8JIV

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.84 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: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L2 C-terminal domain-containing proteinD [auth CA]261Triticum aestivumMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L3E [auth CB]385Triticum aestivumMutation(s): 0 
UniProt
Find proteins for Q7X744 (Triticum aestivum)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4 C-terminal domain-containing proteinF [auth CC]405Triticum aestivumMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L5 eukaryotic C-terminal domain-containing proteinG [auth CD]307Triticum aestivumMutation(s): 0 
UniProt
Find proteins for A0A3B6DD91 (Triticum aestivum)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6H [auth CE]232Triticum aestivumMutation(s): 0 
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Find proteins for A0A3B6QGW3 (Triticum aestivum)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL30I [auth CF]244Triticum aestivumMutation(s): 0 
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Find proteins for A0A3B6DM38 (Triticum aestivum)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7aJ [auth CG]258Triticum aestivumMutation(s): 0 
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Find proteins for A0A3B6RED0 (Triticum aestivum)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L6 alpha-beta domain-containing proteinK [auth CH]189Triticum aestivumMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L10e/L16 domain-containing proteinL [auth CI]217Triticum aestivumMutation(s): 0 
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Find proteins for A0A3B6HUM3 (Triticum aestivum)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11M [auth CJ]180Triticum aestivumMutation(s): 0 
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Find proteins for A0A3B5XX39 (Triticum aestivum)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13N [auth CL]208Triticum aestivumMutation(s): 0 
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Find proteins for A0A3B6QBU0 (Triticum aestivum)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L14e domain-containing proteinO [auth CM]135Triticum aestivumMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L15P [auth CN]204Triticum aestivumMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L13aQ [auth CO]206Triticum aestivumMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL22R [auth CP]170Triticum aestivumMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L18e/L15P domain-containing proteinS [auth CQ]188Triticum aestivumMutation(s): 0 
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Find proteins for A0A3B5ZQE8 (Triticum aestivum)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L19T [auth CR]206Triticum aestivumMutation(s): 0 
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Find proteins for A0A3B6C2W3 (Triticum aestivum)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aU [auth CS]178Triticum aestivumMutation(s): 0 
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Find proteins for A0A3B5Z5M6 (Triticum aestivum)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21V [auth CT]164Triticum aestivumMutation(s): 0 
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Find proteins for F4YWL9 (Triticum aestivum)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Genome assembly, chromosome: IIW [auth CU]129Triticum aestivumMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L17X [auth CV]136Triticum aestivumMutation(s): 0 
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Find proteins for Q5I7K4 (Triticum aestivum)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
TRASH domain-containing proteinY [auth CW]161Triticum aestivumMutation(s): 0 
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Find proteins for A0A3B6ELC9 (Triticum aestivum)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Genome assembly, chromosome: IIZ [auth CX]152Triticum aestivumMutation(s): 0 
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Find proteins for A0A1D5UQZ5 (Triticum aestivum)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
KOW domain-containing proteinAA [auth CY]127Triticum aestivumMutation(s): 0 
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Find proteins for A0A3B6GQI2 (Triticum aestivum)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27BA [auth CZ]137Triticum aestivumMutation(s): 0 
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Find proteins for A0A341XZK6 (Triticum aestivum)
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L18e/L15P domain-containing proteinCA [auth Ca]145Triticum aestivumMutation(s): 0 
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Find proteins for A0A3B6AUW8 (Triticum aestivum)
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29DA [auth Cb]60Triticum aestivumMutation(s): 0 
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Find proteins for A0A1D5RRD3 (Triticum aestivum)
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L7Ae/L30e/S12e/Gadd45 domain-containing proteinEA [auth Cc]112Triticum aestivumMutation(s): 0 
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Find proteins for W4ZRU3 (Triticum aestivum)
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31FA [auth Cd]123Triticum aestivumMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL32GA [auth Ce]133Triticum aestivumMutation(s): 0 
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Find proteins for A0A3B6SDD9 (Triticum aestivum)
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL33HA [auth Cf]111Triticum aestivumMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34IA [auth Cg]119Triticum aestivumMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35JA [auth Ch]124Triticum aestivumMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36KA [auth Ci]111Triticum aestivumMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L37LA [auth Cj]93Triticum aestivumMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38MA [auth Ck]69Triticum aestivumMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L39NA [auth Cl]51Triticum aestivumMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-like domain-containing proteinOA [auth Cm]129Triticum aestivumMutation(s): 0 
UniProt
Find proteins for A0A1D5XNC2 (Triticum aestivum)
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Genome assembly, chromosome: IIPA [auth Co]105Triticum aestivumMutation(s): 0 
UniProt
Find proteins for W5HX73 (Triticum aestivum)
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37a, expressedQA [auth Cp]92Triticum aestivumMutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal L28e/Mak16 domain-containing proteinRA [auth Cr]147Triticum aestivumMutation(s): 0 
UniProt
Find proteins for A0A3B5ZZN9 (Triticum aestivum)
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Entity ID: 1
MoleculeChains LengthOrganismImage
25S rRNAA [auth Aa]3,391Triticum aestivum
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Entity ID: 2
MoleculeChains LengthOrganismImage
5S rRNAB [auth Ab]119Triticum aestivum
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Entity ID: 3
MoleculeChains LengthOrganismImage
5.8S rRNAC [auth Ac]158Triticum aestivum
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
TM [auth Cj],
UM [auth Cm],
WM [auth Co]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K (Subject of Investigation/LOI)
Query on K

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],
BM [auth Ac],
CB [auth Aa],
CC [auth Aa],
CD [auth Aa],
DB [auth Aa],
DC [auth Aa],
DD [auth Aa],
EB [auth Aa],
EC [auth Aa],
FB [auth Aa],
FC [auth Aa],
FM [auth CA],
GB [auth Aa],
GC [auth Aa],
GM [auth CA],
HB [auth Aa],
HC [auth Aa],
IB [auth Aa],
IC [auth Aa],
IM [auth CI],
JB [auth Aa],
JC [auth Aa],
KB [auth Aa],
KC [auth Aa],
KM [auth CL],
LB [auth Aa],
LC [auth Aa],
LM [auth CL],
MB [auth Aa],
MC [auth Aa],
NB [auth Aa],
NC [auth Aa],
OB [auth Aa],
OC [auth Aa],
PB [auth Aa],
PC [auth Aa],
QB [auth Aa],
QC [auth Aa],
QM [auth Cg],
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],
VM [auth Co],
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]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
AE [auth Aa]
AF [auth Aa]
AG [auth Aa]
AH [auth Aa]
AI [auth Aa]
AE [auth Aa],
AF [auth Aa],
AG [auth Aa],
AH [auth Aa],
AI [auth Aa],
AJ [auth Aa],
AK [auth Aa],
AL [auth Aa],
AM [auth Ab],
BE [auth Aa],
BF [auth Aa],
BG [auth Aa],
BH [auth Aa],
BI [auth Aa],
BJ [auth Aa],
BK [auth Aa],
BL [auth Aa],
CE [auth Aa],
CF [auth Aa],
CG [auth Aa],
CH [auth Aa],
CI [auth Aa],
CJ [auth Aa],
CK [auth Aa],
CL [auth Aa],
CM [auth Ac],
DE [auth Aa],
DF [auth Aa],
DG [auth Aa],
DH [auth Aa],
DI [auth Aa],
DJ [auth Aa],
DK [auth Aa],
DL [auth Aa],
DM [auth Ac],
ED [auth Aa],
EE [auth Aa],
EF [auth Aa],
EG [auth Aa],
EH [auth Aa],
EI [auth Aa],
EJ [auth Aa],
EK [auth Aa],
EL [auth Aa],
EM [auth Ac],
FD [auth Aa],
FE [auth Aa],
FF [auth Aa],
FG [auth Aa],
FH [auth Aa],
FI [auth Aa],
FJ [auth Aa],
FK [auth Aa],
FL [auth Aa],
GD [auth Aa],
GE [auth Aa],
GF [auth Aa],
GG [auth Aa],
GH [auth Aa],
GI [auth Aa],
GJ [auth Aa],
GK [auth Aa],
GL [auth Aa],
HD [auth Aa],
HE [auth Aa],
HF [auth Aa],
HG [auth Aa],
HH [auth Aa],
HI [auth Aa],
HJ [auth Aa],
HK [auth Aa],
HL [auth Aa],
HM [auth CB],
ID [auth Aa],
IE [auth Aa],
IF [auth Aa],
IG [auth Aa],
IH [auth Aa],
II [auth Aa],
IJ [auth Aa],
IK [auth Aa],
IL [auth Aa],
JD [auth Aa],
JE [auth Aa],
JF [auth Aa],
JG [auth Aa],
JH [auth Aa],
JI [auth Aa],
JJ [auth Aa],
JK [auth Aa],
JL [auth Aa],
JM [auth CI],
KD [auth Aa],
KE [auth Aa],
KF [auth Aa],
KG [auth Aa],
KH [auth Aa],
KI [auth Aa],
KJ [auth Aa],
KK [auth Aa],
KL [auth Aa],
LD [auth Aa],
LE [auth Aa],
LF [auth Aa],
LG [auth Aa],
LH [auth Aa],
LI [auth Aa],
LJ [auth Aa],
LK [auth Aa],
LL [auth Aa],
MD [auth Aa],
ME [auth Aa],
MF [auth Aa],
MG [auth Aa],
MH [auth Aa],
MI [auth Aa],
MJ [auth Aa],
MK [auth Aa],
ML [auth Aa],
MM [auth CL],
ND [auth Aa],
NE [auth Aa],
NF [auth Aa],
NG [auth Aa],
NH [auth Aa],
NI [auth Aa],
NJ [auth Aa],
NK [auth Aa],
NL [auth Aa],
NM [auth CP],
OD [auth Aa],
OE [auth Aa],
OF [auth Aa],
OG [auth Aa],
OH [auth Aa],
OI [auth Aa],
OJ [auth Aa],
OK [auth Aa],
OL [auth Aa],
OM [auth CR],
PD [auth Aa],
PE [auth Aa],
PF [auth Aa],
PG [auth Aa],
PH [auth Aa],
PI [auth Aa],
PJ [auth Aa],
PK [auth Aa],
PL [auth Aa],
PM [auth CV],
QD [auth Aa],
QE [auth Aa],
QF [auth Aa],
QG [auth Aa],
QH [auth Aa],
QI [auth Aa],
QJ [auth Aa],
QK [auth Aa],
QL [auth Aa],
RD [auth Aa],
RE [auth Aa],
RF [auth Aa],
RG [auth Aa],
RH [auth Aa],
RI [auth Aa],
RJ [auth Aa],
RK [auth Aa],
RL [auth Aa],
RM [auth Cj],
SD [auth Aa],
SE [auth Aa],
SF [auth Aa],
SG [auth Aa],
SH [auth Aa],
SI [auth Aa],
SJ [auth Aa],
SK [auth Aa],
SL [auth Aa],
SM [auth Cj],
TD [auth Aa],
TE [auth Aa],
TF [auth Aa],
TG [auth Aa],
TH [auth Aa],
TI [auth Aa],
TJ [auth Aa],
TK [auth Aa],
TL [auth Aa],
UD [auth Aa],
UE [auth Aa],
UF [auth Aa],
UG [auth Aa],
UH [auth Aa],
UI [auth Aa],
UJ [auth Aa],
UK [auth Aa],
UL [auth Aa],
VD [auth Aa],
VE [auth Aa],
VF [auth Aa],
VG [auth Aa],
VH [auth Aa],
VI [auth Aa],
VJ [auth Aa],
VK [auth Aa],
VL [auth Aa],
WD [auth Aa],
WE [auth Aa],
WF [auth Aa],
WG [auth Aa],
WH [auth Aa],
WI [auth Aa],
WJ [auth Aa],
WK [auth Aa],
WL [auth Aa],
XD [auth Aa],
XE [auth Aa],
XF [auth Aa],
XG [auth Aa],
XH [auth Aa],
XI [auth Aa],
XJ [auth Aa],
XK [auth Aa],
XL [auth Ab],
YD [auth Aa],
YE [auth Aa],
YF [auth Aa],
YG [auth Aa],
YH [auth Aa],
YI [auth Aa],
YJ [auth Aa],
YK [auth Aa],
YL [auth Ab],
ZD [auth Aa],
ZE [auth Aa],
ZF [auth Aa],
ZG [auth Aa],
ZH [auth Aa],
ZI [auth Aa],
ZJ [auth Aa],
ZK [auth Aa],
ZL [auth Ab]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
HIC
Query on HIC
E [auth CB]L-PEPTIDE LINKINGC7 H11 N3 O2HIS
MLZ
Query on MLZ
PA [auth Co]L-PEPTIDE LINKINGC7 H16 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.84 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



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