8AUV

Cryo-EM structure of the plant 40S subunit


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.38 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of the actively translating plant 80S ribosome at 2.2 angstrom resolution.

Smirnova, J.Loerke, J.Kleinau, G.Schmidt, A.Burger, J.Meyer, E.H.Mielke, T.Scheerer, P.Bock, R.Spahn, C.M.T.Zoschke, R.

(2023) Nat Plants 9: 987-1000

  • DOI: https://doi.org/10.1038/s41477-023-01407-y
  • Primary Citation of Related Structures:  
    8AUV, 8AZW, 8B2L

  • PubMed Abstract: 

    In plant cells, translation occurs in three compartments: the cytosol, the plastids and the mitochondria. While the structures of the (prokaryotic-type) ribosomes in plastids and mitochondria are well characterized, high-resolution structures of the eukaryotic 80S ribosomes in the cytosol have been lacking. Here the structure of translating tobacco (Nicotiana tabacum) 80S ribosomes was solved by cryo-electron microscopy with a global resolution of 2.2 Å. The ribosome structure includes two tRNAs, decoded mRNA and the nascent peptide chain, thus providing insights into the molecular underpinnings of the cytosolic translation process in plants. The map displays conserved and plant-specific rRNA modifications and the positions of numerous ionic cofactors, and it uncovers the role of monovalent ions in the decoding centre. The model of the plant 80S ribosome enables broad phylogenetic comparisons that reveal commonalities and differences in the ribosomes of plants and those of other eukaryotes, thus putting our knowledge about eukaryotic translation on a firmer footing.


  • Organizational Affiliation

    Institute of Medical Physics and Biophysics, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany. julia.smirnova@charite.de.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
eS4 (40S ribosomal protein S4)264Nicotiana tabacumMutation(s): 0 
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Find proteins for A0A1S4DQ51 (Nicotiana tabacum)
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
eS6 (40S ribosomal protein S6)B [auth k]249Nicotiana tabacumMutation(s): 0 
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Find proteins for A0A1S3Z3Y7 (Nicotiana tabacum)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
eS10 (40S ribosomal protein S10)D [auth l]208Nicotiana tabacumMutation(s): 0 
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Find proteins for A0A1S4DHU6 (Nicotiana tabacum)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
eS12 (40S ribosomal protein S12)E [auth C]144Nicotiana tabacumMutation(s): 0 
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Find proteins for A0A1S4B129 (Nicotiana tabacum)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
eS17 (40S ribosomal protein S17)F [auth D]149Nicotiana tabacumMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
eS19 (40S ribosomal protein S19)G [auth E]143Nicotiana tabacumMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
eS1 (40S ribosomal protein S3a)H [auth F]261Nicotiana tabacumMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
eS21 (40S ribosomal protein S21)I [auth G]83Nicotiana tabacumMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
eS24 (40S ribosomal protein S24)J [auth H]133Nicotiana tabacumMutation(s): 0 
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Find proteins for A0A1S3ZXI6 (Nicotiana tabacum)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
eS25 (40S ribosomal protein S25)K [auth I]107Nicotiana tabacumMutation(s): 0 
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Find proteins for A0A076L2E2 (Nicotiana tabacum)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
eS26 (40S ribosomal protein S26)L [auth J]127Nicotiana tabacumMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
eS27 (40S ribosomal protein S27)M [auth K]86Nicotiana tabacumMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
eS28 (40S ribosomal protein S28)N [auth L]65Nicotiana tabacumMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
eS30 (40S ribosomal protein S30)O [auth M]62Nicotiana tabacumMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
eS31 (ubiquitin-40S ribosomal protein S27a)P [auth N]156Nicotiana tabacumMutation(s): 0 
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Find proteins for A0A1S4C0C1 (Nicotiana tabacum)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
eS7 (40S ribosomal protein S7)Q [auth O]191Nicotiana tabacumMutation(s): 0 
UniProt
Find proteins for A0A1S3Z906 (Nicotiana tabacum)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
eS8 (40S ribosomal protein S8)R [auth P]224Nicotiana tabacumMutation(s): 0 
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Find proteins for A0A1S4CZK3 (Nicotiana tabacum)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
RACK1 (guanine nucleotide-binding protein subunit beta-like protein)S [auth Q]328Nicotiana tabacumMutation(s): 0 
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Find proteins for A0A1S4ABX7 (Nicotiana tabacum)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
uS10 (40S ribosomal protein S20)T [auth R]122Nicotiana tabacumMutation(s): 0 
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Find proteins for A0A1S3XHL0 (Nicotiana tabacum)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
uS11 (40S ribosomal protein S14)U [auth S]150Nicotiana tabacumMutation(s): 0 
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Find proteins for A0A1S3XAN1 (Nicotiana tabacum)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
uS12 (40S ribosomal protein S23)V [auth T]142Nicotiana tabacumMutation(s): 0 
UniProt
Find proteins for A0A1S4C879 (Nicotiana tabacum)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
uS13 (40S ribosomal protein S18)W [auth U]152Nicotiana tabacumMutation(s): 0 
UniProt
Find proteins for A0A1S3YM01 (Nicotiana tabacum)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
uS14 (40S ribosomal protein S29)X [auth V]56Nicotiana tabacumMutation(s): 0 
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Find proteins for A0A1S4DPT4 (Nicotiana tabacum)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
uS15 (40S ribosomal protein S13)Y [auth W]151Nicotiana tabacumMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
uS17 (40S ribosomal protein S11)Z [auth X]159Nicotiana tabacumMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
uS19 (40S ribosomal protein S15)AA [auth Y]152Nicotiana tabacumMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
uS2 (40S ribosomal protein SA)BA [auth Z]336Nicotiana tabacumMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
uS3 (40S ribosomal protein S3)CA [auth a]248Nicotiana tabacumMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
uS4 (40S ribosomal protein S9)DA [auth b]197Nicotiana tabacumMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
uS5 (40S ribosomal protein S2)EA [auth c]280Nicotiana tabacumMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
uS7 (40S ribosomal protein S5)FA [auth d]210Nicotiana tabacumMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
uS8 (40S ribosomal protein S15a)GA [auth e]130Nicotiana tabacumMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
uS9 (40S ribosomal protein S16)HA [auth f]147Nicotiana tabacumMutation(s): 0 
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Entity ID: 3
MoleculeChains LengthOrganismImage
18S rRNAC [auth h]1,808Nicotiana tabacum
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Entity ID: 35
MoleculeChains LengthOrganismImage
mRNAIA [auth B]12Nicotiana tabacum
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Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SPM
Query on SPM

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UE [auth h],
VE [auth h],
WE [auth h]
SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
SPD
Query on SPD

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TE [auth h]SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
ZN
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EF [auth V],
YE [auth J],
ZE [auth N]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

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AE [auth h]
AF [auth S]
BE [auth h]
BF [auth T]
CE [auth h]
AE [auth h],
AF [auth S],
BE [auth h],
BF [auth T],
CE [auth h],
DE [auth h],
DF [auth U],
ED [auth h],
EE [auth h],
FD [auth h],
FE [auth h],
FF [auth V],
GD [auth h],
GE [auth h],
GF [auth W],
HD [auth h],
HE [auth h],
HF [auth d],
ID [auth h],
IE [auth h],
JD [auth h],
JE [auth h],
KD [auth h],
KE [auth h],
LD [auth h],
LE [auth h],
MD [auth h],
ME [auth h],
ND [auth h],
NE [auth h],
OD [auth h],
OE [auth h],
PD [auth h],
PE [auth h],
QD [auth h],
QE [auth h],
RD [auth h],
RE [auth h],
SD [auth h],
SE [auth h],
TD [auth h],
UD [auth h],
VD [auth h],
WD [auth h],
XD [auth h],
YD [auth h],
ZD [auth h]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

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AB [auth h]
AC [auth h]
AD [auth h]
BB [auth h]
BC [auth h]
AB [auth h],
AC [auth h],
AD [auth h],
BB [auth h],
BC [auth h],
BD [auth h],
CB [auth h],
CC [auth h],
CD [auth h],
CF [auth U],
DB [auth h],
DC [auth h],
DD [auth h],
EB [auth h],
EC [auth h],
FB [auth h],
FC [auth h],
GB [auth h],
GC [auth h],
HB [auth h],
HC [auth h],
IB [auth h],
IC [auth h],
IF [auth B],
JA [auth h],
JB [auth h],
JC [auth h],
KA [auth h],
KB [auth h],
KC [auth h],
LA [auth h],
LB [auth h],
LC [auth h],
MA [auth h],
MB [auth h],
MC [auth h],
NA [auth h],
NB [auth h],
NC [auth h],
OA [auth h],
OB [auth h],
OC [auth h],
PA [auth h],
PB [auth h],
PC [auth h],
QA [auth h],
QB [auth h],
QC [auth h],
RA [auth h],
RB [auth h],
RC [auth h],
SA [auth h],
SB [auth h],
SC [auth h],
TA [auth h],
TB [auth h],
TC [auth h],
UA [auth h],
UB [auth h],
UC [auth h],
VA [auth h],
VB [auth h],
VC [auth h],
WA [auth h],
WB [auth h],
WC [auth h],
XA [auth h],
XB [auth h],
XC [auth h],
XE [auth J],
YA [auth h],
YB [auth h],
YC [auth h],
ZA [auth h],
ZB [auth h],
ZC [auth h]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.38 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany416210002
German Research Foundation (DFG)GermanyINST 335/588-1

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-07
    Type: Initial release
  • Version 1.1: 2023-06-14
    Changes: Structure summary
  • Version 1.2: 2023-06-28
    Changes: Database references
  • Version 1.3: 2024-04-24
    Changes: Data collection