8IDY

human nuclear pre-60S ribosomal particle - State F

  • Classification: RIBOSOME
  • Organism(s): Homo sapiens
  • Mutation(s): No 

  • Deposited: 2023-02-14 Released: 2023-08-09 
  • Deposition Author(s): Zhang, Y., Gao, N.
  • Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Visualizing the nucleoplasmic maturation of human pre-60S ribosomal particles.

Zhang, Y.Liang, X.Luo, S.Chen, Y.Li, Y.Ma, C.Li, N.Gao, N.

(2023) Cell Res 33: 867-878

  • DOI: https://doi.org/10.1038/s41422-023-00853-9
  • Primary Citation of Related Structures:  
    8IDT, 8IDY, 8IE3, 8INE, 8INF, 8INK, 8IPD, 8IPX, 8IPY, 8IR1, 8IR3

  • PubMed Abstract: 

    Eukaryotic ribosome assembly is a highly orchestrated process that involves over two hundred protein factors. After early assembly events on nascent rRNA in the nucleolus, pre-60S particles undergo continuous maturation steps in the nucleoplasm, and prepare for nuclear export. Here, we report eleven cryo-EM structures of the nuclear pre-60S particles isolated from human cells through epitope-tagged GNL2, at resolutions of 2.8-4.3 Å. These high-resolution snapshots provide fine details for several major structural remodeling events at a virtual temporal resolution. Two new human nuclear factors, L10K and C11orf98, were also identified. Comparative structural analyses reveal that many assembly factors act as successive place holders to control the timing of factor association/dissociation events. They display multi-phasic binding properties for different domains and generate complex binding inter-dependencies as a means to guide the rRNA maturation process towards its mature conformation. Overall, our data reveal that nuclear assembly of human pre-60S particles is generally hierarchical with short branch pathways, and a few factors display specific roles as rRNA chaperones by confining rRNA helices locally to facilitate their folding, such as the C-terminal domain of SDAD1.


  • Organizational Affiliation

    State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 6B [auth 6]245Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000242372 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Probable ribosome biogenesis protein RLP24C [auth 7]163Homo sapiensMutation(s): 0 
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PHAROS:  Q9UHA3
GTEx:  ENSG00000137876 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc finger protein 593E [auth 9]134Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142684 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3F [auth B]403Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100316 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29G [auth C]159Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000162244 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4H [auth D]427Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174444 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30I [auth E]115Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000156482 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34J [auth F]117Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000109475 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7aK [auth G]266Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000148303 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35L [auth H]123Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136942 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9M [auth I]192Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163682 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36N [auth K]105Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000130255 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27aO [auth L]148Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000166441 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37P [auth M]97Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145592 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11Q [auth N]178Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142676 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38R [auth O]70Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000172809 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39S [auth P]51Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198918 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13T [auth Q]211Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167526 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14U [auth S]215Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000188846 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15V [auth U]204Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174748 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13aW [auth V]203Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142541 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36aX [auth W]106Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000241343 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37aY [auth X]92Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197756 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18188Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000063177 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19AA [auth a]196Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108298 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aBA [auth b]176Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105640 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21CA [auth c]160Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000122026 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23DA [auth e]140Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125691 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23aEA [auth g]156Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198242 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26FA [auth h]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161970 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27GA [auth i]136Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000131469 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28HA [auth l]137Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108107 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8IA [auth m]257Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161016 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35aJA [auth n]110Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182899 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6KA [auth o]288Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000089009 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7LA [auth p]248Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000147604 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5MA [auth r]297Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000122406 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
G Protein Nucleolar 2NA [auth A]731Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000134697 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Translation machinery-associated protein 16OA [auth R]203Homo sapiensMutation(s): 0 
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Find proteins for Q96EY4 (Homo sapiens)
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GTEx:  ENSG00000198498 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
mRNA turnover protein 4 homologPA [auth J]239Homo sapiensMutation(s): 0 
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Find proteins for Q9UKD2 (Homo sapiens)
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GTEx:  ENSG00000053372 
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UniProt GroupQ9UKD2
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Leydig cell tumor 10 kDa protein homologQA [auth T]99Homo sapiensMutation(s): 0 
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Find proteins for Q9UNZ5 (Homo sapiens)
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GTEx:  ENSG00000104979 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L12SA [auth y]165Homo sapiensMutation(s): 0 
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Find proteins for P30050 (Homo sapiens)
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GTEx:  ENSG00000197958 
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UniProt GroupP30050
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
GTP-binding protein 4TA [auth 4]634Homo sapiensMutation(s): 0 
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Find proteins for Q9BZE4 (Homo sapiens)
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GTEx:  ENSG00000107937 
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UniProt GroupQ9BZE4
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22UA [auth d]128Homo sapiensMutation(s): 0 
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Find proteins for P35268 (Homo sapiens)
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GTEx:  ENSG00000116251 
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UniProt GroupP35268
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31VA [auth j]125Homo sapiensMutation(s): 0 
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Find proteins for P62899 (Homo sapiens)
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GTEx:  ENSG00000071082 
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UniProt GroupP62899
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32WA [auth k]135Homo sapiensMutation(s): 0 
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Find proteins for P62910 (Homo sapiens)
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GTEx:  ENSG00000144713 
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UniProt GroupP62910
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17XA [auth Y]184Homo sapiensMutation(s): 0 
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Find proteins for P18621 (Homo sapiens)
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GTEx:  ENSG00000265681 
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UniProt GroupP18621
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Protein LLP homologYA [auth z]129Homo sapiensMutation(s): 0 
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Find proteins for Q9BRT6 (Homo sapiens)
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GTEx:  ENSG00000139233 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10aZA [auth t]217Homo sapiensMutation(s): 0 
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Find proteins for P62906 (Homo sapiens)
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GTEx:  ENSG00000198755 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Protein SDA1 homologAB [auth u]687Homo sapiensMutation(s): 0 
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Find proteins for Q9NVU7 (Homo sapiens)
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GTEx:  ENSG00000198301 
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UniProt GroupQ9NVU7
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein NSA2 homologBB [auth v]260Homo sapiensMutation(s): 0 
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Find proteins for O95478 (Homo sapiens)
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GTEx:  ENSG00000164346 
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Entity ID: 1
MoleculeChains LengthOrganismImage
5S rRNAA [auth 5]120Homo sapiens
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Entity ID: 4
MoleculeChains LengthOrganismImage
5.8S rRNAD [auth 8]156Homo sapiens
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Entity ID: 44
MoleculeChains LengthOrganismImage
28S rRNARA [auth 2]5,054Homo sapiens
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2_4158:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China32230051;31922036

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-09
    Type: Initial release
  • Version 1.1: 2023-11-15
    Changes: Data collection, Database references