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- PDB-8fl0: Human nucleolar pre-60S ribosomal subunit (State H) -

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Basic information

Entry
Database: PDB / ID: 8fl0
TitleHuman nucleolar pre-60S ribosomal subunit (State H)
Components
  • (60S ribosomal protein ...) x 17
  • (Ribosome biogenesis ...) x 2
  • 28S rRNA
  • 5S rRNA
  • Coiled-coil domain-containing protein 86
  • Eukaryotic translation initiation factor 6
  • GTP-binding protein 4
  • Guanine nucleotide-binding protein-like 3
  • Notchless protein homolog 1
  • Nucleolar GTP-binding protein 2
  • Probable ribosome biogenesis protein RLP24
  • Protein LLP homolog
  • Ribosome production factor 2 homolog
  • mRNA turnover protein 4 homolog
KeywordsRIBOSOME / Pre-60S ribosomal subunit / Assembly intermediate / Nucleoprotein complex
Function / homology
Function and homology information


mitotic nuclear division / positive regulation of protein localization to chromosome, telomeric region / : / dendrite extension / inner cell mass cell differentiation / hematopoietic stem cell homeostasis / preribosome binding / lamin filament / regulation of Notch signaling pathway / regulation of megakaryocyte differentiation ...mitotic nuclear division / positive regulation of protein localization to chromosome, telomeric region / : / dendrite extension / inner cell mass cell differentiation / hematopoietic stem cell homeostasis / preribosome binding / lamin filament / regulation of Notch signaling pathway / regulation of megakaryocyte differentiation / regulation of fatty acid biosynthetic process / miRNA-mediated post-transcriptional gene silencing / negative regulation of G2/M transition of mitotic cell cycle / positive regulation of protein sumoylation / miRNA-mediated gene silencing by inhibition of translation / protein localization to nucleolus / negative regulation of mitotic cell cycle / negative regulation of formation of translation preinitiation complex / ribosomal protein import into nucleus / regulation of G1 to G0 transition / protein-DNA complex disassembly / regulation of glycolytic process / skeletal system morphogenesis / GAIT complex / negative regulation of cell-cell adhesion / regulation of reactive oxygen species metabolic process / maturation of 5.8S rRNA / stem cell division / G1 to G0 transition / mitotic metaphase chromosome alignment / stem cell population maintenance / negative regulation of DNA replication / positive regulation of dendritic spine development / ribosomal large subunit binding / homeostatic process / preribosome, large subunit precursor / macrophage chemotaxis / lung morphogenesis / positive regulation of telomere maintenance / positive regulation of natural killer cell proliferation / nuclear-transcribed mRNA catabolic process / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / ubiquitin ligase inhibitor activity / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / Viral mRNA Translation / positive regulation of signal transduction by p53 class mediator / protein localization to nucleus / negative regulation of ubiquitin-dependent protein catabolic process / somitogenesis / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / hematopoietic progenitor cell differentiation / GTP hydrolysis and joining of the 60S ribosomal subunit / ribosomal subunit export from nucleus / L13a-mediated translational silencing of Ceruloplasmin expression / protein targeting / Major pathway of rRNA processing in the nucleolus and cytosol / maturation of LSU-rRNA / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Notch signaling pathway / 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 / translation initiation factor activity / negative regulation of protein ubiquitination / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / cellular response to interleukin-4 / cytosolic ribosome / negative regulation of cell migration / regulation of signal transduction by p53 class mediator / ribosomal large subunit biogenesis / cytosolic ribosome assembly / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / condensed nuclear chromosome / assembly of large subunit precursor of preribosome / positive regulation of translation / mRNA 3'-UTR binding / kidney development / chromosome segregation / response to insulin / positive regulation of miRNA transcription / cellular response to type II interferon / mRNA 5'-UTR binding / transcription coactivator binding / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / rRNA processing / osteoblast differentiation / positive regulation of canonical Wnt signaling pathway / regulation of cell population proliferation / mitotic cell cycle / large ribosomal subunit / chromosome / ribosome biogenesis / ribosome binding / 5S rRNA binding / cell body / ribosomal large subunit assembly
Similarity search - Function
Coiled-coil domain-containing protein 86 / Ribosome biogenesis protein Rpf2 / Learning associated protein 18-like / LLP homolog / Ribosomal biogenesis regulatory protein / Ribosome biogenesis regulatory protein (RRS1) / Nucleolar GTP-binding protein 2, N-terminal domain / Nucleolar GTP-binding protein 2 / NGP1NT (NUC091) domain / NLE ...Coiled-coil domain-containing protein 86 / Ribosome biogenesis protein Rpf2 / Learning associated protein 18-like / LLP homolog / Ribosomal biogenesis regulatory protein / Ribosome biogenesis regulatory protein (RRS1) / Nucleolar GTP-binding protein 2, N-terminal domain / Nucleolar GTP-binding protein 2 / NGP1NT (NUC091) domain / NLE / NLE (NUC135) domain / Guanine nucleotide-binding protein-like 3, N-terminal domain / GNL3L/Grn1 putative GTPase / : / Ribosomal biogenesis NSA2 family / GTP-binding protein, orthogonal bundle domain superfamily / Ribosome assembly factor Mrt4 / : / : / NOG, C-terminal / Nucleolar GTP-binding protein 1 / NOGCT (NUC087) domain / Nucleolar GTP-binding protein 1, Rossman-fold domain / NOG1, N-terminal helical domain / Nucleolar GTP-binding protein 1 (NOG1) / NOG1 N-terminal helical domain / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile. / Brix domain / Brix domain / Brix domain profile. / Brix / OBG-type guanine nucleotide-binding (G) domain / OBG-type guanine nucleotide-binding (G) domain profile. / Translation initiation factor IF6 / eIF-6 family / translation initiation factor 6 / 50S ribosome-binding GTPase / GTP binding domain / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / 50S ribosomal protein L10, insertion domain superfamily / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Ribosomal protein L28e / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / metallochaperone-like domain / TRASH domain / : / Ribosomal protein L6e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L35Ae, conserved site / 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 signature. / : / Ribosomal Protein L6, KOW domain / Ribosomal protein L6e / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L7, eukaryotic / Ribosomal protein L30, N-terminal / Ribosomal L30 N-terminal domain / 60S ribosomal protein L6E / : / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L18e / Ribosomal protein L14e domain / Ribosomal protein L14 / Ribosomal protein L35A / Ribosomal protein L35Ae / Ribosomal protein L35A superfamily / Ribosomal protein L32e, conserved site / Ribosomal protein L32e signature. / Ribosomal protein L6, conserved site-2 / Ribosomal protein L6 signature 2. / Ribosomal protein L5 eukaryotic/L18 archaeal / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal protein L14 / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L1e signature. / Ribosomal protein L21e / Ribosomal protein L21e, conserved site / Ribosomal protein L21 superfamily / Ribosomal protein L21e / Ribosomal protein L21e signature. / Ribosomal protein L24e-related / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L24e / Ribosomal protein L3, domain 3, archaeal type superfamily / Ribosomal protein L3, archaeal/eukaryotic type
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ribosome biogenesis protein NSA2 homolog ...GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ribosome biogenesis protein NSA2 homolog / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein eL28 / Large ribosomal subunit protein eL14 / Eukaryotic translation initiation factor 6 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein eL18 / Nucleolar GTP-binding protein 2 / Ribosome biogenesis regulatory protein homolog / Protein LLP homolog / Guanine nucleotide-binding protein-like 3 / GTP-binding protein 4 / Coiled-coil domain-containing protein 86 / Ribosome production factor 2 homolog / Notchless protein homolog 1 / Probable ribosome biogenesis protein RLP24 / mRNA turnover protein 4 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.91 Å
AuthorsVanden Broeck, A. / Klinge, S.
Funding supportEuropean Union, United States, 2items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO)ALTF 711-2019European Union
The G. Harold and Leila Y. Mathers FoundationMF-2104-01554 United States
CitationJournal: Science / Year: 2023
Title: Principles of human pre-60 biogenesis.
Authors: Arnaud Vanden Broeck / Sebastian Klinge /
Abstract: During the early stages of human large ribosomal subunit (60) biogenesis, an ensemble of assembly factors establishes and fine-tunes the essential RNA functional centers of pre-60 particles by an ...During the early stages of human large ribosomal subunit (60) biogenesis, an ensemble of assembly factors establishes and fine-tunes the essential RNA functional centers of pre-60 particles by an unknown mechanism. Here, we report a series of cryo-electron microscopy structures of human nucleolar and nuclear pre-60 assembly intermediates at resolutions of 2.5 to 3.2 angstroms. These structures show how protein interaction hubs tether assembly factor complexes to nucleolar particles and how guanosine triphosphatases and adenosine triphosphatase couple irreversible nucleotide hydrolysis steps to the installation of functional centers. Nuclear stages highlight how a conserved RNA-processing complex, the rixosome, couples large-scale RNA conformational changes with pre-ribosomal RNA processing by the RNA degradation machinery. Our ensemble of human pre-60 particles provides a rich foundation with which to elucidate the molecular principles of ribosome formation.
History
DepositionDec 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
BA: 60S ribosomal protein L12
L3: 28S rRNA
L4: 5S rRNA
L5: 60S ribosomal protein L11
L7: 60S ribosomal protein L13a
L8: 60S ribosomal protein L14
LB: 60S ribosomal protein L18
LC: 60S ribosomal protein L18a
LE: 60S ribosomal protein L21
LG: 60S ribosomal protein L23
LL: 60S ribosomal protein L28
LN: 60S ribosomal protein L3
LQ: 60S ribosomal protein L32
LT: 60S ribosomal protein L35a
NB: Guanine nucleotide-binding protein-like 3
NC: Nucleolar GTP-binding protein 2
ND: Ribosome production factor 2 homolog
NF: Ribosome biogenesis protein NSA2 homolog
NJ: Notchless protein homolog 1
NK: Protein LLP homolog
NZ: Coiled-coil domain-containing protein 86
SA: 60S ribosomal protein L4
SB: 60S ribosomal protein L5
SC: 60S ribosomal protein L6
SD: 60S ribosomal protein L7
SG: 60S ribosomal protein L9
SK: Eukaryotic translation initiation factor 6
SQ: mRNA turnover protein 4 homolog
SR: GTP-binding protein 4
ST: Ribosome biogenesis regulatory protein homolog
SV: Probable ribosome biogenesis protein RLP24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,608,75558
Polymers2,607,11031
Non-polymers1,64527
Water00
1


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

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Components

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60S ribosomal protein ... , 17 types, 17 molecules BAL5L7L8LBLCLELGLLLNLQLTSASBSCSDSG

#1: Protein 60S ribosomal protein L12 / Large ribosomal subunit protein uL11


Mass: 17847.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: P30050
#4: 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: HEK293F / References: UniProt: P62913
#5: 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: HEK293F / References: UniProt: P40429
#6: Protein 60S ribosomal protein L14 / CAG-ISL 7 / Large ribosomal subunit protein eL14


Mass: 23485.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: P50914
#7: 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: HEK293F / References: UniProt: Q07020
#8: 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: HEK293F / References: UniProt: Q02543
#9: 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: HEK293F / References: UniProt: P46778
#10: 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: HEK293F / References: UniProt: P62829
#11: 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: HEK293F / References: UniProt: P46779
#12: Protein 60S ribosomal protein L3 / HIV-1 TAR RNA-binding protein B / TARBP-B / Large ribosomal subunit protein uL3


Mass: 46224.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: P39023
#13: 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: HEK293F / References: UniProt: P62910
#14: 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: HEK293F / References: UniProt: P18077
#22: 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: HEK293F / References: UniProt: P36578
#23: 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: HEK293F / References: UniProt: P46777
#24: 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: HEK293F / References: UniProt: Q02878
#25: 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: HEK293F / References: UniProt: P18124
#26: 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: HEK293F / References: UniProt: P32969

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RNA chain , 2 types, 2 molecules L3L4

#2: RNA chain 28S rRNA


Mass: 1640222.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: GenBank: 86475748
#3: RNA chain 5S rRNA


Mass: 38998.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: GenBank: 23898

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Protein , 10 types, 10 molecules NBNCNDNJNKNZSKSQSRSV

#15: Protein Guanine nucleotide-binding protein-like 3 / E2-induced gene 3 protein / Novel nucleolar protein 47 / NNP47 / Nucleolar GTP-binding protein 3 / ...E2-induced gene 3 protein / Novel nucleolar protein 47 / NNP47 / Nucleolar GTP-binding protein 3 / Nucleostemin


Mass: 62098.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q9BVP2
#16: Protein Nucleolar GTP-binding protein 2 / Autoantigen NGP-1


Mass: 83796.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q13823
#17: Protein Ribosome production factor 2 homolog / Brix domain-containing protein 1 / Ribosome biogenesis protein RPF2 homolog


Mass: 35658.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q9H7B2
#19: Protein Notchless protein homolog 1


Mass: 53387.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q9NVX2
#20: Protein Protein LLP homolog / Protein LAPS18-like


Mass: 15268.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q9BRT6
#21: Protein Coiled-coil domain-containing protein 86 / Cytokine-induced protein with coiled-coil domain


Mass: 40312.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q9H6F5
#27: 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: HEK293F / References: UniProt: P56537
#28: Protein mRNA turnover protein 4 homolog / Ribosome assembly factor MRTO4


Mass: 27602.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q9UKD2
#29: Protein GTP-binding protein 4 / Chronic renal failure gene protein / GTP-binding protein NGB / Nucleolar GTP-binding protein 1


Mass: 74107.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q9BZE4
#31: Protein Probable ribosome biogenesis protein RLP24 / Ribosomal L24 domain-containing protein 1 / Ribosomal protein L24-like


Mass: 19666.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q9UHA3

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Ribosome biogenesis ... , 2 types, 2 molecules NFST

#18: Protein Ribosome biogenesis protein NSA2 homolog / Hairy cell leukemia protein 1 / TGF-beta-inducible nuclear protein 1


Mass: 30136.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: O95478
#30: Protein Ribosome biogenesis regulatory protein homolog


Mass: 41278.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q15050

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Non-polymers , 5 types, 27 molecules

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


Mass: 24.305 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Mg
#33: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#34: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#35: 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
#36: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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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 nucleolar pre-60S ribosomal subunit (State H) / Type: RIBOSOME / Entity ID: #1-#31 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human) / Strain: HEK293F
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R3.5/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 283 K
Details: Four applications with manual blotting before last blotting with the vitrobot.

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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: 64000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingAverage exposure time: 2 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 4 / Num. of real images: 172699
EM imaging opticsEnergyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1RELION4particle selection
2SerialEMimage acquisition
4Gctf1.06CTF correction
9RELION4initial Euler assignment
10cryoSPARC3.3.2final Euler assignment
11RELION4classification
12cryoSPARC3.3.2classification
13cryoSPARC3.3.23D reconstruction
20PHENIX1.19.1model refinementphenix.real_space_refine
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 15679142
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 67272 / Symmetry type: POINT
Atomic model buildingSpace: REAL

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