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- PDB-9qiw: Human pre-60S - State 3 -

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Basic information

Entry
Database: PDB / ID: 9qiw
TitleHuman pre-60S - State 3
Components
  • (60S ribosomal protein ...) x 33
  • (Large ribosomal subunit protein ...) x 4
  • (Ribosome biogenesis ...) x 2
  • 28S rRNA
  • 5.8S rRNA
  • 5S rRNA
  • 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 / Human / ribosome biogenesis / NLE1 / RIX1 complex / 5S RNP
Function / homology
Function and homology information


positive regulation of protein localization to chromosome, telomeric region / basal RNA polymerase II transcription machinery binding / dendrite extension / inner cell mass cell differentiation / preribosome binding / hematopoietic stem cell homeostasis / lamin filament / regulation of fatty acid biosynthetic process / regulation of Notch signaling pathway / regulation of megakaryocyte differentiation ...positive regulation of protein localization to chromosome, telomeric region / basal RNA polymerase II transcription machinery binding / dendrite extension / inner cell mass cell differentiation / preribosome binding / hematopoietic stem cell homeostasis / lamin filament / regulation of fatty acid biosynthetic process / regulation of Notch signaling pathway / regulation of megakaryocyte differentiation / 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 / translation at presynapse / 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 / 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 / protein localization to nucleolus / 90S preribosome assembly / negative regulation of mitotic cell cycle / GAIT complex / positive regulation of DNA damage response, signal transduction by p53 class mediator / TORC2 complex binding / alpha-beta T cell differentiation / G1 to G0 transition / regulation of glycolytic process / skeletal system morphogenesis / regulation of reactive oxygen species metabolic process / middle ear morphogenesis / negative regulation of cell-cell adhesion / maturation of 5.8S rRNA / stem cell division / cytoplasmic side of rough endoplasmic reticulum membrane / mitotic metaphase chromosome alignment / negative regulation of ubiquitin protein ligase activity / stem cell population maintenance / homeostatic process / negative regulation of DNA replication / macrophage chemotaxis / positive regulation of dendritic spine development / lung morphogenesis / ribosomal large subunit binding / positive regulation of natural killer cell proliferation / positive regulation of telomere maintenance / preribosome, large subunit precursor / Protein hydroxylation / nuclear-transcribed mRNA catabolic process / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / cellular response to actinomycin D / Eukaryotic Translation Termination / blastocyst development / ubiquitin ligase inhibitor activity / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / negative regulation of ubiquitin-dependent protein catabolic process / positive regulation of signal transduction by p53 class mediator / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / protein localization to nucleus / GTP hydrolysis and joining of the 60S ribosomal subunit / positive regulation of protein binding / L13a-mediated translational silencing of Ceruloplasmin expression / somitogenesis / hematopoietic progenitor cell differentiation / Major pathway of rRNA processing in the nucleolus and cytosol / protein targeting / protein-RNA complex assembly / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / maturation of LSU-rRNA / ribosomal subunit export from nucleus / rough endoplasmic reticulum / 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) / Notch signaling pathway / MDM2/MDM4 family protein binding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / translation initiation factor activity / negative regulation of protein ubiquitination / cytosolic ribosome / cellular response to interleukin-4 / ossification / negative regulation of cell migration / regulation of signal transduction by p53 class mediator / positive regulation of translation / assembly of large subunit precursor of preribosome / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic ribosome assembly / condensed nuclear chromosome / mRNA 3'-UTR binding / innate immune response in mucosa / skeletal system development
Similarity search - Function
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 ...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 / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / GTP binding domain / Ribosomal protein L30e / Ribosomal protein L28e / Ribosomal L15/L27a, N-terminal / 50S ribosomal protein L10, insertion domain superfamily / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / 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 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 L19, eukaryotic / : / Ribosomal protein L6e signature. / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L30e signature 1. / 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 L6, KOW domain / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / 60S ribosomal protein L35 / Ribosomal protein L6e
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 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 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 / Ribosome biogenesis regulatory protein homolog / Protein LLP homolog / Guanine nucleotide-binding protein-like 3 / GTP-binding protein 4 / Ribosome production factor 2 homolog / Notchless protein homolog 1 / Probable ribosome biogenesis protein RLP24 / mRNA turnover protein 4 homolog / Large ribosomal subunit protein eL36
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsThoms, M. / Denk, T. / Beckmann, R.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
Citation
Journal: Nucleic Acids Res / Year: 2025
Title: Highly conserved ribosome biogenesis pathways between human and yeast revealed by the MDN1-NLE1 interaction and NLE1 containing pre-60S subunits.
Authors: Federica Fiorentino / Matthias Thoms / Klemens Wild / Timo Denk / Jingdong Cheng / Jakub Zeman / Irmgard Sinning / Ed Hurt / Roland Beckmann /
Abstract: The assembly of ribosomal subunits, primarily occurring in the nucleolar and nuclear compartments, is a highly complex process crucial for cellular function. This study reveals the conservation of ...The assembly of ribosomal subunits, primarily occurring in the nucleolar and nuclear compartments, is a highly complex process crucial for cellular function. This study reveals the conservation of ribosome biogenesis between yeast and humans, illustrated by the structural similarities of ribosomal subunit intermediates. By using X-ray crystallography and cryo-EM, the interaction between the human AAA+ ATPase MDN1 and the 60S assembly factor NLE1 is compared with the yeast homologs Rea1 and Rsa4. The MDN1-MIDAS and NLE1-Ubl complex structure at 2.3 Å resolution mirrors the highly conserved interaction patterns observed in yeast. Moreover, human pre-60S intermediates bound to the dominant negative NLE1-E85A mutant revealed at 2.8 Å resolution an architecture that largely matched the equivalent yeast structures. Conformation of rRNA, assembly factors and their interaction networks are highly conserved. Additionally, novel human pre-60S intermediates with a non-rotated 5S RNP and processed ITS2/foot structure but incomplete intersubunit surface were identified to be similar to counterparts observed in yeast. These findings confirm that the MDN1-NLE1-driven transition phase of the 60S assembly is essentially identical, supporting the idea that ribosome biogenesis is a highly conserved process across eukaryotic cells, employing an evolutionary preservation of ribosomal assembly mechanisms.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2018
Title: Real-space refinement in PHENIX for cryo-EM and crystallography
Authors: Adams, P.D.
History
DepositionMar 17, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
CA: Eukaryotic translation initiation factor 6
CB: Nucleolar GTP-binding protein 2
CC: Guanine nucleotide-binding protein-like 3
CD: GTP-binding protein 4
CE: Protein LLP homolog
CF: mRNA turnover protein 4 homolog
CG: Notchless protein homolog 1
CH: Ribosome biogenesis protein NSA2 homolog
CI: Probable ribosome biogenesis protein RLP24
CJ: Ribosome production factor 2 homolog
CK: Ribosome biogenesis regulatory protein homolog
L7: 5S rRNA
LA: 60S ribosomal protein L8
LB: 60S ribosomal protein L3
LC: 60S ribosomal protein L4
LD: 60S ribosomal protein L5
LE: Large ribosomal subunit protein eL6
LF: Large ribosomal subunit protein uL30
LG: 60S ribosomal protein L7a
LH: 60S ribosomal protein L9
LJ: 60S ribosomal protein L11
LL: 60S ribosomal protein L13
LM: 60S ribosomal protein L14
LN: 60S ribosomal protein L15
LO: 60S ribosomal protein L13a
LP: 60S ribosomal protein L17
LQ: 60S ribosomal protein L18
LR: 60S ribosomal protein L19
LS: 60S ribosomal protein L18a
LT: 60S ribosomal protein L21
LU: 60S ribosomal protein L22
LV: 60S ribosomal protein L23
LX: 60S ribosomal protein L23a
LY: 60S ribosomal protein L26
LZ: 60S ribosomal protein L27
La: 60S ribosomal protein L27a
Lc: 60S ribosomal protein L30
Ld: 60S ribosomal protein L31
Le: 60S ribosomal protein L32
Lf: 60S ribosomal protein L35a
Lg: 60S ribosomal protein L34
Lh: 60S ribosomal protein L35
Li: 60S ribosomal protein L36
Lj: Large ribosomal subunit protein eL37
Lk: 60S ribosomal protein L38
Ll: 60S ribosomal protein L39
Lp: 60S ribosomal protein L37a
Lr: 60S ribosomal protein L28
Lt: Large ribosomal subunit protein uL11
L5: 28S rRNA
L8: 5.8S rRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,955,97058
Polymers2,954,71851
Non-polymers1,2527
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 9 types, 9 molecules CACBCCCDCECFCGCICJ

#1: 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) / References: UniProt: P56537
#2: 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) / References: UniProt: Q13823
#3: 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) / References: UniProt: Q9BVP2
#4: 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) / References: UniProt: Q9BZE4
#5: 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) / References: UniProt: Q9BRT6
#6: 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) / References: UniProt: Q9UKD2
#7: Protein Notchless protein homolog 1


Mass: 53329.102 Da / Num. of mol.: 1 / Mutation: E85A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NLE1, HUSSY-07 / Production host: Homo sapiens (human) / References: UniProt: Q9NVX2
#9: 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) / References: UniProt: Q9UHA3
#10: 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) / References: UniProt: Q9H7B2

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Ribosome biogenesis ... , 2 types, 2 molecules CHCK

#8: 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) / References: UniProt: O95478
#11: 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) / References: UniProt: Q15050

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RNA chain , 3 types, 3 molecules L7L5L8

#12: RNA chain 5S rRNA


Mass: 38998.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 23898
#50: RNA chain 28S rRNA


Mass: 1640222.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: NR_003287
#51: RNA chain 5.8S rRNA


Mass: 50449.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 555853

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60S ribosomal protein ... , 33 types, 33 molecules LALBLCLDLGLHLJLLLMLNLOLPLQLRLSLTLULVLXLYLZLaLcLdLeLfLgLhLiLk...

#13: 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) / References: UniProt: P62917
#14: 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) / References: UniProt: P39023
#15: 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) / References: UniProt: P36578
#16: 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) / References: UniProt: P46777
#19: 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) / References: UniProt: P62424
#20: 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) / References: UniProt: P32969
#21: 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) / References: UniProt: P62913
#22: 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) / References: UniProt: P26373
#23: 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) / References: UniProt: P50914
#24: 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) / References: UniProt: P61313
#25: 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) / References: UniProt: P40429
#26: 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) / References: UniProt: P18621
#27: 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) / References: UniProt: Q07020
#28: 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) / References: UniProt: P84098
#29: 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) / References: UniProt: Q02543
#30: 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) / References: UniProt: P46778
#31: 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) / References: UniProt: P35268
#32: 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) / References: UniProt: P62829
#33: 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) / References: UniProt: P62750
#34: 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) / References: UniProt: P61254
#35: 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) / References: UniProt: P61353
#36: 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) / References: UniProt: P46776
#37: 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) / References: UniProt: P62888
#38: 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) / References: UniProt: P62899
#39: 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) / References: UniProt: P62910
#40: 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) / References: UniProt: P18077
#41: 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) / References: UniProt: P49207
#42: 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) / References: UniProt: P42766
#43: 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) / References: UniProt: Q9Y3U8
#45: 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) / References: UniProt: P63173
#46: 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) / References: UniProt: P62891
#47: 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) / References: UniProt: P61513
#48: 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) / References: UniProt: P46779

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Large ribosomal subunit protein ... , 4 types, 4 molecules LELFLjLt

#17: Protein Large ribosomal subunit protein eL6 / 60S ribosomal protein L6 / Neoplasm-related protein C140 / Tax-responsive enhancer element-binding ...60S ribosomal protein L6 / 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) / References: UniProt: Q02878
#18: Protein Large ribosomal subunit protein uL30 / 60S ribosomal protein L7


Mass: 29290.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18124
#44: Protein Large ribosomal subunit protein eL37 / 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) / References: UniProt: P61927
#49: Protein Large ribosomal subunit protein uL11 / 60S ribosomal protein L12


Mass: 17847.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P30050

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Non-polymers , 4 types, 7 molecules

#52: 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
#53: 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
#54: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#55: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationN

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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 pre-60S - State 1A / Type: RIBOSOME / Entity ID: #1-#40 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 43.6 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 33891
Details: Resolution given for Consensus refinement - this is a composite map
Symmetry type: POINT

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