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- PDB-7nwg: Mammalian pre-termination 80S ribosome with Hybrid P/E- and A/P-s... -

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Basic information

Entry
Database: PDB / ID: 7nwg
TitleMammalian pre-termination 80S ribosome with Hybrid P/E- and A/P-site tRNA's bound by Blasticidin S.
Components
  • (40S ribosomal protein ...) x 20
  • (60S RIBOSOMAL PROTEIN ...) x 13
  • (Ribosomal protein ...) x 13
  • 18S Ribosomal RNA
  • 28S Ribosomal RNA
  • 5.8S Ribosomal RNA
  • 5S Ribosomal RNA
  • 60S acidic ribosomal protein P0
  • A/P-Site tRNA
  • L13
  • L18
  • L22
  • L38
  • L7a
  • L8
  • L9
  • P/E-Site tRNA
  • Ribosomal protein
  • S19
  • S4
  • Sec61Beta
  • eL14
  • eL21
  • eL28
  • eL29
  • eL30
  • eL31
  • eL32CD59
  • eL33
  • eL39
  • eL42
  • eS31
  • mRNAMessenger RNA
  • uL12
  • uL15
  • uL22
  • uL23
  • uL29
  • uL3
  • uL30
  • uL4
  • uS11
  • uS14
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 / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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) / rough endoplasmic reticulum / DNA-(apurinic or apyrimidinic site) lyase / cytosolic ribosome / cytosolic small ribosomal subunit / small ribosomal subunit / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / nucleolus / RNA binding / cytoplasm
Similarity search - Function
: / metallochaperone-like domain / TRASH domain / Ribosomal protein S21e, conserved site / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S26e signature. / Ribosomal protein S17e, conserved site / Ribosomal protein S21e ...: / metallochaperone-like domain / TRASH domain / Ribosomal protein S21e, conserved site / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S26e signature. / Ribosomal protein S17e, conserved site / 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 L24e, conserved site / Ribosomal protein S6, eukaryotic / Ribosomal protein S19e signature. / Ribosomal S17 / 40S Ribosomal protein S10 / Ribosomal protein S6/S6e/A/B/2, conserved site / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein L1 signature. / Ribosomal protein L19, eukaryotic / Ribosomal protein S17e signature. / Ribosomal protein L27e signature. / Ribosomal protein L10e signature. / Ribosomal protein S7e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L19/L19e conserved site / Ribosomal protein S6e / Ribosomal protein S3Ae signature. / Ribosomal protein S27e signature. / Ribosomal protein L19e signature. / Ribosomal protein L39e, conserved site / Ribosomal protein L24e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L34e signature. / Ribosomal protein S8e signature. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L6e signature. / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L30e signature 1. / Ribosomal protein L30e signature 2. / 60S ribosomal protein L19 / Ribosomal protein L39e signature. / Ribosomal protein L35Ae signature. / Ribosomal protein L39e / Ribosomal protein L24e-related / Ribosomal protein L39e domain superfamily / Ribosomal protein L24e/L24 superfamily / Ribosomal protein S6e 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 L31e signature. / 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. / Ribosomal protein S2 signature 2. / Ubiquitin domain signature. / Ribosomal protein L23 signature. / Ribosomal protein L30 signature. / Ribosomal protein S3 signature. / Ribosomal protein S14 signature. / Ribosomal protein S2 signature 1. / Ribosomal protein L5 signature. / Ribosomal protein L29 signature. / Ribosomal protein S4/S9 N-terminal domain / Type-2 KH domain profile. / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S4, conserved site / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9 / Ribosomal protein S19 signature. / Ribosomal protein S7 signature. / Ribosomal protein S17 signature. / S4 RNA-binding domain / RNA-binding S4 domain / Ribosomal protein S13 signature. / RNA-binding S4 domain superfamily / Ribosomal protein S13 family profile. / S4 domain
Similarity search - Domain/homology
BLASTICIDIN S / : / 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 ...BLASTICIDIN S / : / 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 / 40S ribosomal protein S6 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL33 / Small ribosomal subunit protein eS12 / Large ribosomal subunit protein eL29 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein RACK1 / Ubiquitin-ribosomal protein eS31 fusion protein / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein uL1 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL24 / Small ribosomal subunit protein eS1 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein eS7 / 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 / Large ribosomal subunit protein uL14 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Large ribosomal subunit protein eL30 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein eS8 / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein uL3 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein eL27 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein eL28 / Small ribosomal subunit protein uS14 / Large ribosomal subunit protein eL34 / Small ribosomal subunit protein eS21 / 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: 3.8 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
51: 28S Ribosomal RNA
71: 5S Ribosomal RNA
81: 5.8S Ribosomal RNA
A2: 18S Ribosomal RNA
B2: 40S ribosomal protein SA
C2: 40S ribosomal protein S3a
D2: 40S ribosomal protein S2
E2: 40S ribosomal protein S3
F2: S4
G2: Ribosomal protein S5
H2: 40S ribosomal protein S6
I2: ribosomal protein eS7
J2: 40S ribosomal protein S8
K2: 40S ribosomal protein S9
L2: 40S ribosomal protein S10
M2: 40S ribosomal protein S11
N2: 40S ribosomal protein S12
O2: ribosomal protein uS15
P2: uS11
Q2: 40S ribosomal protein uS19
R2: Ribosomal protein S16
S2: 40S ribosomal protein S17
T2: 40S ribosomal protein uS13
U2: S19
V2: 40S ribosomal protein S20
W2: 40S ribosomal protein S21
X2: Ribosomal protein S15a
Y2: Ribosomal protein S23
Z2: 40S ribosomal protein S24
a2: ribosomal protein eS25
b2: 40S ribosomal protein S26
c2: 40S ribosomal protein S27
d2: 40S ribosomal protein S28
e2: uS14
f2: 40S ribosomal protein S30
g2: eS31
h2: ribosomal protein RACK1
A3: L8
B3: uL3
C3: uL4
D3: 60S ribosomal protein L5
E3: 60S ribosomal protein L6
F3: uL30
G3: L7a
H3: L9
I3: 60S ribosomal protein L10
J3: 60S ribosomal protein L11
L3: L13
M3: Ribosomal protein L14
N3: Ribosomal protein L15
O3: 60S RIBOSOMAL PROTEIN UL13
P3: uL22
Q3: L18
R3: 60S ribosomal protein L19
S3: 60S ribosomal protein L18a
T3: eL21
U3: L22
V3: eL14
X3: uL23
Y3: Ribosomal protein L26
Z3: 60S ribosomal protein L27
a3: uL15
b3: eL29
c3: eL30
d3: eL31
e3: eL32
f3: eL33
g3: 60S ribosomal protein L34
h3: uL29
i3: 60S ribosomal protein L36
j3: Ribosomal protein L37
k3: L38
l3: eL39
m3: 60S RIBOSOMAL PROTEIN EL40
n3: 60s ribosomal protein l41
o3: eL42
p3: ribosomal protein eL43
r3: eL28
q3: A/P-Site tRNA
t3: 60S acidic ribosomal protein P0
u3: uL12
v3: mRNA
33: P/E-Site tRNA
w3: Ribosomal protein
1: Sec61Beta
W: 60S ribosomal protein L24-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,512,378394
Polymers3,504,16586
Non-polymers8,213308
Water0
1


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

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Components

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RNA chain , 7 types, 7 molecules 517181A2q3v333

#1: RNA chain 28S Ribosomal RNA /


Mass: 1226619.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#2: 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
#3: 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)
#4: RNA chain 18S Ribosomal RNA /


Mass: 586374.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#79: RNA chain A/P-Site tRNA


Mass: 23825.205 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#82: RNA chain mRNA / Messenger RNA


Mass: 5719.419 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#83: RNA chain P/E-Site tRNA


Mass: 24118.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)

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40S ribosomal protein ... , 20 types, 20 molecules B2C2D2E2H2J2K2L2M2N2Q2S2T2V2W2Z2b2c2d2f2

#5: Protein 40S ribosomal protein SA / / 37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin ...37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin receptor / 67LR / Laminin receptor 1 / LamR / Laminin-binding protein precursor p40 / LBP/p40


Mass: 32958.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TLT8
#6: 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) / References: UniProt: G1SS70
#7: 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)
#8: 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
#11: Protein 40S ribosomal protein S6 /


Mass: 30070.432 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A5K1UJS7
#13: Protein 40S ribosomal protein S8 /


Mass: 24003.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TJW1
#14: 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
#15: 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
#16: 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) / References: UniProt: G1TRM4
#17: 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
#20: 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
#22: 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
#23: 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
#25: Protein 40S ribosomal protein S20 /


Mass: 14603.080 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#26: 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
#29: 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)
#31: 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
#32: 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) / References: UniProt: G1TZ76
#33: 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
#35: 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

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Protein , 31 types, 31 molecules F2P2U2e2g2A3B3C3F3G3H3L3P3Q3T3U3V3X3a3b3c3d3e3f3h3k3o3r3t3u3w3

#9: Protein S4


Mass: 29523.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#19: Protein uS11


Mass: 18133.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T1F0
#24: Protein S19


Mass: 16106.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TN62
#34: Protein uS14


Mass: 6559.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7M4
#36: Protein eS31


Mass: 7986.440 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SK22
#38: Protein L8


Mass: 26840.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#39: Protein uL3


Mass: 46107.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TL06
#40: Protein uL4


Mass: 47727.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVW5
#43: 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
#44: Protein L7a


Mass: 27480.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1STW0
#45: 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
#48: Protein L13


Mass: 24331.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TKB3
#52: Protein uL22


Mass: 23056.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#53: Protein L18


Mass: 21699.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#56: Protein eL21 /


Mass: 18478.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHQ2
#57: Protein L22


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


Mass: 13972.425 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T6D1
#59: 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
#62: Protein uL15


Mass: 17831.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#63: Protein eL29


Mass: 26708.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SGR6
#64: 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
#65: Protein eL31


Mass: 12635.694 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHG0
#66: Protein eL32 / CD59


Mass: 15022.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TUN8
#67: Protein eL33


Mass: 12449.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SF08
#69: Protein uL29


Mass: 14435.403 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SIT5
#72: Protein L38


Mass: 8107.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#76: Protein eL42


Mass: 16170.214 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#78: 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
#80: 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
#81: Protein uL12


Mass: 21295.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#84: Protein Ribosomal protein /


Mass: 24879.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SKZ8

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Ribosomal protein ... , 13 types, 13 molecules G2I2O2R2X2Y2a2h2M3N3Y3j3p3

#10: Protein Ribosomal protein S5 /


Mass: 23044.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TFM5
#12: Protein ribosomal protein eS7 /


Mass: 21716.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVB0
#18: Protein ribosomal protein uS15 /


Mass: 17057.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SP51
#21: Protein Ribosomal protein S16 /


Mass: 17585.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SGX4
#27: 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)
#28: Protein Ribosomal protein S23 /


Mass: 15626.392 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SZ47
#30: Protein ribosomal protein eS25 /


Mass: 22090.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#37: Protein ribosomal protein RACK1 /


Mass: 34669.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SJB4
#49: 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
#50: Protein Ribosomal protein L15 /


Mass: 24076.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T0C1
#60: Protein Ribosomal protein L26 /


Mass: 15705.556 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SQH0
#71: 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
#77: Protein ribosomal protein eL43 /


Mass: 12010.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)

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60S RIBOSOMAL PROTEIN ... , 13 types, 13 molecules D3E3I3J3O3R3S3Z3g3i3m3n3W

#41: Protein 60S ribosomal protein L5 /


Mass: 34481.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SYJ6
#42: 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
#46: 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
#47: Protein 60S ribosomal protein L11 /


Mass: 20670.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TUB8
#51: 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
#55: 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
#61: Protein 60S ribosomal protein L27 /


Mass: 15704.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TXF6
#68: 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
#70: Protein 60S ribosomal protein L36 /


Mass: 13546.292 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#74: 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)
#75: 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
#86: 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

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Protein/peptide , 2 types, 2 molecules l31

#73: Protein/peptide eL39


Mass: 6324.579 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TTN1
#85: Protein/peptide Sec61Beta


Mass: 1788.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)

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Non-polymers , 3 types, 308 molecules

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


Mass: 24.305 Da / Num. of mol.: 299 / Source method: obtained synthetically / Formula: Mg
#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
#89: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn

-
Details

Has ligand of interestY

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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 Hybrid-P/E and -A/P site tRNAs bound by Blasticidin S.
Type: RIBOSOME
Details: Rabbit reticulocyte lysate derived (in vitro transcription-FLAG affinity purified) ribosomal complex.
Entity ID: #1-#78, #80-#86 / 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.

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI ARCTICA
Details: Collected in super-resolution mode (0.675A pixel size)
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
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: 41.9 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

Software
NameVersionClassificationNB
phenix.real_space_refine1.17.1_3660refinement
PHENIX1.17.1_3660refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
7UCSF Chimeramodel fitting
11RELION3classification
12RELION33D reconstruction
13PHENIXmodel refinement
14Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 730463
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 29879 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingPDB-ID: 6HCJ

6hcj

RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 95.57 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0125236205
ELECTRON MICROSCOPYf_angle_d1.3919346819
ELECTRON MICROSCOPYf_chiral_restr0.071843207
ELECTRON MICROSCOPYf_plane_restr0.012522319
ELECTRON MICROSCOPYf_dihedral_angle_d20.85482888

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