TC [auth Ad],
UA [auth Ad],
UB [auth Ad],
UC [auth Ad],
VA [auth Ad],
VB [auth Ad],
VC [auth Ad],
WA [auth Ad],
WB [auth Ad],
WC [auth Ad],
XA [auth Ad],
XB [auth Ad],
XC [auth Ad],
YA [auth Ad],
YB [auth Ad],
YC [auth Ad],
ZA [auth Ad],
ZB [auth Ad],
ZC [auth Ad]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.88 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-27
    Type: Initial release