[English] 日本語
Yorodumi
- PDB-8ipb: Wheat 80S ribosome pausing on AUG-Stop with cycloheximide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ipb
TitleWheat 80S ribosome pausing on AUG-Stop with cycloheximide
Components
  • (40S ribosomal protein ...) x 31
  • (60S ribosomal protein ...) x 41
  • 18S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • 60S ribosomal RNA
  • RACK1
  • mRNA
  • tRNAi
KeywordsTRANSLATION / ribosome
Function / homology
Function and homology information


endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / 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 LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis ...endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / 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 LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / protein kinase C binding / rRNA processing / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / ribosome biogenesis / ribosome binding / small ribosomal subunit / large ribosomal subunit rRNA binding / 5S rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / positive regulation of protein phosphorylation / mRNA binding / nucleolus / RNA binding / zinc ion binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L2, archaeal-type / Ribosomal protein L28e / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S26e ...Ribosomal protein L2, archaeal-type / Ribosomal protein L28e / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / metallochaperone-like domain / TRASH domain / Ribosomal protein L29e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal L29e protein family / 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 / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S2, eukaryotic/archaeal / : / Ribosomal protein S30 / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein S7e signature. / Ribosomal protein L44e signature. / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L10e / Ribosomal protein L19, eukaryotic / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein S19e / Ribosomal protein S3Ae, conserved site / Ribosomal protein S19e / Ribosomal protein S3Ae signature. / Ribosomal_S19e / Ribosomal protein S27e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / 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 L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein S8e signature. / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L6e signature. / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal L40e family / Ribosomal protein L30e signature 1. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein S6, eukaryotic / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein L23/L25, N-terminal
Similarity search - Domain/homology
Chem-3HE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS8c / Ribosomal protein L35A / 60S ribosomal protein L29 / 40S ribosomal protein S4 ...Chem-3HE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS8c / Ribosomal protein L35A / 60S ribosomal protein L29 / 40S ribosomal protein S4 / Large ribosomal subunit protein uL23 N-terminal domain-containing protein / 60S ribosomal protein L38 / Ubiquitin-like domain-containing protein / Ribosomal protein L37 / 40S ribosomal protein S6 / 60S ribosomal protein L27 / 60S ribosomal protein L11 / 40S ribosomal protein S17 / Large ribosomal subunit protein uL4 C-terminal domain-containing protein / Large ribosomal subunit protein eL28 / Large ribosomal subunit protein uL15/eL18 domain-containing protein / 40S ribosomal protein S8 / 60S ribosomal protein L22 / Ribosomal protein L19 / Large ribosomal subunit protein uL15/eL18 domain-containing protein / Large ribosomal subunit protein eL14 domain-containing protein / Uncharacterized protein / KOW domain-containing protein / Uncharacterized protein / 40S ribosomal protein S16 / Small ribosomal subunit protein eS1 / 40S ribosomal protein S29 / S5 DRBM domain-containing protein / 40S ribosomal protein S26 / 60S ribosomal protein L13 / 40S ribosomal protein S24 / 60S ribosomal protein L6 / 60S ribosomal protein L7a / 60S ribosomal protein L34 / 40S ribosomal protein S30 / 60S ribosomal protein L32 / 30S ribosomal protein S11, chloroplastic / 60S ribosomal protein L37a, expressed / 60S ribosomal protein L21 / 60S ribosomal protein L39 / Small ribosomal subunit protein eS32 / 40S ribosomal protein S7 / Ribosomal protein L17 / Ribosomal protein L13a / 60S ribosomal protein L36 / Cytoplasmatic ribosomal protein S13 / Ribosomal protein L3 / S28 ribosomal protein / 30S ribosomal protein S3, chloroplastic / Large ribosomal subunit protein uL29 / Putative ribosomal protein S18 / Ribosomal protein S20 / Ribosomal protein eL8/eL30/eS12/Gadd45 domain-containing protein / Uncharacterized protein / Plectin/eS10 N-terminal domain-containing protein / Small ribosomal subunit protein uS17 N-terminal domain-containing protein / Large ribosomal subunit protein uL18 C-terminal eukaryotes domain-containing protein / TRASH domain-containing protein / Small ribosomal subunit protein uS7c / Uncharacterized protein / 60S ribosomal protein L18a / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein uL2 C-terminal domain-containing protein / 40S ribosomal protein S21 / 40S ribosomal protein S25 / Ribosomal protein L15 / 30S ribosomal protein S4, chloroplastic / Uncharacterized protein / 40S ribosomal protein S23 / 40S ribosomal protein S19 / 60S ribosomal protein L31 / Uncharacterized protein / 40S ribosomal protein S27 / Large ribosomal subunit protein uL6 alpha-beta domain-containing protein
Similarity search - Component
Biological speciesTriticum aestivum (bread wheat)
Oryza sativa (Asian cultivated rice)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsYokoyama, T. / Tanaka, M. / Saito, H. / Nishimoto, M. / Tsuda, K. / Sotta, N. / Shigematsu, H. / Shirouzu, M. / Iwasaki, S. / Ito, T. / Fujiwara, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP19H05637 Japan
CitationJournal: Nat Chem Biol / Year: 2024
Title: Boric acid intercepts 80S ribosome migration from AUG-stop by stabilizing eRF1.
Authors: Mayuki Tanaka / Takeshi Yokoyama / Hironori Saito / Madoka Nishimoto / Kengo Tsuda / Naoyuki Sotta / Hideki Shigematsu / Mikako Shirouzu / Shintaro Iwasaki / Takuhiro Ito / Toru Fujiwara /
Abstract: In response to environmental changes, cells flexibly and rapidly alter gene expression through translational controls. In plants, the translation of NIP5;1, a boric acid diffusion facilitator, is ...In response to environmental changes, cells flexibly and rapidly alter gene expression through translational controls. In plants, the translation of NIP5;1, a boric acid diffusion facilitator, is downregulated in response to an excess amount of boric acid in the environment through upstream open reading frames (uORFs) that consist of only AUG and stop codons. However, the molecular details of how this minimum uORF controls translation of the downstream main ORF in a boric acid-dependent manner have remained unclear. Here, by combining ribosome profiling, translation complex profile sequencing, structural analysis with cryo-electron microscopy and biochemical assays, we show that the 80S ribosome assembled at AUG-stop migrates into the subsequent RNA segment, followed by downstream translation initiation, and that boric acid impedes this process by the stable confinement of eukaryotic release factor 1 on the 80S ribosome on AUG-stop. Our results provide molecular insight into translation regulation by a minimum and environment-responsive uORF.
History
DepositionMar 14, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
aa: 18S ribosomal RNA
ba: 40S ribosomal protein eS24
ca: 40S ribosomal protein eS8
da: 40S ribosomal protein eS10
ga: 40S ribosomal protein uS12
ha: RACK1
ia: 40S ribosomal protein uS3
ja: 40S ribosomal protein eS4
ka: 40S ribosomal protein uS7
la: 40S ribosomal protein uS9
ma: 40S ribosomal protein uS10
na: 40S ribosomal protein uS11
oa: 40S ribosomal protein uS13
pa: 40S ribosomal protein uS15
qa: 40S ribosomal protein eS17
ra: 40S ribosomal protein eS19
sa: 40S ribosomal protein uS19
ta: 40S ribosomal protein eS25
ua: 40S ribosomal protein eS28
va: 40S ribosomal protein uS8
wa: 40S ribosomal protein uS14
xa: 40S ribosomal protein eS27
ya: 40S ribosomal protein eS30
za: 40S ribosomal protein uS2
bb: 40S ribosomal protein eS1
cb: 40S ribosomal protein eS21
db: 40S ribosomal protein eS26
eb: 40S ribosomal protein uS4
fb: 40S ribosomal protein uS5
gb: 40S ribosomal protein eS6
hb: 40S ribosomal protein eS7
ib: 40S ribosomal protein uS17
AA: 40S ribosomal protein eL8
BA: 60S ribosomal protein eL21
CA: 60S ribosomal protein eL27
DA: 60S ribosomal protein uL2
EA: 60S ribosomal protein uL5
FA: 60S ribosomal protein uL6
GA: 60S ribosomal protein uL14
HA: 60S ribosomal protein eL15
IA: 60S ribosomal protein uL15
JA: 60S ribosomal protein eL18
KA: 60S ribosomal protein uL18
LA: 60S ribosomal protein eL19
MA: 60S ribosomal protein uL22
NA: 60S ribosomal protein uL23
OA: 60S ribosomal protein eL24
PA: 60S ribosomal protein uL24
QA: 60S ribosomal protein eL28
RA: 60S ribosomal protein eL30
SA: 60S ribosomal protein eL31
TA: 60S ribosomal protein eL32
UA: 60S ribosomal protein eL37
VA: 60S ribosomal protein eL39
WA: 60S ribosomal protein eL42
XA: 60S ribosomal protein eL14
YA: 60S ribosomal protein eL20
ZA: 60S ribosomal protein eL22
AB: 60S ribosomal protein eL36
BB: 60S ribosomal protein uL29
CB: 60S ribosomal protein uL30
DB: 60S ribosomal protein uL3
EB: 60S ribosomal protein uL4
FB: 60S ribosomal protein uL13
GB: 60S ribosomal protein eL43
HB: 60S ribosomal protein uL16
IB: 60S ribosomal protein eL41
JB: 60S ribosomal protein eL40
KB: 60S ribosomal protein eL13
LB: 60S ribosomal protein eL6
MB: 60S ribosomal protein eL33
NB: 60S ribosomal protein eL38
OB: 60S ribosomal protein eL29
PB: 60S ribosomal protein eL34
RB: 60S ribosomal RNA
SB: 5.8S ribosomal RNA
TB: 5S ribosomal RNA
al: mRNA
cl: tRNAi
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,193,935349
Polymers3,186,95179
Non-polymers6,984270
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
RNA chain , 6 types, 6 molecules aaRBSBTBalcl

#1: RNA chain 18S ribosomal RNA


Mass: 583613.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: GenBank: 2123606567
#75: RNA chain 60S ribosomal RNA


Mass: 1095659.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#76: RNA chain 5.8S ribosomal RNA


Mass: 51535.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#77: RNA chain 5S ribosomal RNA


Mass: 38716.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#78: RNA chain mRNA


Mass: 2229.403 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)
#79: RNA chain tRNAi


Mass: 24446.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat)

+
40S ribosomal protein ... , 31 types, 31 molecules bacadagaiajakalamanaoapaqarasatauavawaxayazabbcbdbebfbgbhbibAA

#2: Protein 40S ribosomal protein eS24 / 40S ribosomal protein S24


Mass: 15739.685 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6PK86
#3: Protein 40S ribosomal protein eS8 / 40S ribosomal protein S8


Mass: 25341.096 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6AYT7
#4: Protein 40S ribosomal protein eS10 / Plectin/S10 N-terminal domain-containing protein


Mass: 20463.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5AUH7
#5: Protein 40S ribosomal protein uS12 / 40S ribosomal protein S23


Mass: 15696.476 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5FV77
#7: Protein 40S ribosomal protein uS3 / Putative 40S ribosomal protein S3


Mass: 25413.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q8L804
#8: Protein 40S ribosomal protein eS4 / 40S ribosomal protein S4


Mass: 30008.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A1D5SLI4
#9: Protein 40S ribosomal protein uS7 / Ribosomal protein S7 domain-containing protein


Mass: 22350.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5D067
#10: Protein 40S ribosomal protein uS9 / 40S ribosomal protein S16


Mass: 16870.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6HX49
#11: Protein 40S ribosomal protein uS10 / Ribosomal protein S20


Mass: 14128.448 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: U5HTD8
#12: Protein 40S ribosomal protein uS11 / 40S ribosomal protein S14


Mass: 16398.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6SS17
#13: Protein 40S ribosomal protein uS13 / Putative ribosomal protein S18


Mass: 17702.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q8L806
#14: Protein 40S ribosomal protein uS15 / Cytoplasmatic ribosomal protein S13


Mass: 17102.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q5XUU9
#15: Protein 40S ribosomal protein eS17


Mass: 16523.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B5YWZ3
#16: Protein 40S ribosomal protein eS19 / 40S ribosomal protein S19


Mass: 17097.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5FWF5
#17: Protein 40S ribosomal protein uS19 / Genome assembly / chromosome: II


Mass: 17424.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5ASA4
#18: Protein 40S ribosomal protein eS25 / 40S ribosomal protein S25


Mass: 12094.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5EP45
#19: Protein 40S ribosomal protein eS28 / S28 ribosomal protein (Fragment)


Mass: 9815.345 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q7X9K4
#20: Protein 40S ribosomal protein uS8 / 30S ribosomal protein S8 / chloroplastic


Mass: 14924.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A077RZD1
#21: Protein 40S ribosomal protein uS14 / 40S ribosomal protein S29


Mass: 6391.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6LU46
#22: Protein 40S ribosomal protein eS27 / 40S ribosomal protein S27


Mass: 9583.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5HZ68
#23: Protein 40S ribosomal protein eS30 / 40S ribosomal protein S30


Mass: 6934.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6S9M7
#24: Protein 40S ribosomal protein uS2 / 40S ribosomal protein SA


Mass: 33300.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5E2W7
#25: Protein 40S ribosomal protein eS1 / 40S ribosomal protein S3a


Mass: 30043.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6IU74
#26: Protein 40S ribosomal protein eS21 / 40S ribosomal protein S21


Mass: 9194.349 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5EL62
#27: Protein 40S ribosomal protein eS26 / 40S ribosomal protein S26


Mass: 16576.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6LWE1
#28: Protein 40S ribosomal protein uS4 / 30S ribosomal protein S4 / chloroplastic


Mass: 22534.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5FPA7
#29: Protein 40S ribosomal protein uS5 / S5 DRBM domain-containing protein


Mass: 29995.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6LVN2
#30: Protein 40S ribosomal protein eS6 / 40S ribosomal protein S6


Mass: 28488.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A2X0SLI3
#31: Protein 40S ribosomal protein eS7 / 40S ribosomal protein S7


Mass: 22297.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q5I7K2
#32: Protein 40S ribosomal protein uS17 / 40S ribosomal protein S11 N-terminal domain-containing protein


Mass: 17841.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5BFB7
#33: Protein 40S ribosomal protein eL8 / 60S ribosomal protein L7a


Mass: 29407.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6RED0

-
Protein , 1 types, 1 molecules ha

#6: Protein RACK1 / WD_REPEATS_REGION domain-containing protein


Mass: 36200.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5D4F5

+
60S ribosomal protein ... , 41 types, 41 molecules BACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAUAVAWAXAYAZAABBBCBDBEB...

#34: Protein 60S ribosomal protein eL21 / 60S ribosomal protein L21


Mass: 18719.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: F4YWL9
#35: Protein 60S ribosomal protein eL27 / 60S ribosomal protein L27


Mass: 15615.687 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A341XZK6
#36: Protein 60S ribosomal protein uL2 / Ribosomal protein L2 C-terminal domain-containing protein


Mass: 28251.521 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5ECL2
#37: Protein 60S ribosomal protein uL5 / 60S ribosomal protein L11


Mass: 20725.115 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B5XX39
#38: Protein 60S ribosomal protein uL6 / Ribosomal protein L6 alpha-beta domain-containing protein


Mass: 21329.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5I5G5
#39: Protein 60S ribosomal protein uL14 / Ribosomal protein L17


Mass: 15040.856 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q5I7K4
#40: Protein 60S ribosomal protein eL15 / Ribosomal protein L15


Mass: 24488.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5FEX7
#41: Protein 60S ribosomal protein uL15 / Ribosomal protein L18e/L15P domain-containing protein


Mass: 16054.964 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6DCS5
#42: Protein 60S ribosomal protein eL18 / Ribosomal protein L18e/L15P domain-containing protein


Mass: 21292.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6ATQ1
#43: Protein 60S ribosomal protein uL18 / Ribosomal protein L5 eukaryotic C-terminal domain-containing protein


Mass: 34486.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5BZZ2
#44: Protein 60S ribosomal protein eL19 / Ribosomal protein L19


Mass: 24692.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6DA12
#45: Protein 60S ribosomal protein uL22


Mass: 19525.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5FSM8
#46: Protein 60S ribosomal protein uL23 / Genome assembly / chromosome: II


Mass: 16920.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A1D5UQZ5
#47: Protein 60S ribosomal protein eL24 / TRASH domain-containing protein


Mass: 18450.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5CDW4
#48: Protein 60S ribosomal protein uL24 / KOW domain-containing protein


Mass: 17585.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6GQI2
#49: Protein 60S ribosomal protein eL28 / Ribosomal L28e/Mak16 domain-containing protein


Mass: 16607.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B5ZZN9
#50: Protein 60S ribosomal protein eL30 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 domain-containing protein


Mass: 12372.487 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W4ZRU3
#51: Protein 60S ribosomal protein eL31 / 60S ribosomal protein L31


Mass: 14152.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5G990
#52: Protein 60S ribosomal protein eL32


Mass: 15737.636 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6SDD9
#53: Protein 60S ribosomal protein eL37 / Ribosomal protein L37


Mass: 10765.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A1D6BC85
#54: Protein 60S ribosomal protein eL39 / 60S ribosomal protein L39


Mass: 9439.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: M7ZU91
#55: Protein 60S ribosomal protein eL42 / Genome assembly / chromosome: II


Mass: 12139.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5HX73
#56: Protein 60S ribosomal protein eL14 / Ribosomal protein L14e domain-containing protein


Mass: 15490.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6DGT8
#57: Protein 60S ribosomal protein eL20 / 60S ribosomal protein L18a


Mass: 21380.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5D7B8
#58: Protein 60S ribosomal protein eL22


Mass: 14503.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6C0D4
#59: Protein 60S ribosomal protein eL36 / 60S ribosomal protein L36


Mass: 12563.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q5I7L5
#60: Protein 60S ribosomal protein uL29 / 60S ribosomal protein L35


Mass: 14401.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q8L805
#61: Protein 60S ribosomal protein uL30


Mass: 28161.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6DM38
#62: Protein 60S ribosomal protein uL3 / Ribosomal protein L3


Mass: 44722.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q7X748
#63: Protein 60S ribosomal protein uL4 / 60S ribosomal protein L4 C-terminal domain-containing protein


Mass: 44285.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B5ZXX7
#64: Protein 60S ribosomal protein uL13 / Ribosomal protein L13a


Mass: 23581.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q5I7L1
#65: Protein 60S ribosomal protein eL43 / 60S ribosomal protein L37a / expressed


Mass: 10266.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: D8L9P6
#66: Protein 60S ribosomal protein uL16 / Ribosomal protein L10e/L16 domain-containing protein


Mass: 24516.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6HUM3
#67: Protein/peptide 60S ribosomal protein eL41 / 60S ribosomal protein L41


Mass: 3445.437 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryza sativa (Asian cultivated rice) / References: UniProt: P62125
#68: Protein 60S ribosomal protein eL40 / Ubiquitin-like domain-containing protein


Mass: 14828.420 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A1D5XNC2
#69: Protein 60S ribosomal protein eL13 / 60S ribosomal protein L13


Mass: 24185.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6NJZ9
#70: Protein 60S ribosomal protein eL6 / 60S ribosomal protein L6


Mass: 24575.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6QGW3
#71: Protein 60S ribosomal protein eL33


Mass: 12704.744 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A0C4BK99
#72: Protein 60S ribosomal protein eL38 / 60S ribosomal protein L38


Mass: 8067.592 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: The sequence refer to database XP_044323325.1 / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A1D5W6Q2
#73: Protein 60S ribosomal protein eL29 / 60S ribosomal protein L29


Mass: 6994.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A1D5RRD3
#74: Protein 60S ribosomal protein eL34 / 60S ribosomal protein L34


Mass: 13798.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: A0A3B6RFY8

-
Non-polymers , 3 types, 270 molecules

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


Mass: 24.305 Da / Num. of mol.: 265 / Source method: obtained synthetically / Formula: Mg
#81: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#82: Chemical ChemComp-3HE / 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione


Mass: 281.347 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23NO4

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Wheat 80S ribosome pausing on AUG-Stop with cycloheximide
Type: RIBOSOME / Entity ID: #1-#79 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Triticum aestivum (bread wheat)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 23500 X / Nominal defocus max: 3500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: OTHER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

EM software
IDNameCategory
1RELIONparticle selection
2SerialEMimage acquisition
4CTFFINDCTF correction
7Cootmodel fitting
9RELIONinitial Euler assignment
10RELIONfinal Euler assignment
11RELIONclassification
12RELION3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 52217 / 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