[English] 日本語
Yorodumi
- PDB-8azw: Cryo-EM structure of the plant 60S subunit -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8azw
TitleCryo-EM structure of the plant 60S subunit
Components
  • 25S rRNA
  • 5.8S rRNA
  • 5S rRNA
  • eL13 (60S ribosomal protein L13)
  • eL14 (60S ribosomal protein L14)
  • eL15 (60S ribosomal protein L15)
  • eL18 (60S ribosomal protein L18)
  • eL19 (60S ribosomal protein L19)
  • eL20 (60S ribosomal protein L18a)
  • eL21 (60S ribosomal protein L21)
  • eL22 (60S ribosomal protein L22)
  • eL24 (60S ribosomal protein L24)
  • eL27 (60S ribosomal protein L27)
  • eL28 (60S ribosomal protein L28)
  • eL29 (60S ribosomal protein L29)
  • eL30 (60S ribosomal protein L30)
  • eL31 (60S ribosomal protein L31)
  • eL32 (60S ribosomal protein L32)
  • eL33 (60S ribosomal protein L35a)
  • eL34 (60S ribosomal protein L34)
  • eL36 (60S ribosomal protein L36)
  • eL37 (60S ribosomal protein L37)
  • eL38 (60S ribosomal protein L38)
  • eL39 (60S ribosomal protein L39)
  • eL40 (60S ribosomal protein L40)
  • eL41 (60S ribosomal protein L41)
  • eL42 (60S ribosomal protein L42)
  • eL43 (60S ribosomal protein L37a)
  • eL6 (60S ribosomal protein L6)
  • eL8 (60S ribosomal protein L7a)
  • nascent chain
  • uL13 (60S ribosomal protein L13a)
  • uL14 (60S ribosomal protein L23)
  • uL15 (60S ribosomal protein L27a)
  • uL16 (60S ribosomal protein L10)
  • uL18 (60S ribosomal protein L5)
  • uL2 (60S ribosomal protein L8)
  • uL22 (60S ribosomal protein L17)
  • uL23 (60S ribosomal protein L23a)
  • uL24 (60S ribosomal protein L26)
  • uL29 (60S ribosomal protein L35)
  • uL3 (60S ribosomal protein L3)
  • uL30 (60S ribosomal protein L7)
  • uL4 (60S ribosomal protein L4)
  • uL5 (60S ribosomal protein L11)
  • uL6 (60S ribosomal protein L9)
KeywordsRIBOSOME / Plant / 80S / rRNA Modifications
Function / homology
Function and homology information


protein-RNA complex assembly / maturation of LSU-rRNA / cytosolic ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / ribosome biogenesis / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit ...protein-RNA complex assembly / maturation of LSU-rRNA / cytosolic ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / ribosome biogenesis / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / zinc ion binding
Similarity search - Function
Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L28e / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / metallochaperone-like domain / TRASH domain / Ribosomal protein L41 ...Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L28e / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / metallochaperone-like domain / TRASH domain / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L19, eukaryotic / Ribosomal protein L10e / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L44e signature. / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / : / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein L44e / Ribosomal protein L44 / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L30e signature 1. / Ribosomal protein L36e signature. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L35Ae, conserved site / Ribosomal protein L35Ae signature. / : / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal Protein L6, KOW domain / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein L30e signature 2. / Ribosomal protein L39e, conserved site / Ribosomal protein L30e, conserved site / Ribosomal protein L39e signature. / Ribosomal protein L6e / 60S ribosomal protein L35 / : / 60S ribosomal protein L19 / Ribosomal protein L34Ae / Ribosomal protein L34e / 60S ribosomal protein L6E / Ribosomal protein L7A/L8 / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L30/YlxQ / Ribosomal protein L7, eukaryotic / Ribosomal protein L30, N-terminal / Ribosomal L30 N-terminal domain / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L31e, conserved site / Ribosomal protein L31e signature. / Ribosomal protein L18e / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e / Ribosomal protein L19e, C-terminal domain / Ribosomal_L19e / Ribosomal protein L19/L19e / Ribosomal protein L14e domain / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e, N-terminal domain / Ribosomal protein L14 / Ribosomal protein L37ae / Ribosomal L37ae protein family / Ribosomal protein L32e, conserved site / Ribosomal protein L32e signature. / Ribosomal protein L35A / Ribosomal protein L35Ae / Ribosomal protein L35A superfamily / Ribosomal protein L6, conserved site-2 / Ribosomal protein L6 signature 2.
Similarity search - Domain/homology
: / SPERMIDINE / SPERMINE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 60S ribosomal protein L35-like ...: / SPERMIDINE / SPERMINE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 60S ribosomal protein L35-like / 60S ribosomal protein L30 / Ribosomal protein L19 / 60S ribosomal protein L4 / 60S ribosomal protein L37a / 60S ribosomal protein L11-1 / 60S ribosomal protein L21-1-like / 60S ribosomal protein L5-like / 60S ribosomal protein L23 / 60S ribosomal protein L35a-3 / 60S ribosomal protein L8-like / 60S ribosomal protein L31 / 60S ribosomal protein L29 / 60S ribosomal protein L39-3 / 60S ribosomal protein L10 / 60S ribosomal protein L32-1 / 60S ribosomal protein L3 / 60S ribosomal protein L7-4 / 60S ribosomal protein L14-1 / 60S ribosomal protein L27 / 60S ribosomal protein L44 / 60S ribosomal protein L6 isoform X1 / 60S ribosomal protein L27a-3-like / 60S ribosomal protein L24 / Large ribosomal subunit protein eL22 / 60S ribosomal protein L9-1 / 60S ribosomal protein L38 / 60S ribosomal protein L17-1 / 60S ribosomal protein L18a / 60S ribosomal protein L13 / 60S ribosomal protein L28-1 / 60S ribosomal protein L36 / Ribosomal protein L15 / 60S ribosomal protein L7a / 60S ribosomal protein L18-2 / 60S ribosomal protein L13a-4 / Ribosomal protein L37 / 60S ribosomal protein L26-1 / Large ribosomal subunit protein eL34 / Small ribosomal subunit protein eS32 / Large ribosomal subunit protein uL23
Similarity search - Component
Biological speciesNicotiana tabacum (common tobacco)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.14 Å
AuthorsSmirnova, J. / Loerke, J. / Kleinau, G. / Schmidt, A. / Buerger, J. / Meyer, E.H. / Mielke, T. / Scheerer, P. / Bock, R. / Spahn, C.M.T. / Zoschke, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)416210002 Germany
CitationJournal: Nat Plants / Year: 2023
Title: Structure of the actively translating plant 80S ribosome at 2.2 Å resolution.
Authors: Julia Smirnova / Justus Loerke / Gunnar Kleinau / Andrea Schmidt / Jörg Bürger / Etienne H Meyer / Thorsten Mielke / Patrick Scheerer / Ralph Bock / Christian M T Spahn / Reimo Zoschke /
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 ...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.
History
DepositionSep 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jul 24, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: 5S rRNA
D: eL13 (60S ribosomal protein L13)
E: eL14 (60S ribosomal protein L14)
F: eL15 (60S ribosomal protein L15)
G: eL18 (60S ribosomal protein L18)
H: eL19 (60S ribosomal protein L19)
I: eL20 (60S ribosomal protein L18a)
J: eL21 (60S ribosomal protein L21)
K: eL22 (60S ribosomal protein L22)
L: eL24 (60S ribosomal protein L24)
M: eL27 (60S ribosomal protein L27)
N: eL28 (60S ribosomal protein L28)
O: eL29 (60S ribosomal protein L29)
P: eL30 (60S ribosomal protein L30)
Q: eL31 (60S ribosomal protein L31)
R: eL32 (60S ribosomal protein L32)
S: eL33 (60S ribosomal protein L35a)
T: eL34 (60S ribosomal protein L34)
U: eL36 (60S ribosomal protein L36)
V: eL37 (60S ribosomal protein L37)
W: eL38 (60S ribosomal protein L38)
X: eL39 (60S ribosomal protein L39)
Y: eL40 (60S ribosomal protein L40)
p: eL41 (60S ribosomal protein L41)
Z: eL42 (60S ribosomal protein L42)
a: eL43 (60S ribosomal protein L37a)
b: eL6 (60S ribosomal protein L6)
c: eL8 (60S ribosomal protein L7a)
d: uL13 (60S ribosomal protein L13a)
e: uL14 (60S ribosomal protein L23)
f: uL15 (60S ribosomal protein L27a)
g: uL16 (60S ribosomal protein L10)
h: uL18 (60S ribosomal protein L5)
j: uL22 (60S ribosomal protein L17)
k: uL23 (60S ribosomal protein L23a)
m: uL24 (60S ribosomal protein L26)
n: uL29 (60S ribosomal protein L35)
o: uL2 (60S ribosomal protein L8)
q: uL30 (60S ribosomal protein L7)
r: uL3 (60S ribosomal protein L3)
s: uL4 (60S ribosomal protein L4)
t: uL5 (60S ribosomal protein L11)
u: uL6 (60S ribosomal protein L9)
l: nascent chain
A: 25S rRNA
B: 5.8S rRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,992,120207
Polymers1,986,17546
Non-polymers5,945161
Water79,3744406
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area492250 Å2
ΔGint-3585 kcal/mol
Surface area605770 Å2
MethodPISA

-
Components

-
RNA chain , 3 types, 3 molecules CAB

#1: RNA chain 5S rRNA


Mass: 38328.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: GenBank: 2276356346
#45: RNA chain 25S rRNA


Mass: 1098268.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco)
#46: RNA chain 5.8S rRNA


Mass: 52563.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: GenBank: 1782605526

+
Protein , 41 types, 41 molecules DEFGHIJKLMNOPQRSTUVWXYZabcdefg...

#2: Protein eL13 (60S ribosomal protein L13) / 60S ribosomal protein L13


Mass: 23595.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4CSN1
#3: Protein eL14 (60S ribosomal protein L14) / 60S ribosomal protein L14-1


Mass: 15443.432 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4A807
#4: Protein eL15 (60S ribosomal protein L15) / Ribosomal protein L15


Mass: 24228.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4D5P7
#5: Protein eL18 (60S ribosomal protein L18) / 60S ribosomal protein L18-2-like


Mass: 20905.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4DF55
#6: Protein eL19 (60S ribosomal protein L19) / Ribosomal protein L19


Mass: 25055.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3X0I4
#7: Protein eL20 (60S ribosomal protein L18a) / 60S ribosomal protein L18a


Mass: 21513.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4CP52
#8: Protein eL21 (60S ribosomal protein L21) / 60S ribosomal protein L21-1-like


Mass: 18716.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3XCW6
#9: Protein eL22 (60S ribosomal protein L22) / 60S ribosomal protein L22-2-like


Mass: 14277.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4BSU3
#10: Protein eL24 (60S ribosomal protein L24) / 60S ribosomal protein L24-like


Mass: 18606.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4BHF2
#11: Protein eL27 (60S ribosomal protein L27) / 60S ribosomal protein L27


Mass: 15722.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4AEL0
#12: Protein eL28 (60S ribosomal protein L28) / 60S ribosomal protein L28-1-like


Mass: 15954.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4D1U6
#13: Protein eL29 (60S ribosomal protein L29) / 60S ribosomal protein L29


Mass: 7132.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3YR12
#14: Protein eL30 (60S ribosomal protein L30) / 60S ribosomal protein L30-like


Mass: 12420.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3WZ09
#15: Protein eL31 (60S ribosomal protein L31) / 60S ribosomal protein L31


Mass: 13894.171 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3Y3V5
#16: Protein eL32 (60S ribosomal protein L32) / 60S ribosomal protein L32-1


Mass: 15665.528 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3Z2X4
#17: Protein eL33 (60S ribosomal protein L35a) / 60S ribosomal protein L35a-3


Mass: 12959.179 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3XU79
#18: Protein eL34 (60S ribosomal protein L34) / 60S ribosomal protein L34


Mass: 13788.358 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: P41098
#19: Protein eL36 (60S ribosomal protein L36) / 60S ribosomal protein L36


Mass: 12361.817 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4D2I2
#20: Protein eL37 (60S ribosomal protein L37) / Ribosomal protein L37


Mass: 10879.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4DN51
#21: Protein eL38 (60S ribosomal protein L38) / 60S ribosomal protein L38


Mass: 8101.704 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4C4G8
#22: Protein eL39 (60S ribosomal protein L39) / 60S ribosomal protein L39-3


Mass: 6503.839 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3YR32
#23: Protein eL40 (60S ribosomal protein L40) / 60S ribosomal protein L40


Mass: 14717.386 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco)
#25: Protein eL42 (60S ribosomal protein L42) / 60S ribosomal protein L44


Mass: 12037.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4AVP7
#26: Protein eL43 (60S ribosomal protein L37a) / 60S ribosomal protein L37a


Mass: 10280.108 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3X5Y9
#27: Protein eL6 (60S ribosomal protein L6) / 60S ribosomal protein L6-like isoform X1


Mass: 25536.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4B0G2
#28: Protein eL8 (60S ribosomal protein L7a) / 60S ribosomal protein L7a


Mass: 29432.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4D668
#29: Protein uL13 (60S ribosomal protein L13a) / 60S ribosomal protein L13a-4


Mass: 23525.217 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4DN49
#30: Protein uL14 (60S ribosomal protein L23) / 60S ribosomal protein L23


Mass: 15040.858 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3XSQ1
#31: Protein uL15 (60S ribosomal protein L27a) / 60S ribosomal protein L27a-3-like


Mass: 16578.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4BFD5
#32: Protein uL16 (60S ribosomal protein L10) / 60S ribosomal protein L10-like


Mass: 25012.420 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3Z2D7
#33: Protein uL18 (60S ribosomal protein L5) / 60S ribosomal protein L5-like


Mass: 34627.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3XE16
#34: Protein uL22 (60S ribosomal protein L17) / 50S ribosomal protein L22 / chloroplastic


Mass: 20136.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4CCH0
#35: Protein uL23 (60S ribosomal protein L23a) / 60S ribosomal protein L23a / L25


Mass: 17321.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: Q07761
#36: Protein uL24 (60S ribosomal protein L26) / 60S ribosomal protein L26-1-like


Mass: 16748.537 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4DPM5
#37: Protein uL29 (60S ribosomal protein L35) / 60S ribosomal protein L35-like


Mass: 14352.466 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3WY31
#38: Protein uL2 (60S ribosomal protein L8) / 60S ribosomal protein L8-like


Mass: 28220.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3XXQ5
#39: Protein uL30 (60S ribosomal protein L7) / 60S ribosomal protein L7-4-like


Mass: 28148.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4A5Z2
#40: Protein uL3 (60S ribosomal protein L3) / 60S ribosomal protein L3


Mass: 44507.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3ZLI9
#41: Protein uL4 (60S ribosomal protein L4) / 60S ribosomal protein L4-like


Mass: 44706.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3X0M5
#42: Protein uL5 (60S ribosomal protein L11) / 60S ribosomal protein L11-1


Mass: 20794.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3XAW1
#43: Protein uL6 (60S ribosomal protein L9) / 60S ribosomal protein L9-1-like


Mass: 22057.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4C068

-
Protein/peptide , 2 types, 2 molecules pl

#24: Protein/peptide eL41 (60S ribosomal protein L41) / 60S ribosomal protein L41


Mass: 3445.437 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: P62121
#44: Protein/peptide nascent chain


Mass: 2060.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco)

-
Non-polymers , 6 types, 4567 molecules

#47: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 60 / Source method: obtained synthetically / Formula: Mg
#48: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 94 / Source method: obtained synthetically / Formula: K
#49: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#50: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H19N3
#51: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H26N4
#52: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4406 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: 40S subunit of the cytosolic 80S ribosome from tobacco
Type: RIBOSOME / Entity ID: #1-#35 / Source: NATURAL
Source (natural)Organism: Nicotiana tabacum (common tobacco)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 27 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

CTF correctionType: NONE
3D reconstructionResolution: 2.14 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 335291 / Symmetry type: POINT

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more