8AZW

Cryo-EM structure of the plant 60S subunit


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.14 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

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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
eL13 (60S ribosomal protein L13)B [auth D]206Nicotiana tabacumMutation(s): 0 
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Find proteins for A0A1S4CSN1 (Nicotiana tabacum)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
eL14 (60S ribosomal protein L14)C [auth E]134Nicotiana tabacumMutation(s): 0 
UniProt
Find proteins for A0A1S4A807 (Nicotiana tabacum)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
eL15 (60S ribosomal protein L15)D [auth F]204Nicotiana tabacumMutation(s): 0 
UniProt
Find proteins for A0A1S4D5P7 (Nicotiana tabacum)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
eL18 (60S ribosomal protein L18)E [auth G]187Nicotiana tabacumMutation(s): 0 
UniProt
Find proteins for A0A1S4DF55 (Nicotiana tabacum)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
eL19 (60S ribosomal protein L19)F [auth H]214Nicotiana tabacumMutation(s): 0 
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Find proteins for A0A1S3X0I4 (Nicotiana tabacum)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
eL20 (60S ribosomal protein L18a)G [auth I]178Nicotiana tabacumMutation(s): 0 
UniProt
Find proteins for A0A1S4CP52 (Nicotiana tabacum)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
eL21 (60S ribosomal protein L21)H [auth J]164Nicotiana tabacumMutation(s): 0 
UniProt
Find proteins for A0A1S3XCW6 (Nicotiana tabacum)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
eL22 (60S ribosomal protein L22)I [auth K]127Nicotiana tabacumMutation(s): 0 
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Find proteins for A0A1S4BSU3 (Nicotiana tabacum)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
eL24 (60S ribosomal protein L24)J [auth L]164Nicotiana tabacumMutation(s): 0 
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Find proteins for A0A1S4BHF2 (Nicotiana tabacum)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
eL27 (60S ribosomal protein L27)K [auth M]135Nicotiana tabacumMutation(s): 0 
UniProt
Find proteins for A0A1S4AEL0 (Nicotiana tabacum)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
eL28 (60S ribosomal protein L28)L [auth N]143Nicotiana tabacumMutation(s): 0 
UniProt
Find proteins for A0A1S4D1U6 (Nicotiana tabacum)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
eL29 (60S ribosomal protein L29)M [auth O]61Nicotiana tabacumMutation(s): 0 
UniProt
Find proteins for A0A1S3YR12 (Nicotiana tabacum)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
eL30 (60S ribosomal protein L30)N [auth P]113Nicotiana tabacumMutation(s): 0 
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Find proteins for A0A1S3WZ09 (Nicotiana tabacum)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
eL31 (60S ribosomal protein L31)O [auth Q]120Nicotiana tabacumMutation(s): 0 
UniProt
Find proteins for A0A1S3Y3V5 (Nicotiana tabacum)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
eL32 (60S ribosomal protein L32)P [auth R]133Nicotiana tabacumMutation(s): 0 
UniProt
Find proteins for A0A1S3Z2X4 (Nicotiana tabacum)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
eL33 (60S ribosomal protein L35a)Q [auth S]112Nicotiana tabacumMutation(s): 0 
UniProt
Find proteins for A0A1S3XU79 (Nicotiana tabacum)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
eL34 (60S ribosomal protein L34)R [auth T]120Nicotiana tabacumMutation(s): 0 
UniProt
Find proteins for P41098 (Nicotiana tabacum)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
eL36 (60S ribosomal protein L36)S [auth U]110Nicotiana tabacumMutation(s): 0 
UniProt
Find proteins for A0A1S4D2I2 (Nicotiana tabacum)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
eL37 (60S ribosomal protein L37)T [auth V]95Nicotiana tabacumMutation(s): 0 
UniProt
Find proteins for A0A1S4DN51 (Nicotiana tabacum)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
eL38 (60S ribosomal protein L38)U [auth W]69Nicotiana tabacumMutation(s): 0 
UniProt
Find proteins for A0A1S4C4G8 (Nicotiana tabacum)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
eL39 (60S ribosomal protein L39)V [auth X]51Nicotiana tabacumMutation(s): 0 
UniProt
Find proteins for A0A1S3YR32 (Nicotiana tabacum)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
eL40 (60S ribosomal protein L40)W [auth Y]128Nicotiana tabacumMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
eL41 (60S ribosomal protein L41)X [auth p]25Nicotiana tabacumMutation(s): 0 
UniProt
Find proteins for P62121 (Nicotiana tabacum)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
eL42 (60S ribosomal protein L42)Y [auth Z]105Nicotiana tabacumMutation(s): 0 
UniProt
Find proteins for A0A1S4AVP7 (Nicotiana tabacum)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
eL43 (60S ribosomal protein L37a)Z [auth a]92Nicotiana tabacumMutation(s): 0 
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Find proteins for A0A1S3X5Y9 (Nicotiana tabacum)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
eL6 (60S ribosomal protein L6)AA [auth b]230Nicotiana tabacumMutation(s): 0 
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Find proteins for A0A1S4B0G2 (Nicotiana tabacum)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
eL8 (60S ribosomal protein L7a)BA [auth c]258Nicotiana tabacumMutation(s): 0 
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Find proteins for A0A1S4D668 (Nicotiana tabacum)
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
uL13 (60S ribosomal protein L13a)CA [auth d]206Nicotiana tabacumMutation(s): 0 
UniProt
Find proteins for A0A1S4DN49 (Nicotiana tabacum)
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
uL14 (60S ribosomal protein L23)DA [auth e]140Nicotiana tabacumMutation(s): 0 
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Find proteins for A0A1S3XSQ1 (Nicotiana tabacum)
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
uL15 (60S ribosomal protein L27a)EA [auth f]148Nicotiana tabacumMutation(s): 0 
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Find proteins for A0A1S4BFD5 (Nicotiana tabacum)
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
uL16 (60S ribosomal protein L10)FA [auth g]221Nicotiana tabacumMutation(s): 0 
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Find proteins for A0A1S3Z2D7 (Nicotiana tabacum)
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
uL18 (60S ribosomal protein L5)GA [auth h]301Nicotiana tabacumMutation(s): 0 
UniProt
Find proteins for A0A1S3XE16 (Nicotiana tabacum)
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
uL22 (60S ribosomal protein L17)HA [auth j]175Nicotiana tabacumMutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
uL23 (60S ribosomal protein L23a)IA [auth k]154Nicotiana tabacumMutation(s): 0 
UniProt
Find proteins for Q07761 (Nicotiana tabacum)
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
uL24 (60S ribosomal protein L26)JA [auth m]146Nicotiana tabacumMutation(s): 0 
UniProt
Find proteins for A0A1S4DPM5 (Nicotiana tabacum)
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
uL29 (60S ribosomal protein L35)KA [auth n]123Nicotiana tabacumMutation(s): 0 
UniProt
Find proteins for A0A1S3WY31 (Nicotiana tabacum)
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
uL2 (60S ribosomal protein L8)LA [auth o]260Nicotiana tabacumMutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
uL30 (60S ribosomal protein L7)MA [auth q]242Nicotiana tabacumMutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
uL3 (60S ribosomal protein L3)NA [auth r]389Nicotiana tabacumMutation(s): 0 
UniProt
Find proteins for A0A1S3ZLI9 (Nicotiana tabacum)
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
uL4 (60S ribosomal protein L4)OA [auth s]405Nicotiana tabacumMutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
uL5 (60S ribosomal protein L11)PA [auth t]181Nicotiana tabacumMutation(s): 0 
UniProt
Find proteins for A0A1S3XAW1 (Nicotiana tabacum)
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
uL6 (60S ribosomal protein L9)QA [auth u]194Nicotiana tabacumMutation(s): 0 
UniProt
Find proteins for A0A1S4C068 (Nicotiana tabacum)
Explore A0A1S4C068 
Go to UniProtKB:  A0A1S4C068
Entity Groups  
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UniProt GroupA0A1S4C068
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
nascent chainRA [auth l]24Nicotiana tabacumMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
5S rRNAA [auth C]119Nicotiana tabacum
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Entity ID: 45
MoleculeChains LengthOrganismImage
25S rRNASA [auth A]3,390Nicotiana tabacum
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Entity ID: 46
MoleculeChains LengthOrganismImage
5.8S rRNATA [auth B]163Nicotiana 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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QD [auth A],
RD [auth A]
SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
SPD
Query on SPD

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PD [auth A]SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
ZN
Query on ZN

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BB [auth V],
DB [auth Y],
FB [auth Z],
GB [auth a]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

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AB [auth T]
AE [auth A]
AF [auth A]
AG [auth A]
BE [auth A]
AB [auth T],
AE [auth A],
AF [auth A],
AG [auth A],
BE [auth A],
BF [auth A],
BG [auth A],
CE [auth A],
CF [auth A],
CG [auth A],
DE [auth A],
DF [auth A],
DG [auth A],
EB [auth Z],
EE [auth A],
EF [auth A],
EG [auth A],
FE [auth A],
FF [auth A],
FG [auth A],
GE [auth A],
GF [auth A],
GG [auth A],
HE [auth A],
HF [auth A],
HG [auth A],
IB [auth f],
IE [auth A],
IF [auth A],
IG [auth A],
JB [auth g],
JE [auth A],
JF [auth A],
JG [auth A],
KE [auth A],
KF [auth A],
KG [auth A],
LB [auth o],
LE [auth A],
LF [auth A],
LG [auth A],
MB [auth o],
ME [auth A],
MF [auth A],
MG [auth A],
NE [auth A],
NF [auth A],
NG [auth A],
OE [auth A],
OF [auth A],
OG [auth A],
PE [auth A],
PF [auth A],
PG [auth A],
QB [auth r],
QE [auth A],
QF [auth A],
QG [auth A],
RE [auth A],
RF [auth A],
RG [auth A],
SD [auth A],
SE [auth A],
SF [auth A],
SG [auth A],
TD [auth A],
TE [auth A],
TF [auth A],
TG [auth A],
UD [auth A],
UE [auth A],
UF [auth A],
UG [auth A],
VD [auth A],
VE [auth A],
VF [auth A],
VG [auth A],
WD [auth A],
WE [auth A],
WF [auth A],
WG [auth A],
XD [auth A],
XE [auth A],
XF [auth A],
XG [auth B],
YA [auth D],
YD [auth A],
YE [auth A],
YF [auth A],
YG [auth B],
ZA [auth R],
ZD [auth A],
ZE [auth A],
ZF [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

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AC [auth A]
AD [auth A]
BC [auth A]
BD [auth A]
CB [auth V]
AC [auth A],
AD [auth A],
BC [auth A],
BD [auth A],
CB [auth V],
CC [auth A],
CD [auth A],
DC [auth A],
DD [auth A],
EC [auth A],
ED [auth A],
FC [auth A],
FD [auth A],
GC [auth A],
GD [auth A],
HB [auth e],
HC [auth A],
HD [auth A],
IC [auth A],
ID [auth A],
JC [auth A],
JD [auth A],
KB [auth j],
KC [auth A],
KD [auth A],
LC [auth A],
LD [auth A],
MC [auth A],
MD [auth A],
NB [auth q],
NC [auth A],
ND [auth A],
OB [auth r],
OC [auth A],
OD [auth A],
PB [auth r],
PC [auth A],
QC [auth A],
RB [auth A],
RC [auth A],
SB [auth A],
SC [auth A],
TB [auth A],
TC [auth A],
UA [auth C],
UB [auth A],
UC [auth A],
VA [auth C],
VB [auth A],
VC [auth A],
WA [auth C],
WB [auth A],
WC [auth A],
XA [auth C],
XB [auth A],
XC [auth A],
YB [auth A],
YC [auth A],
ZB [auth A],
ZC [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.14 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany416210002

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-07
    Type: Initial release
  • Version 1.1: 2023-06-28
    Changes: Database references