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- PDB-7nwh: Mammalian pre-termination 80S ribosome with eRF1 and eRF3 bound b... -

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Basic information

Entry
Database: PDB / ID: 7nwh
TitleMammalian pre-termination 80S ribosome with eRF1 and eRF3 bound by Blasticidin S.
Components
  • (40S ribosomal protein ...) x 23
  • (60S RIBOSOMAL PROTEIN ...) x 16
  • (Ribosomal protein ...) x 10
  • 18S Ribosomal RNA
  • 28S Ribosomal RNA
  • 40S_SA_C domain-containing protein
  • 5.8S Ribosomal RNA
  • 5S Ribosomal RNA
  • 60S acidic ribosomal protein P0
  • Epididymis tissue sperm binding protein Li 3a
  • Eukaryotic peptide chain release factor subunit 1
  • L22
  • L38
  • L7a
  • L9
  • S29
  • S7
  • eL14
  • eL18
  • eL21
  • eL28
  • eL29
  • eL30
  • eL31
  • eL33
  • eL39
  • eL42
  • eRF3a
  • eS19
  • mRNAMessenger RNA
  • uL12
  • uL22
  • uL23
  • uL29
  • uL3
  • uL30
  • uL4
  • uS11
KeywordsRIBOSOME / Inhibitor 80S Termination Complex Blasticidin S Translation NMD
Function / homology
Function and homology information


L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Major pathway of rRNA processing in the nucleolus and cytosol / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition ...L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Major pathway of rRNA processing in the nucleolus and cytosol / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Major pathway of rRNA processing in the nucleolus and cytosol / GTP hydrolysis and joining of the 60S ribosomal subunit / translation termination factor activity / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Downregulation of ERBB4 signaling / Spry regulation of FGF signaling / Downregulation of ERBB2:ERBB3 signaling / NOD1/2 Signaling Pathway / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / APC-Cdc20 mediated degradation of Nek2A / EGFR downregulation / TCF dependent signaling in response to WNT / NRIF signals cell death from the nucleus / p75NTR recruits signalling complexes / NF-kB is activated and signals survival / Activated NOTCH1 Transmits Signal to the Nucleus / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Senescence-Associated Secretory Phenotype (SASP) / Regulation of innate immune responses to cytosolic DNA / activated TAK1 mediates p38 MAPK activation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of FZD by ubiquitination / PINK1-PRKN Mediated Mitophagy / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of TNFR1 signaling / TNFR1-induced NF-kappa-B signaling pathway / Translesion synthesis by POLK / Translesion synthesis by POLI / Regulation of necroptotic cell death / MAP3K8 (TPL2)-dependent MAPK1/3 activation / HDR through Homologous Recombination (HRR) / Josephin domain DUBs / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / DNA Damage Recognition in GG-NER / Formation of Incision Complex in GG-NER / Gap-filling DNA repair synthesis and ligation in GG-NER / Dual Incision in GG-NER / Fanconi Anemia Pathway / Regulation of TP53 Activity through Phosphorylation / Regulation of TP53 Degradation / Regulation of TP53 Activity through Methylation / Negative regulation of MET activity / Cyclin D associated events in G1 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Downregulation of ERBB2 signaling / E3 ubiquitin ligases ubiquitinate target proteins / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) / Regulation of expression of SLITs and ROBOs / Interferon alpha/beta signaling / Endosomal Sorting Complex Required For Transport (ESCRT) / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / IKK complex recruitment mediated by RIP1 / IRAK2 mediated activation of TAK1 complex / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Alpha-protein kinase 1 signaling pathway / RAS processing / Pexophagy / Inactivation of CSF3 (G-CSF) signaling / Negative regulation of FLT3 / Regulation of BACH1 activity / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of NF-kappa B signaling / Termination of translesion DNA synthesis / Ovarian tumor domain proteases / Negative regulators of DDX58/IFIH1 signaling / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Negative regulation of MAPK pathway / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Iron uptake and transport / Deactivation of the beta-catenin transactivating complex / Metalloprotease DUBs / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Activation of NF-kappaB in B cells / L13a-mediated translational silencing of Ceruloplasmin expression / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A
Similarity search - Function
Peptide chain release factor eRF1/aRF1 / eRF1, domain 1 / eRF1 domain 2 / eRF1 domain 2 / eRF1 domain 1 / eRF1 domain 1/Pelota-like / eRF1 domain 3 / eRF1, domain 2 superfamily / eRF1 domain 3 / eRF1_1 ...Peptide chain release factor eRF1/aRF1 / eRF1, domain 1 / eRF1 domain 2 / eRF1 domain 2 / eRF1 domain 1 / eRF1 domain 1/Pelota-like / eRF1 domain 3 / eRF1, domain 2 superfamily / eRF1 domain 3 / eRF1_1 / : / Ribosomal protein L2, archaeal-type / : / metallochaperone-like domain / TRASH domain / Ribosomal protein S21e, conserved site / Ribosomal protein S26e / Ribosomal protein S26e superfamily / S27a-like superfamily / Ribosomal protein S26e / Ribosomal protein S26e signature. / Ribosomal protein S17e, conserved site / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S21e signature. / Ribosomal protein S12e signature. / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal protein S27a / Ribosomal protein L24e, conserved site / Ribosomal S17 / 40S Ribosomal protein S10 / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein L19, eukaryotic / Ribosomal protein S17e signature. / Ribosomal protein L10e signature. / Ribosomal protein L27e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L19/L19e conserved site / Ribosomal protein L39e, conserved site / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L19e signature. / Ribosomal protein L24e signature. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L34e signature. / Ribosomal protein L6e signature. / Ribosomal protein L30e signature 1. / Ribosomal protein L30e signature 2. / 60S ribosomal protein L19 / Ribosomal protein L39e signature. / Ribosomal protein L39e / Ribosomal protein L24e-related / Ribosomal protein L39e domain superfamily / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L35Ae signature. / Ribosomal_L19e / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal L39 protein / Ribosomal protein L19e / Ribosomal protein S28e signature. / Ribosomal protein L24e / Ribosomal protein L5 eukaryotic/L18 archaeal / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal protein L32e signature. / Ribosomal protein L6 signature 2. / Ribosomal protein L1e signature. / Ribosomal protein L15e signature. / Ribosomal protein L21e signature. / Ribosomal protein L37e signature. / 50S ribosomal protein L30e-like / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ribosomal protein L23 signature. / Ribosomal protein L30 signature. / Ribosomal protein S3 signature. / Ubiquitin family / Ribosomal protein L5 signature. / Ribosomal protein L2, conserved site / Ribosomal protein L2 signature. / Ribosomal protein L29 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S4, conserved site / Type-2 KH domain profile. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9 / Ribosomal protein S19 signature. / Ubiquitin homologues / Ribosomal protein L2, domain 3
Similarity search - Domain/homology
BLASTICIDIN S / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL24 / Small ribosomal subunit protein eS32 / Small ribosomal subunit protein uS4 ...BLASTICIDIN S / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL24 / Small ribosomal subunit protein eS32 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein eL20 / 40S ribosomal protein S10 / Large ribosomal subunit protein uL16 / Epididymis tissue sperm binding protein Li 3a / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL33 / Small ribosomal subunit protein eS12 / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL14 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein eL15 / Small ribosomal subunit protein uS11 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Small ribosomal subunit protein eS25 / Large ribosomal subunit protein eL30 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein eS28 / Large ribosomal subunit protein uL3 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS13 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein eL27 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein eL28 / Large ribosomal subunit protein eL34 / Eukaryotic peptide chain release factor subunit 1 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein eS21 / 60S ribosomal protein L8 / Large ribosomal subunit protein eL19 / 40S ribosomal protein S17 / 40S ribosomal protein S26 / Large ribosomal subunit protein eL37
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsPowers, K.T. / Yadav, S.K.N. / Bufton, J.C. / Schaffitzel, C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust210701/Z/18/Z United Kingdom
CitationJournal: Nucleic Acids Res / Year: 2021
Title: Blasticidin S inhibits mammalian translation and enhances production of protein encoded by nonsense mRNA.
Authors: Kyle T Powers / Flint Stevenson-Jones / Sathish K N Yadav / Beate Amthor / Joshua C Bufton / Ufuk Borucu / Dakang Shen / Jonas P Becker / Daria Lavysh / Matthias W Hentze / Andreas E Kulozik ...Authors: Kyle T Powers / Flint Stevenson-Jones / Sathish K N Yadav / Beate Amthor / Joshua C Bufton / Ufuk Borucu / Dakang Shen / Jonas P Becker / Daria Lavysh / Matthias W Hentze / Andreas E Kulozik / Gabriele Neu-Yilik / Christiane Schaffitzel /
Abstract: Deciphering translation is of paramount importance for the understanding of many diseases, and antibiotics played a pivotal role in this endeavour. Blasticidin S (BlaS) targets translation by binding ...Deciphering translation is of paramount importance for the understanding of many diseases, and antibiotics played a pivotal role in this endeavour. Blasticidin S (BlaS) targets translation by binding to the peptidyl transferase center of the large ribosomal subunit. Using biochemical, structural and cellular approaches, we show here that BlaS inhibits both translation elongation and termination in Mammalia. Bound to mammalian terminating ribosomes, BlaS distorts the 3'CCA tail of the P-site tRNA to a larger extent than previously reported for bacterial ribosomes, thus delaying both, peptide bond formation and peptidyl-tRNA hydrolysis. While BlaS does not inhibit stop codon recognition by the eukaryotic release factor 1 (eRF1), it interferes with eRF1's accommodation into the peptidyl transferase center and subsequent peptide release. In human cells, BlaS inhibits nonsense-mediated mRNA decay and, at subinhibitory concentrations, modulates translation dynamics at premature termination codons leading to enhanced protein production.
History
DepositionMar 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: 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
Revision 1.2Jan 11, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: 60S ribosomal protein L8
C: uL4
d: eL31
DD: 40S ribosomal protein S3
dd: S29
D: 60S ribosomal protein L5
e: Ribosomal protein L32
EE: 40S ribosomal protein S4
ee: 40S ribosomal protein S30
b: eL29
E: 60S ribosomal protein L6
f: eL33
FF: Ribosomal protein S5
ff: 40S ribosomal protein S27a
F: uL30
g: 60S ribosomal protein L34
BB: 40S ribosomal protein S3a
GG: 40S ribosomal protein S6
gg: Epididymis tissue sperm binding protein Li 3a
G: L7a
h: uL29
HH: S7
hh: mRNA
bb: 40S ribosomal protein S27
H: L9
i: 60S ribosomal protein L36
II: 40S ribosomal protein S8
ii: Eukaryotic peptide chain release factor subunit 1
I: 60S ribosomal protein L10
j: Ribosomal protein L37
JJ: 40S ribosomal protein S9
jj: eRF3a
J: 60S ribosomal protein L11
k: L38
KK: 40S ribosomal protein S10
L: 60S ribosomal protein L13
l: eL39
LL: 40S ribosomal protein S11
M: Ribosomal protein L14
m: 60S RIBOSOMAL PROTEIN EL40
MM: 40S ribosomal protein S12
N: Ribosomal protein L15
n: 60s ribosomal protein l41
NN: ribosomal protein uS15
O: 60S RIBOSOMAL PROTEIN UL13
o: eL42
OO: uS11
P: uL22
p: ribosomal protein eL43
PP: 40S ribosomal protein uS19
Q: eL18
r: eL28
QQ: Ribosomal protein S16
R: 60S ribosomal protein L19
s: 60S acidic ribosomal protein P0
RR: 40S ribosomal protein S17
S: 60S ribosomal protein L18a
t: uL12
SS: 40S ribosomal protein uS13
T: eL21
TT: eS19
U: L22
UU: 40S ribosomal protein S20
V: eL14
VV: 40S ribosomal protein S21
W: 60S ribosomal protein L24-like protein
5: 28S Ribosomal RNA
WW: Ribosomal protein S15a
X: uL23
7: 5S Ribosomal RNA
XX: 40S ribosomal protein uS12
Y: Ribosomal protein L26
8: 5.8S Ribosomal RNA
YY: 40S ribosomal protein S24
Z: 60S ribosomal protein L27
9: 18S Ribosomal RNA
ZZ: 40S ribosomal protein S25
a: 60S ribosomal protein L27a
AA: 40S_SA_C domain-containing protein
aa: 40S ribosomal protein S26
B: uL3
c: eL30
CC: 40S ribosomal protein S2
cc: 40S ribosomal protein S28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,476,517375
Polymers3,468,22184
Non-polymers8,297291
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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60S RIBOSOMAL PROTEIN ... , 16 types, 16 molecules ADEgiIJLmnORSWZa

#1: Protein 60S ribosomal protein L8 /


Mass: 27129.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: Q3T0S6
#6: Protein 60S ribosomal protein L5 /


Mass: 34350.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SYJ6
#11: Protein 60S ribosomal protein L6 /


Mass: 33028.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SKF7
#16: Protein 60S ribosomal protein L34 /


Mass: 14210.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U945
#26: Protein 60S ribosomal protein L36 /


Mass: 12317.796 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#29: Protein 60S ribosomal protein L10 / / Ribosomal protein L10 (Predicted)


Mass: 24643.057 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZQ2
#33: Protein 60S ribosomal protein L11 /


Mass: 20086.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TUB8
#36: Protein 60S ribosomal protein L13 /


Mass: 24331.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#40: Protein 60S RIBOSOMAL PROTEIN EL40 /


Mass: 14695.310 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#43: Protein/peptide 60s ribosomal protein l41 / / eL41


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A087WNH4
#45: Protein 60S RIBOSOMAL PROTEIN UL13 /


Mass: 23533.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#54: Protein 60S ribosomal protein L19 /


Mass: 23535.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: Q3T0W9
#57: Protein 60S ribosomal protein L18a /


Mass: 20827.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A287APR1
#66: Protein 60S ribosomal protein L24-like protein / Ribosome


Mass: 15538.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A061I3X8
#75: Protein 60S ribosomal protein L27 /


Mass: 15835.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TXF6
#78: Protein 60S ribosomal protein L27a /


Mass: 16489.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SNY0

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Protein , 30 types, 30 molecules CdddbfFggGhHHHiijjkloOOPQrstTTTUVXAABc

#2: Protein uL4


Mass: 42825.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVW5
#3: Protein eL31


Mass: 12766.890 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#5: Protein S29


Mass: 6690.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#10: Protein eL29


Mass: 24931.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SGR6
#12: Protein eL33


Mass: 12580.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SF08
#15: Protein uL30


Mass: 29514.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SV32
#19: Protein Epididymis tissue sperm binding protein Li 3a


Mass: 34800.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: E9KL35
#20: Protein L7a


Mass: 27611.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#21: Protein uL29


Mass: 14566.599 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SIT5
#22: Protein S7


Mass: 21847.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#25: Protein L9


Mass: 21627.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SWI6
#28: Protein Eukaryotic peptide chain release factor subunit 1 / Eukaryotic release factor 1 / eRF1


Mass: 49092.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P62497
#32: Protein eRF3a


Mass: 48056.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#34: Protein L38


Mass: 8238.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#37: Protein eL39


Mass: 6455.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TTN1
#46: Protein eL42


Mass: 16170.214 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#47: Protein uS11


Mass: 16916.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T1F0
#48: Protein uL22


Mass: 23056.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#51: Protein eL18


Mass: 21699.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#52: Protein eL28


Mass: 15783.614 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7L1
#55: Protein 60S acidic ribosomal protein P0 /


Mass: 34380.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SPK4
#58: Protein uL12


Mass: 21426.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#60: Protein eL21 /


Mass: 18609.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHQ2
#61: Protein eS19


Mass: 16106.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#62: Protein L22


Mass: 14798.989 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#64: Protein eL14


Mass: 14103.620 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#69: Protein uL23


Mass: 17768.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SE76
#79: Protein 40S_SA_C domain-containing protein


Mass: 32958.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#81: Protein uL3


Mass: 45976.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TL06
#82: Protein eL30


Mass: 12807.065 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TDL2

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40S ribosomal protein ... , 23 types, 23 molecules DDEEeeffBBGGbbIIJJKKLLMMPPRRSSUUVVXXYYZZaaCCcc

#4: Protein 40S ribosomal protein S3 /


Mass: 31146.607 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
References: UniProt: G1TNM3, DNA-(apurinic or apyrimidinic site) lyase
#8: Protein 40S ribosomal protein S4 /


Mass: 29654.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#9: Protein 40S ribosomal protein S30 /


Mass: 14498.884 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T8A2
#14: Protein 40S ribosomal protein S27a /


Mass: 7986.440 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P62992
#17: Protein 40S ribosomal protein S3a /


Mass: 29942.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#18: Protein 40S ribosomal protein S6 /


Mass: 30201.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#24: Protein 40S ribosomal protein S27 /


Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#27: Protein 40S ribosomal protein S8 /


Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#31: Protein 40S ribosomal protein S9 /


Mass: 22655.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A1S3APZ1
#35: Protein 40S ribosomal protein S10 /


Mass: 17422.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A2F0BDG8
#38: Protein 40S ribosomal protein S11 /


Mass: 18513.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#41: Protein 40S ribosomal protein S12 /


Mass: 13709.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SFR8
#50: Protein 40S ribosomal protein uS19 /


Mass: 17049.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U0Q2
#56: Protein 40S ribosomal protein S17 /


Mass: 16782.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: S7Q348
#59: Protein 40S ribosomal protein uS13 /


Mass: 17759.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPG3
#63: Protein 40S ribosomal protein S20 /


Mass: 13268.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#65: Protein 40S ribosomal protein S21 /


Mass: 9124.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: Q32PB8
#71: Protein 40S ribosomal protein uS12 /


Mass: 15757.587 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SZ47
#74: Protein 40S ribosomal protein S24 /


Mass: 17007.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#77: Protein 40S ribosomal protein S25 /


Mass: 13450.798 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TDB3
#80: Protein 40S ribosomal protein S26 /


Mass: 13147.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: T0M5X4
#83: Protein 40S ribosomal protein S2 /


Mass: 27995.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#84: Protein 40S ribosomal protein S28 /


Mass: 7836.005 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TIB4

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Ribosomal protein ... , 10 types, 10 molecules eFFjMNNNpQQWWY

#7: Protein Ribosomal protein L32 /


Mass: 15153.217 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U437
#13: Protein Ribosomal protein S5 /


Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TFM5
#30: Protein Ribosomal protein L37 /


Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: U3KPD5
#39: Protein Ribosomal protein L14 /


Mass: 23870.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SZ12
#42: Protein Ribosomal protein L15 /


Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T0C1
#44: Protein ribosomal protein uS15 /


Mass: 17188.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#49: Protein ribosomal protein eL43 /


Mass: 12010.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#53: Protein Ribosomal protein S16 /


Mass: 17716.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#68: Protein Ribosomal protein S15a / Ribosome


Mass: 15778.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#72: Protein Ribosomal protein L26 /


Mass: 15891.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SQH0

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RNA chain , 5 types, 5 molecules hh5789

#23: RNA chain mRNA / Messenger RNA


Mass: 4753.857 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#67: RNA chain 28S Ribosomal RNA /


Mass: 1199695.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#70: RNA chain 5S Ribosomal RNA /


Mass: 38691.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: GenBank: 4CXE_4
#73: RNA chain 5.8S Ribosomal RNA /


Mass: 48545.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#76: RNA chain 18S Ribosomal RNA /


Mass: 573842.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)

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Non-polymers , 4 types, 291 molecules

#85: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#86: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 281 / Source method: obtained synthetically / Formula: Mg
#87: Chemical ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-PCP, energy-carrying molecule analogue*YM
#88: Chemical ChemComp-BLS / BLASTICIDIN S / Blasticidin S


Mass: 422.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H26N8O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Mammalian pre-termination 80S ribosome with eRF1 and eRF3 bound by Blasticidin S.
Type: RIBOSOME
Details: Rabbit reticulocyte lysate derived (in vitro transcription-FLAG affinity purified) ribosomal complex.
Entity ID: #1-#84 / Source: NATURAL
Molecular weightValue: 3.8 MDa / Experimental value: NO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Buffer solutionpH: 7.4
Details: 50 mM HEPES pH 7.4 100 mM KOAc 5 mM Mg(Oac)2 1mM DTT
SpecimenConc.: 0.63 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 165nM (OD260nm~10.5)
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 70 % / Chamber temperature: 288.15 K
Details: 30s sample incubation on grid followed by 1.1s blotting time.

-
Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Details: Collected in super-resolution mode (0.675A pixel size)
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy / Calibrated magnification: 79000 X / Calibrated defocus min: 400 nm / Calibrated defocus max: 2000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 8 sec. / Electron dose: 41.92 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3500
Image scansMovie frames/image: 40

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFIND4CTF correction
7UCSF Chimeramodel fitting
11RELION3classification
13PHENIXmodel refinement
14Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 730463
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18937 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingPDB-ID: 5LZT

5lzt

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