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- PDB-8a3d: Human mature large subunit of the ribosome with eIF6 and homoharr... -

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Basic information

Entry
Database: PDB / ID: 8a3d
TitleHuman mature large subunit of the ribosome with eIF6 and homoharringtonine bound
Components
  • (60S ribosomal protein ...) x 39
  • 28S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • Eukaryotic translation initiation factor 6
  • Ribosomal protein uL29
  • Ubiquitin-60S ribosomal protein L40
KeywordsTRANSLATION / Ribosome / human / rna modifications / water / magnesium / potassium / homoharringtonine
Function / homology
Function and homology information


lamin filament / regulation of fatty acid biosynthetic process / regulation of megakaryocyte differentiation / miRNA-mediated post-transcriptional gene silencing / miRNA-mediated gene silencing by inhibition of translation / embryonic brain development / translation at presynapse / exit from mitosis / optic nerve development / eukaryotic 80S initiation complex ...lamin filament / regulation of fatty acid biosynthetic process / regulation of megakaryocyte differentiation / miRNA-mediated post-transcriptional gene silencing / miRNA-mediated gene silencing by inhibition of translation / embryonic brain development / translation at presynapse / exit from mitosis / optic nerve development / eukaryotic 80S initiation complex / negative regulation of protein neddylation / regulation of translation involved in cellular response to UV / axial mesoderm development / negative regulation of formation of translation preinitiation complex / regulation of G1 to G0 transition / retinal ganglion cell axon guidance / ribosomal protein import into nucleus / protein-DNA complex disassembly / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / 90S preribosome assembly / alpha-beta T cell differentiation / GAIT complex / positive regulation of DNA damage response, signal transduction by p53 class mediator / regulation of glycolytic process / TORC2 complex binding / G1 to G0 transition / regulation of reactive oxygen species metabolic process / middle ear morphogenesis / maturation of 5.8S rRNA / cytoplasmic side of rough endoplasmic reticulum membrane / negative regulation of ubiquitin protein ligase activity / homeostatic process / macrophage chemotaxis / ribosomal large subunit binding / lung morphogenesis / positive regulation of natural killer cell proliferation / Protein hydroxylation / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / cellular response to actinomycin D / Eukaryotic Translation Termination / blastocyst development / negative regulation of ubiquitin-dependent protein catabolic process / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / ubiquitin ligase inhibitor activity / Viral mRNA Translation / positive regulation of signal transduction by p53 class mediator / protein localization to nucleus / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / positive regulation of protein binding / Major pathway of rRNA processing in the nucleolus and cytosol / protein targeting / ribosomal subunit export from nucleus / protein-RNA complex assembly / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / maturation of LSU-rRNA / rough endoplasmic reticulum / translation regulator activity / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / translation initiation factor activity / MDM2/MDM4 family protein binding / embryo implantation / cellular response to interleukin-4 / cytosolic ribosome / ossification / assembly of large subunit precursor of preribosome / regulation of signal transduction by p53 class mediator / positive regulation of translation / cytosolic ribosome assembly / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA 3'-UTR binding / innate immune response in mucosa / skeletal system development / DNA damage response, signal transduction by p53 class mediator / sensory perception of sound / cellular response to gamma radiation / response to insulin / bone development / mRNA 5'-UTR binding / cellular response to type II interferon / transcription coactivator binding / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / rRNA processing / antimicrobial humoral immune response mediated by antimicrobial peptide / cellular response to UV / antibacterial humoral response / presynapse / heparin binding / regulation of translation / large ribosomal subunit / ribosome binding / retina development in camera-type eye / cell body / 5S rRNA binding
Similarity search - Function
Translation initiation factor IF6 / eIF-6 family / translation initiation factor 6 / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L30e / Ribosomal protein L28e / Ribosomal L15/L27a, N-terminal / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type ...Translation initiation factor IF6 / eIF-6 family / translation initiation factor 6 / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L30e / Ribosomal protein L28e / Ribosomal L15/L27a, N-terminal / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / metallochaperone-like domain / TRASH domain / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L19, eukaryotic / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L44e signature. / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L24e, conserved site / : / Ribosomal protein L24e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L10e / Ribosomal protein L6e signature. / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / : / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal L40e family / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein L44e / Ribosomal protein L44 / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L30e signature 1. / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein L36e signature. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L35Ae, conserved site / Ribosomal protein L35Ae signature. / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / : / Ribosomal Protein L6, KOW domain / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / 60S ribosomal protein L19 / : / Ribosomal protein L34Ae / Ribosomal protein L34e / Ribosomal protein L7A/L8 / Ribosomal protein L6e / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L30/YlxQ / 60S ribosomal protein L6E / Ribosomal protein L7, eukaryotic / Ribosomal protein L30, N-terminal / Ribosomal L30 N-terminal domain / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L31e, conserved site / Ribosomal protein L31e signature. / Ribosomal protein L18e / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e / Ribosomal protein L19e, C-terminal domain / Ribosomal_L19e / Ribosomal protein L19/L19e / Ribosomal protein L14e domain / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e, N-terminal domain
Similarity search - Domain/homology
Chem-HMT / : / SPERMINE / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) ...Chem-HMT / : / SPERMINE / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ubiquitin-ribosomal protein eL40 fusion protein / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein eL28 / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein eL34 / Eukaryotic translation initiation factor 6 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein eL27 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein eL37 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein eL38 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein eL18 / Large ribosomal subunit protein eL14 / Large ribosomal subunit protein eL36
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.67 Å
AuthorsFaille, A. / Warren, A.J. / Dent, K.C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)SBAG/191 United Kingdom
CitationJournal: bioRxiv / Year: 2023
Title: The chemical landscape of the human ribosome at 1.67 Å resolution.
Authors: Alexandre Faille / Kyle C Dent / Simone Pellegrino / Pekka Jaako / Alan J Warren
Abstract: The ability of ribosomes to translate the genetic code into protein requires a finely tuned ion and solvent ecosystem. However, the lack of high-resolution structures has precluded accurate ...The ability of ribosomes to translate the genetic code into protein requires a finely tuned ion and solvent ecosystem. However, the lack of high-resolution structures has precluded accurate positioning of all the functional elements of the ribosome and limited our understanding of the specific role of ribosomal RNA chemical modifications in modulating ribosome function in health and disease. Here, using a new sample preparation methodology based on functionalised pristine graphene-coated grids, we solve the cryo-EM structure of the human large ribosomal subunit to a resolution of 1.67 Å. The accurate assignment of water molecules, magnesium and potassium ions in our model highlights the fundamental biological role of ribosomal RNA methylation in harnessing unconventional carbon-oxygen hydrogen bonds to establish chemical interactions with the environment and fine-tune the functional interplay with tRNA. In addition, the structures of three translational inhibitors bound to the human large ribosomal subunit at better than 2 Å resolution provide mechanistic insights into how three key druggable pockets of the ribosome are targeted and illustrate the potential of this methodology to accelerate high-throughput structure-based design of anti-cancer therapeutics.
History
DepositionJun 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 28S ribosomal RNA
B: 5S ribosomal RNA
C: 5.8S ribosomal RNA
D: 60S ribosomal protein L8
E: 60S ribosomal protein L3
F: 60S ribosomal protein L4
G: 60S ribosomal protein L5
H: 60S ribosomal protein L6
m: 60S ribosomal protein L7
n: 60S ribosomal protein L7a
o: 60S ribosomal protein L9
p: 60S ribosomal protein L10
q: 60S ribosomal protein L11
r: 60S ribosomal protein L13
s: 60S ribosomal protein L14
l: 60S ribosomal protein L15
I: 60S ribosomal protein L13a
J: 60S ribosomal protein L17
K: 60S ribosomal protein L18
L: 60S ribosomal protein L19
M: 60S ribosomal protein L18a
N: 60S ribosomal protein L21
O: 60S ribosomal protein L22
P: 60S ribosomal protein L23
Q: 60S ribosomal protein L24
R: 60S ribosomal protein L23a
S: 60S ribosomal protein L26
T: 60S ribosomal protein L27
U: 60S ribosomal protein L27a
V: 60S ribosomal protein L29
W: 60S ribosomal protein L30
X: 60S ribosomal protein L31
Y: 60S ribosomal protein L32
Z: 60S ribosomal protein L35a
a: 60S ribosomal protein L34
b: Ribosomal protein uL29
c: 60S ribosomal protein L36
d: 60S ribosomal protein L37
e: 60S ribosomal protein L38
f: 60S ribosomal protein L39
g: Ubiquitin-60S ribosomal protein L40
i: 60S ribosomal protein L36a
j: 60S ribosomal protein L37a
k: 60S ribosomal protein L28
h: Eukaryotic translation initiation factor 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,599,218439
Polymers2,586,23345
Non-polymers12,985394
Water215,69411973
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation, Sucrose density gradient
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 3 types, 3 molecules ABC

#1: RNA chain 28S ribosomal RNA


Mass: 1640812.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / Plasmid details: Thermofisher / Variant: Expi293 / References: GenBank: 86475748
#2: RNA chain 5S ribosomal RNA


Mass: 38998.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / Plasmid details: Thermofisher / Variant: Expi293 / References: GenBank: 23898
#3: RNA chain 5.8S ribosomal RNA


Mass: 50463.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / Plasmid details: Thermofisher / Variant: Expi293 / References: GenBank: 555853

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60S ribosomal protein ... , 39 types, 39 molecules DEFGHmnopqrslIJKLMNOPQRSTUVWXY...

#4: Protein 60S ribosomal protein L8 / Large ribosomal subunit protein uL2


Mass: 28088.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / Plasmid details: Thermofisher / Variant: Expi293 / References: UniProt: P62917
#5: Protein 60S ribosomal protein L3 / HIV-1 TAR RNA-binding protein B / TARBP-B / Large ribosomal subunit protein uL3


Mass: 46211.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / Plasmid details: Thermofisher / Variant: Expi293 / References: UniProt: P39023
#6: Protein 60S ribosomal protein L4 / 60S ribosomal protein L1 / Large ribosomal subunit protein uL4


Mass: 47804.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / Plasmid details: Thermofisher / Variant: Expi293 / References: UniProt: P36578
#7: Protein 60S ribosomal protein L5 / Large ribosomal subunit protein uL18


Mass: 34426.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / Plasmid details: Thermofisher / Variant: Expi293 / References: UniProt: P46777
#8: Protein 60S ribosomal protein L6 / Large ribosomal subunit protein eL6 / Neoplasm-related protein C140 / Tax-responsive enhancer ...Large ribosomal subunit protein eL6 / Neoplasm-related protein C140 / Tax-responsive enhancer element-binding protein 107 / TaxREB107


Mass: 32810.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / Plasmid details: Thermofisher / Variant: Expi293 / References: UniProt: Q02878
#9: Protein 60S ribosomal protein L7 / Large ribosomal subunit protein uL30


Mass: 29290.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / Plasmid details: Thermofisher / Variant: Expi293 / References: UniProt: P18124
#10: Protein 60S ribosomal protein L7a / Large ribosomal subunit protein eL8 / PLA-X polypeptide / Surfeit locus protein 3


Mass: 30061.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / Plasmid details: Thermofisher / Variant: Expi293 / References: UniProt: P62424
#11: Protein 60S ribosomal protein L9 / Large ribosomal subunit protein uL6


Mass: 21899.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / Plasmid details: Thermofisher / Variant: Expi293 / References: UniProt: P32969
#12: Protein 60S ribosomal protein L10 / Laminin receptor homolog / Large ribosomal subunit protein uL16 / Protein QM / Ribosomal protein ...Laminin receptor homolog / Large ribosomal subunit protein uL16 / Protein QM / Ribosomal protein L10 / Tumor suppressor QM


Mass: 24630.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / Plasmid details: Thermofisher / Variant: Expi293 / References: UniProt: P27635
#13: Protein 60S ribosomal protein L11 / CLL-associated antigen KW-12 / Large ribosomal subunit protein uL5


Mass: 20288.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / Plasmid details: Thermofisher / Variant: Expi293 / References: UniProt: P62913
#14: Protein 60S ribosomal protein L13 / Breast basic conserved protein 1 / Large ribosomal subunit protein eL13


Mass: 24321.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / Plasmid details: Thermofisher / Variant: Expi293 / References: UniProt: P26373
#15: Protein 60S ribosomal protein L14


Mass: 23840.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / Plasmid details: Thermofisher / Variant: Expi293 / References: UniProt: Q6IPH7
#16: Protein 60S ribosomal protein L15 / Large ribosomal subunit protein eL15


Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / Plasmid details: Thermofisher / Variant: Expi293 / References: UniProt: P61313
#17: Protein 60S ribosomal protein L13a / 23 kDa highly basic protein / Large ribosomal subunit protein uL13


Mass: 23633.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / Plasmid details: Thermofisher / Variant: Expi293 / References: UniProt: P40429
#18: Protein 60S ribosomal protein L17 / 60S ribosomal protein L23 / Large ribosomal subunit protein uL22 / PD-1


Mass: 21443.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / Plasmid details: Thermofisher / Variant: Expi293 / References: UniProt: P18621
#19: Protein 60S ribosomal protein L18 / Large ribosomal subunit protein eL18


Mass: 21687.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / Plasmid details: Thermofisher / Variant: Expi293 / References: UniProt: Q07020
#20: Protein 60S ribosomal protein L19 / Large ribosomal subunit protein eL19


Mass: 23535.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / Plasmid details: Thermofisher / Variant: Expi293 / References: UniProt: P84098
#21: Protein 60S ribosomal protein L18a / Large ribosomal subunit protein eL20


Mass: 20808.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / Plasmid details: Thermofisher / Variant: Expi293 / References: UniProt: Q02543
#22: Protein 60S ribosomal protein L21 / Large ribosomal subunit protein eL21


Mass: 18609.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / Plasmid details: Thermofisher / Variant: Expi293 / References: UniProt: P46778
#23: Protein 60S ribosomal protein L22 / EBER-associated protein / EAP / Epstein-Barr virus small RNA-associated protein / Heparin-binding ...EBER-associated protein / EAP / Epstein-Barr virus small RNA-associated protein / Heparin-binding protein HBp15 / Large ribosomal subunit protein eL22


Mass: 14813.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / Plasmid details: Thermofisher / Variant: Expi293 / References: UniProt: P35268
#24: Protein 60S ribosomal protein L23 / 60S ribosomal protein L17 / Large ribosomal subunit protein uL14


Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / Plasmid details: Thermofisher / Variant: Expi293 / References: UniProt: P62829
#25: Protein 60S ribosomal protein L24 / 60S ribosomal protein L30 / Large ribosomal subunit protein eL24


Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / Plasmid details: Thermofisher / Variant: Expi293 / References: UniProt: P83731
#26: Protein 60S ribosomal protein L23a / Large ribosomal subunit protein uL23


Mass: 17740.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / Plasmid details: Thermofisher / Variant: Expi293 / References: UniProt: P62750
#27: Protein 60S ribosomal protein L26 / Large ribosomal subunit protein uL24


Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / Plasmid details: Thermofisher / Variant: Expi293 / References: UniProt: P61254
#28: Protein 60S ribosomal protein L27 / Large ribosomal subunit protein eL27


Mass: 15835.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / Plasmid details: Thermofisher / Variant: Expi293 / References: UniProt: P61353
#29: Protein 60S ribosomal protein L27a / Large ribosomal subunit protein uL15


Mass: 16604.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / Plasmid details: Thermofisher / Variant: Expi293 / References: UniProt: P46776
#30: Protein 60S ribosomal protein L29 / Cell surface heparin-binding protein HIP / Large ribosomal subunit protein eL29


Mass: 17804.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / Plasmid details: Thermofisher / Variant: Expi293 / References: UniProt: P47914
#31: Protein 60S ribosomal protein L30 / Large ribosomal subunit protein eL30


Mass: 12805.092 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / Plasmid details: Thermofisher / Variant: Expi293 / References: UniProt: P62888
#32: Protein 60S ribosomal protein L31 / Large ribosomal subunit protein eL31


Mass: 14494.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / Plasmid details: Thermofisher / Variant: Expi293 / References: UniProt: P62899
#33: Protein 60S ribosomal protein L32 / Large ribosomal subunit protein eL32


Mass: 15898.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / Plasmid details: Thermofisher / Variant: Expi293 / References: UniProt: P62910
#34: Protein 60S ribosomal protein L35a / Cell growth-inhibiting gene 33 protein / Large ribosomal subunit protein eL33


Mass: 12564.743 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / Plasmid details: Thermofisher / Variant: Expi293 / References: UniProt: P18077
#35: Protein 60S ribosomal protein L34 / Large ribosomal subunit protein eL34


Mass: 13326.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / Plasmid details: Thermofisher / Variant: Expi293 / References: UniProt: P49207
#37: Protein 60S ribosomal protein L36 / Large ribosomal subunit protein eL36


Mass: 12290.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / Plasmid details: Thermofisher / Variant: Expi293 / References: UniProt: Q9Y3U8
#38: Protein 60S ribosomal protein L37 / G1.16 / Large ribosomal subunit protein eL37


Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / Plasmid details: Thermofisher / Variant: Expi293 / References: UniProt: P61927
#39: Protein 60S ribosomal protein L38 / Large ribosomal subunit protein eL38


Mass: 8238.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / Plasmid details: Thermofisher / Variant: Expi293 / References: UniProt: P63173
#40: Protein 60S ribosomal protein L39 / Large ribosomal subunit protein eL39


Mass: 6426.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / Plasmid details: Thermofisher / Variant: Expi293 / References: UniProt: P62891
#42: Protein 60S ribosomal protein L36a / 60S ribosomal protein L44 / Cell growth-inhibiting gene 15 protein / Cell migration-inducing gene 6 ...60S ribosomal protein L44 / Cell growth-inhibiting gene 15 protein / Cell migration-inducing gene 6 protein / Large ribosomal subunit protein eL42


Mass: 12476.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / Plasmid details: Thermofisher / Variant: Expi293 / References: UniProt: P83881
#43: Protein 60S ribosomal protein L37a / Large ribosomal subunit protein eL43


Mass: 10299.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / Plasmid details: Thermofisher / Variant: Expi293 / References: UniProt: P61513
#44: Protein 60S ribosomal protein L28 / Large ribosomal subunit protein eL28


Mass: 15784.622 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / Plasmid details: Thermofisher / Variant: Expi293 / References: UniProt: P46779

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Protein , 3 types, 3 molecules bgh

#36: Protein Ribosomal protein uL29


Mass: 21730.748 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / Plasmid details: Thermofisher / Variant: Expi293
#41: Protein Ubiquitin-60S ribosomal protein L40 / Ubiquitin A-52 residue ribosomal protein fusion product 1


Mass: 11470.713 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / Plasmid details: Thermofisher / Variant: Expi293 / References: UniProt: A0A3Q0DRJ6
#45: Protein Eukaryotic translation initiation factor 6 / eIF-6 / B(2)GCN homolog / B4 integrin interactor / CAB / p27(BBP)


Mass: 26620.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / Plasmid details: Thermofisher / Variant: Expi293 / References: UniProt: P56537

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Non-polymers , 8 types, 12367 molecules

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


Mass: 24.305 Da / Num. of mol.: 229 / Source method: obtained synthetically / Formula: Mg
#47: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: K
#48: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#49: Chemical ChemComp-HMT / (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine / Homoharringtonine / Cephalotaxine / [3(R)]-4-methyl 2-hydroxy-2-(4-hydroxy-4-methylpentyl)butanedioate


Mass: 545.621 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H39NO9
#50: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#51: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#52: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#53: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11973 / 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: Human mature large subunit of the ribosome with eIF6 bound
Type: RIBOSOME / Entity ID: #1-#45 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMHEPES1
25 mMmagnesium chlorideMgCl21
3100 mMpotassium chlorideKCl1
42 mMDTT1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Grid was functionalised with 1-pyrenemethylamine. See methods section in published article.
Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: 30 seconds 'wait' time

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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 / Nominal magnification: 105000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.2 sec. / Electron dose: 51 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9973

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Processing

SoftwareName: REFMAC / Version: 5.8.0267 / Classification: refinement
EM software
IDNameVersionCategory
2EPU2.5image acquisition
4CTFFIND4.1CTF correction
7UCSF ChimeraX1model fitting
9cryoSPARC3initial Euler assignment
10RELION3.1final Euler assignment
11cryoSPARC3.1classification
12RELION3.13D reconstruction
13REFMAC5.5model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1147785
3D reconstructionResolution: 1.67 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1088709 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 40 / Protocol: AB INITIO MODEL / Space: REAL
Atomic model buildingPDB-ID: 6EK0

6ek0
PDB Unreleased entry


Accession code: 6EK0 / Source name: PDB / Type: experimental model
RefinementResolution: 1.67→270.25 Å / Cor.coef. Fo:Fc: 0.688
RfactorNum. reflection% reflection
Rwork0.26991 --
obs0.26991 6590753 100 %
Displacement parametersBiso mean: 35.442 Å2
LS refinement shellHighest resolution: 1.67 Å /
Rfactor% reflection
Rfree0 -
Rwork0.496 -
obs-100 %

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