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- PDB-7ls1: 80S ribosome from mouse bound to eEF2 (Class II) -

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Basic information

Entry
Database: PDB / ID: 7ls1
Title80S ribosome from mouse bound to eEF2 (Class II)
Components
  • (28S rRNA) x 2
  • (40S ribosomal protein ...) x 31
  • (60S ribosomal protein ...) x 43
  • 5.8S rRNA
  • 5S rRNA
  • 60S acidic ribosomal protein P0
  • Elongation factor 2
  • Isoform 3 of Plasminogen activator inhibitor 1 RNA-binding protein
  • Receptor of activated protein C kinase 1
  • Ubiquitin-40S ribosomal protein S27a
  • Ubiquitin-60S ribosomal protein L40
  • tRNA
KeywordsRIBOSOME / regulation / translation
Function / homology
Function and homology information


Peptide chain elongation / Synthesis of diphthamide-EEF2 / 5.8S rRNA binding / TNFR1-mediated ceramide production / cellular response to Thyroid stimulating hormone / Protein hydroxylation / positive regulation of amide metabolic process / Formation of the ternary complex, and subsequently, the 43S complex / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 ...Peptide chain elongation / Synthesis of diphthamide-EEF2 / 5.8S rRNA binding / TNFR1-mediated ceramide production / cellular response to Thyroid stimulating hormone / Protein hydroxylation / positive regulation of amide metabolic process / Formation of the ternary complex, and subsequently, the 43S complex / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / APC-Cdc20 mediated degradation of Nek2A / ER Quality Control Compartment (ERQC) / Regulation of PTEN localization / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / IRAK2 mediated activation of TAK1 complex / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Gap-filling DNA repair synthesis and ligation in GG-NER / Fanconi Anemia Pathway / Endosomal Sorting Complex Required For Transport (ESCRT) / Negative regulation of FLT3 / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of expression of SLITs and ROBOs / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Downregulation of ERBB4 signaling / E3 ubiquitin ligases ubiquitinate target proteins / Alpha-protein kinase 1 signaling pathway / Stabilization of p53 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Pexophagy / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Translesion synthesis by REV1 / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Translesion synthesis by POLK / Regulation of NF-kappa B signaling / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Regulation of TP53 Activity through Methylation / Formation of a pool of free 40S subunits / NRIF signals cell death from the nucleus / Translesion synthesis by POLI / Regulation of BACH1 activity / Recognition of DNA damage by PCNA-containing replication complex / p75NTR recruits signalling complexes / HDR through Homologous Recombination (HRR) / Interferon alpha/beta signaling / Negative regulation of MAPK pathway / Spry regulation of FGF signaling / SRP-dependent cotranslational protein targeting to membrane / Regulation of TP53 Degradation / Translesion Synthesis by POLH / Activated NOTCH1 Transmits Signal to the Nucleus / DNA Damage Recognition in GG-NER / Formation of TC-NER Pre-Incision Complex / Major pathway of rRNA processing in the nucleolus and cytosol / Negative regulation of MET activity / TRAF6-mediated induction of TAK1 complex within TLR4 complex / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Termination of translesion DNA synthesis / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Senescence-Associated Secretory Phenotype (SASP) / Josephin domain DUBs / Dual Incision in GG-NER / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Ubiquitin-dependent degradation of Cyclin D / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR1-induced NF-kappa-B signaling pathway / Downregulation of ERBB2 signaling / Dual incision in TC-NER / Oncogene Induced Senescence / PINK1-PRKN Mediated Mitophagy / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SCF(Skp2)-mediated degradation of p27/p21 / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Formation of Incision Complex in GG-NER / Assembly of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6 / Inactivation of CSF3 (G-CSF) signaling / Gap-filling DNA repair synthesis and ligation in TC-NER / TCF dependent signaling in response to WNT / Metalloprotease DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / EGFR downregulation / Translation initiation complex formation / Ribosomal scanning and start codon recognition / Autodegradation of the E3 ubiquitin ligase COP1 / Regulation of TNFR1 signaling / MAP3K8 (TPL2)-dependent MAPK1/3 activation / G2/M Checkpoints
Similarity search - Function
Intracellular hyaluronan-binding protein 4, N-terminal domain / Intracellular hyaluronan-binding protein 4 N-terminal / Hyaluronan / mRNA binding family / RNA binding protein HABP4/SERBP1 / Hyaluronan/mRNA-binding protein / Hyaluronan / mRNA binding family / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / 40S ribosomal protein SA ...Intracellular hyaluronan-binding protein 4, N-terminal domain / Intracellular hyaluronan-binding protein 4 N-terminal / Hyaluronan / mRNA binding family / RNA binding protein HABP4/SERBP1 / Hyaluronan/mRNA-binding protein / Hyaluronan / mRNA binding family / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Elongation Factor G, domain II / Elongation Factor G, domain III / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ubiquitin-like protein FUBI / Ribosomal protein L30e / Ribosomal protein L2, archaeal-type / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Ribosomal L15/L27a, N-terminal / Elongation factor G C-terminus / Ribosomal protein L28e / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / 50S ribosomal protein L10, insertion domain superfamily / Ribosomal protein L23 / EF-G domain III/V-like / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / metallochaperone-like domain / TRASH domain / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein L1, conserved site / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein L1 signature. / : / Ribosomal protein S12e signature. / Ribosomal protein L1 / Ribosomal protein S12e / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S2, eukaryotic / S27a-like superfamily / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Translation elongation factor EFTu-like, domain 2 / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L10e / 40S Ribosomal protein S10 / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / : / Ribosomal protein S7e signature. / Ribosomal protein L44e signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / : / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L19, eukaryotic / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L6e signature. / Ribosomal protein L13e / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein L13e / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S27a
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein uL15 ...GUANOSINE-5'-DIPHOSPHATE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL13 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein eL18 / Large ribosomal subunit protein eL28 / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein eL36 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL1 / Elongation factor 2 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein eL27 / Large ribosomal subunit protein eL43 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein eS4 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein eS6 / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein eS26 / Small ribosomal subunit protein eS28 / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL31 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein eS32 / Ubiquitin-ribosomal protein eS31 fusion protein / Ubiquitin-ribosomal protein eL40 fusion protein / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein eS10 / Large ribosomal subunit protein eL22 / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein uL16-like / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein uS7 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein eS27-like / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein eS21 / Large ribosomal subunit protein eL14 / Large ribosomal subunit protein uL5 / SERPINE1 mRNA-binding protein 1 / Large ribosomal subunit protein eL15 / Small ribosomal subunit protein eS19 / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein eL37 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein eL38
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLoerch, S. / Smith, P.R. / Kunder, N. / Stanowick, A.D. / Lou, T.-F. / Campbell, Z.T.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS100788 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS114018 United States
CitationJournal: Nat Commun / Year: 2021
Title: Functionally distinct roles for eEF2K in the control of ribosome availability and p-body abundance.
Authors: Patrick R Smith / Sarah Loerch / Nikesh Kunder / Alexander D Stanowick / Tzu-Fang Lou / Zachary T Campbell /
Abstract: Processing bodies (p-bodies) are a prototypical phase-separated RNA-containing granule. Their abundance is highly dynamic and has been linked to translation. Yet, the molecular mechanisms responsible ...Processing bodies (p-bodies) are a prototypical phase-separated RNA-containing granule. Their abundance is highly dynamic and has been linked to translation. Yet, the molecular mechanisms responsible for coordinate control of the two processes are unclear. Here, we uncover key roles for eEF2 kinase (eEF2K) in the control of ribosome availability and p-body abundance. eEF2K acts on a sole known substrate, eEF2, to inhibit translation. We find that the eEF2K agonist nelfinavir abolishes p-bodies in sensory neurons and impairs translation. To probe the latter, we used cryo-electron microscopy. Nelfinavir stabilizes vacant 80S ribosomes. They contain SERBP1 in place of mRNA and eEF2 in the acceptor site. Phosphorylated eEF2 associates with inactive ribosomes that resist splitting in vitro. Collectively, the data suggest that eEF2K defines a population of inactive ribosomes resistant to recycling and protected from degradation. Thus, eEF2K activity is central to both p-body abundance and ribosome availability in sensory neurons.
History
DepositionFeb 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A1: 60S ribosomal protein L7
B1: 60S ribosomal protein L7a
C1: 60S ribosomal protein L9
D1: 60S ribosomal protein L10-like
E1: 60S ribosomal protein L11
F1: 60S ribosomal protein L13
G1: 60S ribosomal protein L14
H1: 60S ribosomal protein L15
A2: 28S rRNA
B2: 5S rRNA
C2: 5.8S rRNA
D2: 60S ribosomal protein L8
E2: 60S ribosomal protein L3
F2: 60S ribosomal protein L4
G2: 60S ribosomal protein L5
H2: 60S ribosomal protein L6
I2: 60S ribosomal protein L13a
J2: 60S ribosomal protein L17
K2: 60S ribosomal protein L18
L2: 60S ribosomal protein L19
M2: 60S ribosomal protein L18a
N2: 60S ribosomal protein L21
O2: 60S ribosomal protein L22
P2: 60S ribosomal protein L23
Q2: 60S ribosomal protein L24
R2: 60S ribosomal protein L23a
S2: 60S ribosomal protein L26
T2: 60S ribosomal protein L27
U2: 60S ribosomal protein L27a
V2: 60S ribosomal protein L29
W2: 60S ribosomal protein L30
X2: 60S ribosomal protein L31
Y2: 60S ribosomal protein L32
Z2: 60S ribosomal protein L35a
a2: 60S ribosomal protein L34
b2: 60S ribosomal protein L35
c2: 60S ribosomal protein L36
d2: 60S ribosomal protein L37
e2: 60S ribosomal protein L38
f2: 60S ribosomal protein L39
g2: Ubiquitin-60S ribosomal protein L40
h2: 60S ribosomal protein L41
i2: 60S ribosomal protein L36a
j2: 60S ribosomal protein L37a
k2: 60S ribosomal protein L28
m2: 28S rRNA
n2: tRNA
p2: 40S ribosomal protein S3a
q2: 40S ribosomal protein S3
r2: 40S ribosomal protein S4, X isoform
w2: 40S ribosomal protein S11
z2: 40S ribosomal protein S17
o2: 40S ribosomal protein SA
s2: 40S ribosomal protein S5
v2: 40S ribosomal protein S10
x2: 40S ribosomal protein S15
y2: 40S ribosomal protein S16
A3: 40S ribosomal protein S18
B3: 40S ribosomal protein S19
C3: 40S ribosomal protein S20
D3: 40S ribosomal protein S21
E3: 40S ribosomal protein S23
F3: 40S ribosomal protein S26
G3: 40S ribosomal protein S28
H3: 40S ribosomal protein S29
I3: Receptor of activated protein C kinase 1
J3: 40S ribosomal protein S2
K3: 40S ribosomal protein S6
L3: 40S ribosomal protein S9
M3: 40S ribosomal protein S12
N3: 40S ribosomal protein S13
O3: 40S ribosomal protein S14
P3: 40S ribosomal protein S15a
Q3: 40S ribosomal protein S24
R3: 40S ribosomal protein S25
S3: 40S ribosomal protein S27-like
T3: 40S ribosomal protein S30
U3: Ubiquitin-40S ribosomal protein S27a
m: Elongation factor 2
j: 60S acidic ribosomal protein P0
k: 60S ribosomal protein L12
A: Isoform 3 of Plasminogen activator inhibitor 1 RNA-binding protein
t: 40S ribosomal protein S7
u: 40S ribosomal protein S8
L1: 60S ribosomal protein L10a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,928,76394
Polymers3,927,83785
Non-polymers9259
Water362
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 ... , 43 types, 43 molecules A1B1C1D1E1F1G1H1D2E2F2G2H2I2J2K2L2M2N2O2P2Q2R2S2T2U2V2W2X2Y2...

#1: Protein 60S ribosomal protein L7


Mass: 31492.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P14148
#2: Protein 60S ribosomal protein L7a / Surfeit locus protein 3


Mass: 30042.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P12970
#3: Protein 60S ribosomal protein L9


Mass: 21917.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P51410
#4: Protein 60S ribosomal protein L10-like


Mass: 24612.045 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P86048
#5: Protein 60S ribosomal protein L11


Mass: 20288.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CXW4
#6: Protein 60S ribosomal protein L13 / A52


Mass: 24364.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P47963
#7: Protein 60S ribosomal protein L14


Mass: 23620.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CR57
#8: Protein 60S ribosomal protein L15


Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CZM2
#12: Protein 60S ribosomal protein L8


Mass: 28088.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62918
#13: Protein 60S ribosomal protein L3 / J1 protein


Mass: 46212.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P27659
#14: Protein 60S ribosomal protein L4


Mass: 47272.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D8E6
#15: Protein 60S ribosomal protein L5


Mass: 34464.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P47962
#16: Protein 60S ribosomal protein L6 / TAX-responsive enhancer element-binding protein 107 / TAXREB107


Mass: 33593.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P47911
#17: Protein 60S ribosomal protein L13a / Transplantation antigen P198 / Tum-P198 antigen


Mass: 23519.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P19253
#18: Protein 60S ribosomal protein L17


Mass: 21470.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CPR4
#19: Protein 60S ribosomal protein L18


Mass: 21698.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P35980
#20: Protein 60S ribosomal protein L19


Mass: 23535.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P84099
#21: Protein 60S ribosomal protein L18a


Mass: 20778.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62717
#22: Protein 60S ribosomal protein L21


Mass: 18607.994 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: O09167
#23: Protein 60S ribosomal protein L22 / Heparin-binding protein HBp15


Mass: 14784.962 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P67984
#24: Protein 60S ribosomal protein L23


Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62830
#25: Protein 60S ribosomal protein L24


Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8BP67
#26: Protein 60S ribosomal protein L23a


Mass: 17740.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62751
#27: Protein 60S ribosomal protein L26 / Silica-induced gene 20 protein / SIG-20


Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P61255
#28: Protein 60S ribosomal protein L27


Mass: 15835.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P61358
#29: Protein 60S ribosomal protein L27a / L29


Mass: 16648.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P14115
#30: Protein 60S ribosomal protein L29


Mass: 17635.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P47915
#31: Protein 60S ribosomal protein L30


Mass: 12805.092 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62889
#32: Protein 60S ribosomal protein L31


Mass: 14494.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62900
#33: Protein 60S ribosomal protein L32


Mass: 15898.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62911
#34: Protein 60S ribosomal protein L35a


Mass: 12580.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: O55142
#35: Protein 60S ribosomal protein L34


Mass: 13325.022 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D1R9
#36: Protein 60S ribosomal protein L35


Mass: 14595.702 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6ZWV7
#37: Protein 60S ribosomal protein L36


Mass: 12249.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P47964
#38: Protein 60S ribosomal protein L37


Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D823
#39: Protein 60S ribosomal protein L38


Mass: 8224.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9JJI8
#40: Protein 60S ribosomal protein L39


Mass: 6426.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62892
#42: Protein/peptide 60S ribosomal protein L41


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62947
#43: Protein 60S ribosomal protein L36a / 60S ribosomal protein L44


Mass: 12476.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P83882
#44: Protein 60S ribosomal protein L37a


Mass: 10299.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P61514
#45: Protein 60S ribosomal protein L28


Mass: 15770.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P41105
#81: Protein 60S ribosomal protein L12


Mass: 17833.592 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P35979
#85: Protein 60S ribosomal protein L10a / CSA-19 / Neural precursor cell expressed developmentally down-regulated protein 6 / NEDD-6


Mass: 24965.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P53026

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RNA chain , 5 types, 5 molecules A2B2C2m2n2

#9: RNA chain 28S rRNA


Mass: 1532193.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#10: RNA chain 5S rRNA


Mass: 38998.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: GenBank: 396138
#11: RNA chain 5.8S rRNA


Mass: 55920.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#46: RNA chain 28S rRNA


Mass: 603714.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#47: RNA chain tRNA


Mass: 24231.510 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Protein , 6 types, 6 molecules g2I3U3mjA

#41: Protein Ubiquitin-60S ribosomal protein L40 / Ubiquitin A-52 residue ribosomal protein fusion product 1


Mass: 14771.411 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62984
#66: Protein Receptor of activated protein C kinase 1 / 12-3 / Guanine nucleotide-binding protein subunit beta-2-like 1 / Receptor for activated C kinase / ...12-3 / Guanine nucleotide-binding protein subunit beta-2-like 1 / Receptor for activated C kinase / Receptor of activated protein kinase C 1 / p205


Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P68040
#78: Protein Ubiquitin-40S ribosomal protein S27a / Ubiquitin carboxyl extension protein 80


Mass: 17990.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62983
#79: Protein Elongation factor 2 / EF-2


Mass: 95581.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P58252
#80: Protein 60S acidic ribosomal protein P0 / 60S ribosomal protein L10E


Mass: 34252.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P14869
#82: Protein Isoform 3 of Plasminogen activator inhibitor 1 RNA-binding protein / PAI1 RNA-binding protein 1 / PAI-RBP1 / SERPINE1 mRNA-binding protein 1


Mass: 42317.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CY58

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40S ribosomal protein ... , 31 types, 31 molecules p2q2r2w2z2o2s2v2x2y2A3B3C3D3E3F3G3H3J3K3L3M3N3O3P3Q3R3S3T3tu

#48: Protein 40S ribosomal protein S3a / Protein TU-11


Mass: 29942.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P97351
#49: Protein 40S ribosomal protein S3


Mass: 26715.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P62908, DNA-(apurinic or apyrimidinic site) lyase
#50: Protein 40S ribosomal protein S4, X isoform


Mass: 29654.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62702
#51: Protein 40S ribosomal protein S11


Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62281
#52: Protein 40S ribosomal protein S17


Mass: 15552.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P63276
#53: Protein 40S ribosomal protein SA / 37 kDa laminin receptor precursor / 37LRP / 37 kDa oncofetal antigen / 37/67 kDa laminin receptor / ...37 kDa laminin receptor precursor / 37LRP / 37 kDa oncofetal antigen / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin receptor / 67LR / Laminin receptor 1 / LamR / Laminin-binding protein precursor p40 / LBP/p40 / OFA/iLRP


Mass: 32867.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P14206
#54: Protein 40S ribosomal protein S5


Mass: 22926.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P97461
#55: Protein 40S ribosomal protein S10


Mass: 18951.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P63325
#56: Protein 40S ribosomal protein S15 / RIG protein


Mass: 17076.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62843
#57: Protein 40S ribosomal protein S16


Mass: 16477.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P14131
#58: Protein 40S ribosomal protein S18 / Ke-3 / Ke3


Mass: 17759.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62270
#59: Protein 40S ribosomal protein S19


Mass: 16117.560 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CZX8
#60: Protein 40S ribosomal protein S20


Mass: 13398.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P60867
#61: Protein 40S ribosomal protein S21


Mass: 9154.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQR2
#62: Protein 40S ribosomal protein S23


Mass: 15844.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62267
#63: Protein 40S ribosomal protein S26


Mass: 13047.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62855
#64: Protein 40S ribosomal protein S28


Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62858
#65: Protein 40S ribosomal protein S29


Mass: 6690.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62274
#67: Protein 40S ribosomal protein S2 / 40S ribosomal protein S4 / Protein LLRep3


Mass: 31283.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P25444
#68: Protein 40S ribosomal protein S6 / Phosphoprotein NP33


Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62754
#69: Protein 40S ribosomal protein S9


Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6ZWN5
#70: Protein 40S ribosomal protein S12


Mass: 14549.001 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P63323
#71: Protein 40S ribosomal protein S13


Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62301
#72: Protein 40S ribosomal protein S14


Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62264
#73: Protein 40S ribosomal protein S15a


Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62245
#74: Protein 40S ribosomal protein S24


Mass: 15463.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62849
#75: Protein 40S ribosomal protein S25


Mass: 13776.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62852
#76: Protein 40S ribosomal protein S27-like


Mass: 9496.229 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6ZWY3
#77: Protein 40S ribosomal protein S30


Mass: 14441.718 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q642K5
#83: Protein 40S ribosomal protein S7


Mass: 22168.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62082
#84: Protein 40S ribosomal protein S8


Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62242

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Non-polymers , 4 types, 11 molecules

#86: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#87: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#88: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#89: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: 80S ribosome from mous ebound to eEF2 / Type: RIBOSOME / Entity ID: #1-#78, #80-#85 / Source: NATURAL
Molecular weightValue: 4.5 MDa / Experimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277.15 K / Details: 3 second blotting, force 3

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 1 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsEnergyfilter slit width: 20 eV

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.19.1_4122refinement
PHENIX1.19.1_4122refinement
EM software
IDNameVersionCategory
2SerialEM3.8image acquisition
4cisTEMCTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10cisTEMinitial Euler assignment
11cisTEMfinal Euler assignment
12cisTEMclassification
13cisTEM3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 193794
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11878 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 160.78 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0019243520
ELECTRON MICROSCOPYf_angle_d0.4928356644
ELECTRON MICROSCOPYf_chiral_restr0.030344153
ELECTRON MICROSCOPYf_plane_restr0.003623679
ELECTRON MICROSCOPYf_dihedral_angle_d13.8224109965

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