[English] 日本語
Yorodumi
- PDB-8auv: Cryo-EM structure of the plant 40S subunit -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8auv
TitleCryo-EM structure of the plant 40S subunit
Components
  • 18S rRNA
  • RACK1 (guanine nucleotide-binding protein subunit beta-like protein)
  • eS1 (40S ribosomal protein S3a)
  • eS10 (40S ribosomal protein S10)
  • eS12 (40S ribosomal protein S12)
  • eS17 (40S ribosomal protein S17)
  • eS19 (40S ribosomal protein S19)
  • eS21 (40S ribosomal protein S21)
  • eS24 (40S ribosomal protein S24)
  • eS25 (40S ribosomal protein S25)
  • eS26 (40S ribosomal protein S26)
  • eS27 (40S ribosomal protein S27)
  • eS28 (40S ribosomal protein S28)
  • eS30 (40S ribosomal protein S30)
  • eS31 (ubiquitin-40S ribosomal protein S27a)
  • eS4 (40S ribosomal protein S4)
  • eS6 (40S ribosomal protein S6)
  • eS7 (40S ribosomal protein S7)
  • eS8 (40S ribosomal protein S8)
  • mRNA
  • uS10 (40S ribosomal protein S20)
  • uS11 (40S ribosomal protein S14)
  • uS12 (40S ribosomal protein S23)
  • uS13 (40S ribosomal protein S18)
  • uS14 (40S ribosomal protein S29)
  • uS15 (40S ribosomal protein S13)
  • uS17 (40S ribosomal protein S11)
  • uS19 (40S ribosomal protein S15)
  • uS2 (40S ribosomal protein SA)
  • uS3 (40S ribosomal protein S3)
  • uS4 (40S ribosomal protein S9)
  • uS5 (40S ribosomal protein S2)
  • uS7 (40S ribosomal protein S5)
  • uS8 (40S ribosomal protein S15a)
  • uS9 (40S ribosomal protein S16)
KeywordsRIBOSOME / Plant / 80S / Modifications
Function / homology
Function and homology information


endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation regulator activity / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rescue of stalled ribosome / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / protein kinase C binding / maintenance of translational fidelity ...endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation regulator activity / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rescue of stalled ribosome / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / protein kinase C binding / maintenance of translational fidelity / modification-dependent protein catabolic process / rRNA processing / protein tag activity / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / positive regulation of protein phosphorylation / mRNA binding / ubiquitin protein ligase binding / nucleolus / RNA binding / zinc ion binding / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
: / Ribosomal protein S26e signature. / : / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S12e signature. / Ribosomal protein S12e ...: / Ribosomal protein S26e signature. / : / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S2, eukaryotic / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / 40S Ribosomal protein S10 / S27a-like superfamily / Ribosomal protein S10, eukaryotic/archaeal / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S2, eukaryotic/archaeal / : / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S30 / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S7e signature. / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal protein S3Ae, conserved site / Ribosomal protein S19e / Ribosomal protein S3Ae signature. / Ribosomal_S19e / Ribosomal protein S27e signature. / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S19A/S15e / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / Ribosomal protein S6, eukaryotic / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein S7e / Ribosomal protein S7e / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S24e / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S24e / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S6e signature. / Ribosomal protein S27 / Ribosomal protein S27 / Ribosomal protein S8e / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S3Ae / Ribosomal protein S28e conserved site / Ribosomal S3Ae family / Ribosomal protein S28e signature. / Ribosomal S3Ae family / Ribosomal protein S28e / Ribosomal protein S28e / Ribosomal protein S6e / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S8e / Ribosomal protein S14/S29 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Similarity search - Domain/homology
: / SPERMIDINE / SPERMINE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S25 / 40S ribosomal protein S14-2 ...: / SPERMIDINE / SPERMINE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S25 / 40S ribosomal protein S14-2 / 40S ribosomal protein S2-3-like / 40S ribosomal protein S30 / 40S ribosomal protein S20-2 / 40S ribosomal protein S27 / Small ribosomal subunit protein uS2 / 40S ribosomal protein S19-3 / 40S ribosomal protein S18 / 40S ribosomal protein S6 / 40S ribosomal protein S7 / 40S ribosomal protein S17-like / 40S ribosomal protein S13 / 40S ribosomal protein S24 / 40S ribosomal protein S21 / Guanine nucleotide-binding protein subunit beta-like protein / 40S ribosomal protein S28 / 40S ribosomal protein S16 / 40S ribosomal protein S12 / 40S ribosomal protein S9-2-like / 40S ribosomal protein S11-like / 40S ribosomal protein S5-like / 40S ribosomal protein S3-2-like / Ubiquitin-40S ribosomal protein S27a-like / 40S ribosomal protein S23 / 40S ribosomal protein S26 / 40S ribosomal protein S8 / 40S ribosomal protein S15a-1 / 40S ribosomal protein S15-like / 40S ribosomal protein S10-1-like / 40S ribosomal protein S29 / 40S ribosomal protein S4 / Small ribosomal subunit protein eS1
Similarity search - Component
Biological speciesNicotiana tabacum (common tobacco)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.38 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, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)416210002 Germany
German Research Foundation (DFG)INST 335/588-1 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
DepositionAug 25, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Jun 28, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Apr 24, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: eS4 (40S ribosomal protein S4)
k: eS6 (40S ribosomal protein S6)
h: 18S rRNA
l: eS10 (40S ribosomal protein S10)
C: eS12 (40S ribosomal protein S12)
D: eS17 (40S ribosomal protein S17)
E: eS19 (40S ribosomal protein S19)
F: eS1 (40S ribosomal protein S3a)
G: eS21 (40S ribosomal protein S21)
H: eS24 (40S ribosomal protein S24)
I: eS25 (40S ribosomal protein S25)
J: eS26 (40S ribosomal protein S26)
K: eS27 (40S ribosomal protein S27)
L: eS28 (40S ribosomal protein S28)
M: eS30 (40S ribosomal protein S30)
N: eS31 (ubiquitin-40S ribosomal protein S27a)
O: eS7 (40S ribosomal protein S7)
P: eS8 (40S ribosomal protein S8)
Q: RACK1 (guanine nucleotide-binding protein subunit beta-like protein)
R: uS10 (40S ribosomal protein S20)
S: uS11 (40S ribosomal protein S14)
T: uS12 (40S ribosomal protein S23)
U: uS13 (40S ribosomal protein S18)
V: uS14 (40S ribosomal protein S29)
W: uS15 (40S ribosomal protein S13)
X: uS17 (40S ribosomal protein S11)
Y: uS19 (40S ribosomal protein S15)
Z: uS2 (40S ribosomal protein SA)
a: uS3 (40S ribosomal protein S3)
b: uS4 (40S ribosomal protein S9)
c: uS5 (40S ribosomal protein S2)
d: uS7 (40S ribosomal protein S5)
e: uS8 (40S ribosomal protein S15a)
f: uS9 (40S ribosomal protein S16)
B: mRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,221,466165
Polymers1,216,83335
Non-polymers4,633130
Water42,7322372
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area259430 Å2
ΔGint-2082 kcal/mol
Surface area363680 Å2

-
Components

+
Protein , 33 types, 33 molecules AklCDEFGHIJKLMNOPQRSTUVWXYZabc...

#1: Protein eS4 (40S ribosomal protein S4) / 40S ribosomal protein S4


Mass: 29971.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4DQ51
#2: Protein eS6 (40S ribosomal protein S6) / 40S ribosomal protein S6


Mass: 28368.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3Z3Y7
#4: Protein eS10 (40S ribosomal protein S10)


Mass: 23121.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4DHU6
#5: Protein eS12 (40S ribosomal protein S12)


Mass: 15190.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4B129
#6: Protein eS17 (40S ribosomal protein S17) / 40S ribosomal protein S10-1-like


Mass: 16643.303 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3Z9G2
#7: Protein eS19 (40S ribosomal protein S19) / 40S ribosomal protein S12


Mass: 16034.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3Y949
#8: Protein eS1 (40S ribosomal protein S3a) / 40S ribosomal protein S17-like


Mass: 29782.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: Q285L8
#9: Protein eS21 (40S ribosomal protein S21) / 40S ribosomal protein S19-3


Mass: 9307.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4A3T4
#10: Protein eS24 (40S ribosomal protein S24) / 40S ribosomal protein S3a / Protein cyc07


Mass: 15429.315 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3ZXI6
#11: Protein eS25 (40S ribosomal protein S25) / 40S ribosomal protein S21


Mass: 11795.916 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A076L2E2
#12: Protein eS26 (40S ribosomal protein S26) / 40S ribosomal protein S24


Mass: 14540.069 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4CWI7
#13: Protein eS27 (40S ribosomal protein S27) / 40S ribosomal protein S25


Mass: 9613.144 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3XJK0
#14: Protein eS28 (40S ribosomal protein S28) / 40S ribosomal protein S26


Mass: 7481.715 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4AS05
#15: Protein eS30 (40S ribosomal protein S30) / 40S ribosomal protein S27


Mass: 6953.253 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3XGJ0
#16: Protein eS31 (ubiquitin-40S ribosomal protein S27a) / 40S ribosomal protein S28


Mass: 17739.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4C0C1
#17: Protein eS7 (40S ribosomal protein S7) / 40S ribosomal protein S30


Mass: 22121.541 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3Z906
#18: Protein eS8 (40S ribosomal protein S8) / ubiquitin-40S ribosomal protein S27a-like


Mass: 25164.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4CZK3
#19: Protein RACK1 (guanine nucleotide-binding protein subunit beta-like protein) / 40S ribosomal protein S7


Mass: 36061.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4ABX7
#20: Protein uS10 (40S ribosomal protein S20) / 40S ribosomal protein S8


Mass: 13651.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3XHL0
#21: Protein uS11 (40S ribosomal protein S14) / guanine nucleotide-binding protein subunit beta-like protein


Mass: 16375.829 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3XAN1
#22: Protein uS12 (40S ribosomal protein S23) / 40S ribosomal protein S20-2


Mass: 15771.567 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4C879
#23: Protein uS13 (40S ribosomal protein S18) / 40S ribosomal protein S14-2


Mass: 17578.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3YM01
#24: Protein uS14 (40S ribosomal protein S29) / 40S ribosomal protein S23


Mass: 6455.581 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4DPT4
#25: Protein uS15 (40S ribosomal protein S13) / 40S ribosomal protein S18


Mass: 17099.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3ZRI7
#26: Protein uS17 (40S ribosomal protein S11) / 40S ribosomal protein S29


Mass: 17724.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4BW10
#27: Protein uS19 (40S ribosomal protein S15) / 30S ribosomal protein S15 / chloroplastic


Mass: 17274.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4DFI4
#28: Protein uS2 (40S ribosomal protein SA) / 40S ribosomal protein S11-like


Mass: 35894.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3Y4M0
#29: Protein uS3 (40S ribosomal protein S3) / 40S ribosomal protein S15-like


Mass: 27758.545 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4BXU2
#30: Protein uS4 (40S ribosomal protein S9) / 40S ribosomal protein SA


Mass: 23103.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4B907
#31: Protein uS5 (40S ribosomal protein S2) / 40S ribosomal protein S3-2-like


Mass: 30652.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S3XAX8
#32: Protein uS7 (40S ribosomal protein S5) / 40S ribosomal protein S9-2-like


Mass: 23373.857 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4BXT5
#33: Protein uS8 (40S ribosomal protein S15a) / 40S ribosomal protein S2-3-like


Mass: 14815.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4DBQ8
#34: Protein uS9 (40S ribosomal protein S16) / 40S ribosomal protein S5-like


Mass: 16731.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: UniProt: A0A1S4AU23

-
RNA chain , 2 types, 2 molecules hB

#3: RNA chain 18S rRNA


Mass: 583622.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / References: GenBank: HQ384692
#35: RNA chain mRNA / 40S ribosomal protein S15a-1 / 40S ribosomal protein S15a-1 isoform X1


Mass: 3629.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco)

-
Non-polymers , 6 types, 2502 molecules

#36: Chemical...
ChemComp-MG / MAGNESIUM ION / 40S ribosomal protein S16


Mass: 24.305 Da / Num. of mol.: 76 / Source method: obtained synthetically / Formula: Mg
#37: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 47 / Source method: obtained synthetically / Formula: K
#38: 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
#39: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H26N4
#40: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#41: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2372 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
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: 2.38 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 335672 / 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://pdbjlvh1.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