PDB-8fl7: Human nuclear pre-60S ribosomal subunit (State J2)

ID or keywords:

Entry

Database: PDB / ID: 8fl7

Title

Human nuclear pre-60S ribosomal subunit (State J2)

Components

(60S ribosomal protein ...) x 40
(Ribosome biogenesis protein ...) x 2
28S rRNA
5.8S rRNA
5S rRNA
Eukaryotic translation initiation factor 6
GTP-binding protein 4
MKI67 FHA domain-interacting nucleolar phosphoprotein
Nucleolar GTP-binding protein 2
Pescadillo homolog
Probable ribosome biogenesis protein RLP24
Protein LLP homolog
Zinc finger protein 593
mRNA turnover protein 4 homolog

Keywords

RIBOSOME / Pre-60S ribosomal subunit / Assembly intermediate / Nucleoprotein complex

Function / homology

Function and homology information

protein localization to nucleoplasm / negative regulation of transcription of nucleolar large rRNA by RNA polymerase I / negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / regulation of RIG-I signaling pathway / basal RNA polymerase II transcription machinery binding / negative regulation of collagen binding / dendrite extension / preribosome binding / lamin filament / regulation of fatty acid biosynthetic process ...protein localization to nucleoplasm / negative regulation of transcription of nucleolar large rRNA by RNA polymerase I / negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / regulation of RIG-I signaling pathway / basal RNA polymerase II transcription machinery binding / negative regulation of collagen binding / dendrite extension / preribosome binding / lamin filament / regulation of fatty acid biosynthetic process / regulation of megakaryocyte differentiation / PeBoW complex / miRNA-mediated post-transcriptional gene silencing / negative regulation of signal transduction by p53 class mediator / miRNA-mediated gene silencing by inhibition of translation / eukaryotic 80S initiation complex / negative regulation of protein neddylation / translation at presynapse / axial mesoderm development / ribosomal protein import into nucleus / negative regulation of formation of translation preinitiation complex / 90S preribosome assembly / blastocyst formation / positive regulation of protein K63-linked deubiquitination / protein localization to nucleolus / TORC2 complex binding / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / GAIT complex / middle ear morphogenesis / regulation of glycolytic process / maturation of 5.8S rRNA / A band / regulation of reactive oxygen species metabolic process / alpha-beta T cell differentiation / cytoplasmic side of rough endoplasmic reticulum membrane / regulation of G1 to G0 transition / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / negative regulation of ubiquitin protein ligase activity / regulation of aerobic respiration / response to aldosterone / regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of cell-cell adhesion / positive regulation of dendritic spine development / homeostatic process / rRNA metabolic process / G1 to G0 transition / negative regulation of DNA replication / macrophage chemotaxis / lung morphogenesis / Protein hydroxylation / mitotic G2 DNA damage checkpoint signaling / ribosomal large subunit binding / Peptide chain elongation / rRNA transcription / preribosome, large subunit precursor / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / nuclear-transcribed mRNA catabolic process / Formation of a pool of free 40S subunits / blastocyst development / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / protein localization to nucleus / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / 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 / Major pathway of rRNA processing in the nucleolus and cytosol / protein targeting / negative regulation of protein-containing complex assembly / protein-RNA complex assembly / cellular response to interleukin-4 / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / cellular response to actinomycin D / negative regulation of ubiquitin-dependent protein catabolic process / ribonucleoprotein complex binding / ribosomal subunit export from nucleus / rough endoplasmic reticulum / MDM2/MDM4 family protein binding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein ubiquitination / maturation of LSU-rRNA / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / cytosolic ribosome / embryo implantation / translation initiation factor activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ossification / assembly of large subunit precursor of preribosome / ribosomal large subunit biogenesis / cytosolic ribosome assembly / negative regulation of cell migration / regulation of signal transduction by p53 class mediator / innate immune response in mucosa
Similarity search - Function

MKI67 FHA domain-interacting nucleolar phosphoprotein, FHA Ki67 binding / FHA Ki67 binding domain of hNIFK / Learning associated protein 18-like / LLP homolog / Ribosome biogenesis protein Nop53/GLTSCR2 / Nop53 (60S ribosomal biogenesis) / : / Nucleolar GTP-binding protein 2, N-terminal domain / Nucleolar GTP-binding protein 2 / NGP1NT (NUC091) domain ...MKI67 FHA domain-interacting nucleolar phosphoprotein, FHA Ki67 binding / FHA Ki67 binding domain of hNIFK / Learning associated protein 18-like / LLP homolog / Ribosome biogenesis protein Nop53/GLTSCR2 / Nop53 (60S ribosomal biogenesis) / : / Nucleolar GTP-binding protein 2, N-terminal domain / Nucleolar GTP-binding protein 2 / NGP1NT (NUC091) domain / Zinc-finger double-stranded RNA-binding / Zinc finger, double-stranded RNA binding / : / Pescadillo / Pescadillo N-terminus / Ribosomal protein L24e / GTP-binding protein, orthogonal bundle domain superfamily / Ribosomal biogenesis NSA2 family / Ribosome assembly factor Mrt4 / : / BRCT domain, a BRCA1 C-terminus domain / 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. / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / 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 / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L30e / GTP binding domain / Ribosomal protein L2, archaeal-type / Ribosomal L15/L27a, N-terminal / Ribosomal protein L28e / Ribosomal protein L23 / 50S ribosomal protein L10, insertion domain superfamily / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Ribosomal protein L18e / Ribosomal protein 60S L18 and 50S L18e / metallochaperone-like domain / TRASH domain / breast cancer carboxy-terminal domain / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L13e, conserved site / Ribosomal protein L13e 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 L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L44e signature. / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L19, eukaryotic / 60S ribosomal protein L18a/ L20, eukaryotes / : / Ribosomal protein L24e, conserved site / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L24e signature. / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / : / Ribosomal protein L30e signature 1. / Ribosomal protein L6e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein L30e signature 2. / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein L30e, conserved site / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family
Similarity search - Domain/homology

GUANOSINE-5'-DIPHOSPHATE / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL42 ...GUANOSINE-5'-DIPHOSPHATE / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL42 / Zinc finger protein 593 / Pescadillo homolog / Ribosome biogenesis protein NSA2 homolog / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein uL11 / 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 uL29 / 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 / Large ribosomal subunit protein eL14 / 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 eL19 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein eL18 / Nucleolar GTP-binding protein 2 / Ribosomal protein uL30-like / Protein LLP homolog / MKI67 FHA domain-interacting nucleolar phosphoprotein / GTP-binding protein 4 / Ribosome biogenesis protein NOP53 / Probable ribosome biogenesis protein RLP24 / mRNA turnover protein 4 homolog / Large ribosomal subunit protein eL36
Similarity search - Component

Biological species

Homo sapiens (human)

Method

ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.55 Å

Authors

Vanden Broeck, A. / Klinge, S.

Funding support

European Union,

United States, 2items

Citation

Journal: 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 ...

History

Deposition	Dec 21, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 12, 2023	Provider: repository / Type: Initial release
Revision 1.1	Jul 19, 2023	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2	Jul 26, 2023	Group: Database references / Category: citation / citation_author Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8fl7.cif.gz	3.3 MB	Display	PDBx/mmCIF format
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Validation report

Summary document	8fl7_validation.pdf.gz	2.1 MB	Display	wwPDB validaton report
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Data in CIF	8fl7_validation.cif.gz	454.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fl/8fl7 ftp://data.pdbj.org/pub/pdb/validation_reports/fl/8fl7	HTTPS FTP

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Related structure data

Related structure data	29269MC 29104C 29105C 29106C 29107C 29108C 29109C 29110C 29111C 29112C 29113C 29114C 29115C 29116C 29117C 29118C 29119C 29120C 29121C 29122C 29123C 29124C 29125C 29126C 29127C 29128C 29129C 29130C 29131C 29132C 29133C 29134C 29135C 29136C 29137C 29138C 29139C 29140C 29141C 29142C 29143C 29144C 29145C 29146C 29147C 29148C 29149C 29150C 29151C 29152C 29153C 29154C 29155C 29156C 29157C 29158C 29159C 29160C 29161C 29162C 29163C 29164C 29165C 29166C 29167C 29168C 29169C 29170C 29171C 29173C 29174C 29175C 29176C 29177C 29178C 29179C 29180C 29181C 29182C 29183C 29184C 29185C 29186C 29187C 29188C 29189C 29192C 29193C 29194C 29195C 29196C 29197C 29198C 29199C 29200C 29201C 29202C 29204C 29205C 29206C 29252C 29253C 29254C 29255C 29256C 29257C 29258C 29259C 29260C 29261C 29262C 29263C 29265C 29266C 29267C 29268C 29271C 29272C 29273C 29274C 29275C 29276C 29277C 8fkpC 8fkqC 8fkrC 8fksC 8fktC 8fkuC 8fkvC 8fkwC 8fkxC 8fkyC 8fkzC 8fl0C 8fl2C 8fl3C 8fl4C 8fl6C 8fl9C 8flaC 8flbC 8flcC 8fldC 8fleC 8flfC C: citing same article (ref.) M: map data used to model this data
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

29269MC

C: citing same article (ref.)

M: map data used to model this data

Similar structure data

Similarity search - Function & homology

F&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#121 - Jan 2010 70S Ribosomes similarity (89) #130 - Oct 2010 Riboswitches similarity (2) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #10 - Oct 2000 Ribosome similarity (82) #157 - Jan 2013 Transfer-Messenger RNA similarity (5) #253 - Jan 2021 Expressome similarity (8) #260 - Aug 2021 Ribonuclease P similarity (8) #181 - Jan 2015 Cascade and CRISPR similarity (1) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (3) #15 - Mar 2001 Transfer RNA similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1) #161 - May 2013 Ricin similarity (141) #87 - Mar 2007 Zinc Fingers similarity (5) #210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #266 - Feb 2022 Oligosaccharyltransferase similarity (115) #245 - May 2020 Spliceosomes similarity (5) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (3) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (5) #65 - May 2005 Self-splicing RNA similarity (2) #105 - Sep 2008 Ribonuclease A similarity (1) #98 - Feb 2008 Small Interfering RNA similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (13) #230 - Feb 2019 Initiation Factor eIF4E similarity (5) #227 - Nov 2018 Telomerase similarity (2) #106 - Oct 2008 Poly(A) Polymerase similarity (4) #104 - Aug 2008 Selenocysteine Synthase similarity (2) #143 - Nov 2011 Toll-like Receptors similarity (1) #81 - Sep 2006 Elongation Factors similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #60 - Dec 2004 Ubiquitin similarity (12) #241 - Jan 2020 Twenty Years of Molecules similarity (1) #55 - Jul 2004 DNA Ligase similarity (4) #122 - Feb 2010 Enhanceosome similarity (5) #150 - Jun 2012 Sliding Clamps similarity (4) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (4) #257 - May 2021 Fetal Hemoglobin similarity (4) #165 - Sep 2013 Designed Protein Cages similarity (1) #62 - Feb 2005 Major Histocompatibility Complex similarity (1) #86 - Feb 2007 Exosomes similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

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Deposited unit

BA: 60S ribosomal protein L12

L1: 5.8S rRNA

L3: 28S rRNA

L4: 5S rRNA

L5: 60S ribosomal protein L11

L6: 60S ribosomal protein L13

L7: 60S ribosomal protein L13a

L8: 60S ribosomal protein L14

L9: 60S ribosomal protein L15

LA: 60S ribosomal protein L17

LB: 60S ribosomal protein L18

LC: 60S ribosomal protein L18a

LD: 60S ribosomal protein L19

LE: 60S ribosomal protein L21

LF: 60S ribosomal protein L22

LG: 60S ribosomal protein L23

LH: 60S ribosomal protein L23a

LI: 60S ribosomal protein L26

LJ: 60S ribosomal protein L27

LK: 60S ribosomal protein L27a

LL: 60S ribosomal protein L28

LM: 60S ribosomal protein L29

LN: 60S ribosomal protein L3

LO: 60S ribosomal protein L30

LP: 60S ribosomal protein L31

LQ: 60S ribosomal protein L32

LR: 60S ribosomal protein L34

LS: 60S ribosomal protein L35

LT: 60S ribosomal protein L35a

LU: 60S ribosomal protein L36

LV: 60S ribosomal protein L36a

LW: 60S ribosomal protein L37

LX: 60S ribosomal protein L37a

LY: 60S ribosomal protein L38

LZ: 60S ribosomal protein L39

NC: Nucleolar GTP-binding protein 2

NF: Ribosome biogenesis protein NSA2 homolog

NK: Protein LLP homolog

NL: Ribosome biogenesis protein NOP53

NP: Zinc finger protein 593

SA: 60S ribosomal protein L4

SB: 60S ribosomal protein L5

SC: 60S ribosomal protein L6

SD: 60S ribosomal protein L7

SE: 60S ribosomal protein L7a

SF: 60S ribosomal protein L8

SG: 60S ribosomal protein L9

SH: MKI67 FHA domain-interacting nucleolar phosphoprotein

SI: 60S ribosomal protein L7-like 1

SK: Eukaryotic translation initiation factor 6

SM: Pescadillo homolog

SQ: mRNA turnover protein 4 homolog

SR: GTP-binding protein 4

SV: Probable ribosome biogenesis protein RLP24

hetero molecules

3 MDa, 54 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: electron microscopy

+
60S ribosomal protein ... , 40 types, 40 molecules BAL5L6L7L8L9LALBLCLDLELFLGLHLILJLKLLLMLNLOLPLQLRLSLTLULVLWLX...

#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
#5: 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
#6: 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: HEK293F / References: UniProt: P26373
#7: 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
#8: 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
#9: 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: HEK293F / References: UniProt: P61313
#10: 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: HEK293F / References: UniProt: P18621
#11: 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
#12: 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
#13: 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: HEK293F / References: UniProt: P84098
#14: 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
#15: 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: HEK293F / References: UniProt: P35268
#16: 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
#17: 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: HEK293F / References: UniProt: P62750
#18: 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: HEK293F / References: UniProt: P61254
#19: 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: HEK293F / References: UniProt: P61353
#20: 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: HEK293F / References: UniProt: P46776
#21: 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
#22: 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: HEK293F / References: UniProt: P47914
#23: 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
#24: 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: HEK293F / References: UniProt: P62888
#25: 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: HEK293F / References: UniProt: P62899
#26: 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
#27: 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: HEK293F / References: UniProt: P49207
#28: Protein	60S ribosomal protein L35 / Large ribosomal subunit protein uL29 Mass: 14593.624 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: P42766
#29: 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
#30: 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: HEK293F / References: UniProt: Q9Y3U8
#31: Protein	60S ribosomal protein L36a Mass: 12476.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: J3KQN4
#32: Protein	60S ribosomal protein L37 / G1.16 Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: P61927
#33: 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: HEK293F / References: UniProt: P61513
#34: Protein	60S ribosomal protein L38 Mass: 8238.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: P63173
#35: Protein	60S ribosomal protein L39 Mass: 6426.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: P62891
#41: 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
#42: 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
#43: 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
#44: 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
#45: 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: HEK293F / References: UniProt: P62424
#46: 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: HEK293F / References: UniProt: P62917
#47: 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
#49: Protein	60S ribosomal protein L7-like 1 / Large ribosomal subunit protein uL30-like 1 Mass: 29730.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q6DKI1

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RNA chain , 3 types, 3 molecules L1L3L4

#2: RNA chain	5.8S rRNA Mass: 50463.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: GenBank: 555853
#3: RNA chain	28S rRNA Mass: 1641203.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: GenBank: 86475748
#4: 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 , 9 types, 9 molecules NCNKNPSHSKSMSQSRSV

#36: 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
#38: 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
#40: Protein	Zinc finger protein 593 / Zinc finger protein T86 Mass: 15230.225 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: O00488
#48: Protein	MKI67 FHA domain-interacting nucleolar phosphoprotein / Nucleolar phosphoprotein Nopp34 / Nucleolar protein interacting with the FHA domain of pKI-67 / hNIFK Mass: 34285.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q9BYG3
#50: 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
#51: Protein	Pescadillo homolog Mass: 68114.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: O00541
#52: 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
#53: 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
#54: 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 protein ... , 2 types, 2 molecules NFNL

#37: 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
#39: Protein	Ribosome biogenesis protein NOP53 / Glioma tumor suppressor candidate region gene 2 protein / Protein interacting with carboxyl ...Glioma tumor suppressor candidate region gene 2 protein / Protein interacting with carboxyl terminus 1 / PICT-1 / p60 Mass: 54498.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q9NZM5

#37: 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

#39: Protein

Ribosome biogenesis protein NOP53 / Glioma tumor suppressor candidate region gene 2 protein / Protein interacting with carboxyl ...

Mass: 54498.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural)

Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q9NZM5

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Non-polymers , 4 types, 96 molecules

#55: Chemical	... ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 88 / Source method: obtained synthetically / Formula: Mg
#56: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#57: 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
#58: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: K

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Details

Has ligand of interest	N

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Experiment

Experiment	Method: ELECTRON MICROSCOPY
EM experiment	Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component	Name: Human nuclear pre-60S ribosomal subunit (State J2) / Type: RIBOSOME / Entity ID: #1-#54 / Source: NATURAL
Molecular weight	Experimental value: NO
Source (natural)	Organism: Homo sapiens (human) / Strain: HEK293F
Buffer solution	pH: 7.6
Specimen	Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen support	Grid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R3.5/1
Vitrification	Instrument: 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
Microscopy	Model: FEI TITAN KRIOS
Electron gun	Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lens	Mode: BRIGHT FIELD / Nominal magnification: 64000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recording	Average 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 optics	Energyfilter slit width: 20 eV

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Processing

EM software

ID	Name	Version	Category	Details
1	RELION	4	particle selection
2	SerialEM		image acquisition
4	Gctf	1.06	CTF correction
9	PHENIX	1.19.1	model refinement	phenix.real_space_refine
10	RELION	4	initial Euler assignment
11	cryoSPARC	3.3.2	final Euler assignment
12	RELION	4	classification
13	cryoSPARC	3.3.2	classification
14	cryoSPARC	3.3.2	3D reconstruction

CTF correction

Type: PHASE FLIPPING AND AMPLITUDE CORRECTION

Particle selection

Num. of particles selected: 15679142

Symmetry

Point symmetry: C₁ (asymmetric)

3D reconstruction

Resolution: 2.55 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 74556 / Symmetry type: POINT

Atomic model building

Space: REAL

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60S ribosomal protein ... , 40 types, 40 molecules BAL5L6L7L8L9LALBLCLDLELFLGLHLILJLKLLLMLNLOLPLQLRLSLTLULVLWLX...

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RNA chain , 3 types, 3 molecules L1L3L4

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Protein , 9 types, 9 molecules NCNKNPSHSKSMSQSRSV

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Ribosome biogenesis protein ... , 2 types, 2 molecules NFNL

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Non-polymers , 4 types, 96 molecules

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+60S ribosomal protein ... , 40 types, 40 molecules BAL5L6L7L8L9LALBLCLDLELFLGLHLILJLKLLLMLNLOLPLQLRLSLTLULVLWLX...

-RNA chain , 3 types, 3 molecules L1L3L4

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60S ribosomal protein ... , 40 types, 40 molecules BAL5L6L7L8L9LALBLCLDLELFLGLHLILJLKLLLMLNLOLPLQLRLSLTLULVLWLX...

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RNA chain , 3 types, 3 molecules L1L3L4

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Protein , 9 types, 9 molecules NCNKNPSHSKSMSQSRSV

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Ribosome biogenesis protein ... , 2 types, 2 molecules NFNL

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Non-polymers , 4 types, 96 molecules

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