8IR1

human nuclear pre-60S ribosomal particle - State A

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

  • Deposited: 2023-03-17 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: 3.30 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: 1
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L12A [auth y]165Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197958 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
GTP-binding protein 4B [auth 4]634Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000107937 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 6C [auth 6]245Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000242372 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Probable ribosome biogenesis protein RLP24D [auth 7]163Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137876 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3E [auth B]403Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100316 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4F [auth D]427Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174444 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30G [auth E]115Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000156482 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34H [auth F]117Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000109475 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7aI [auth G]266Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000148303 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35J [auth H]123Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136942 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9K [auth I]192Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163682 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36L [auth K]105Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000130255 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27aM [auth L]148Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000166441 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37N [auth M]97Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145592 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39O [auth P]51Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198918 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13P [auth Q]211Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167526 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14Q [auth S]215Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000188846 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15R [auth U]204Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174748 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13aS [auth V]203Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142541 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37aT [auth X]92Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197756 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18U [auth Z]188Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000063177 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19V [auth a]196Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108298 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aW [auth b]176Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105640 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21X [auth c]160Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000122026 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23Y [auth e]140Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125691 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26Z [auth h]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161970 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27AA [auth i]136Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000131469 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28BA [auth l]137Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108107 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8CA [auth m]257Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161016 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35aDA [auth n]110Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182899 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6EA [auth o]288Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000089009 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7FA [auth p]248Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000147604 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Protein LLP homologGA [auth z]129Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000139233 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11HA [auth A]178Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142676 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5IA [auth C]297Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000122406 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein NSA2 homologJA [auth J]260Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000164346 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Notchless protein homolog 1KA [auth N]485Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000073536 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis regulatory protein homologLA [auth R]365Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000179041 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein-like 3MA [auth u]549Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163938 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
mRNA turnover protein 4 homologNA [auth v]239Homo sapiensMutation(s): 0 
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Go to UniProtKB:  Q9UKD2
PHAROS:  Q9UKD2
GTEx:  ENSG00000053372 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
G Protein Nucleolar 2OA [auth w]731Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000134697 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Coiled-coil domain-containing protein 86PA [auth r]360Homo sapiensMutation(s): 0 
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Find proteins for Q9H6F5 (Homo sapiens)
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PHAROS:  Q9H6F5
GTEx:  ENSG00000110104 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23aSA [auth g]156Homo sapiensMutation(s): 0 
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Find proteins for P62750 (Homo sapiens)
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GTEx:  ENSG00000198242 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22TA [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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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31UA [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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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32VA [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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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17WA [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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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38XA [auth O]70Homo sapiensMutation(s): 0 
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Find proteins for P63173 (Homo sapiens)
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GTEx:  ENSG00000172809 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome production factor 2 homologZA [auth T]306Homo sapiensMutation(s): 0 
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Find proteins for Q9H7B2 (Homo sapiens)
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PHAROS:  Q9H7B2
GTEx:  ENSG00000197498 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
pre-rRNA 2'-O-ribose RNA methyltransferase FTSJ3AB [auth 9]847Homo sapiensMutation(s): 0 
EC: 2.1.1
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Find proteins for Q8IY81 (Homo sapiens)
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GTEx:  ENSG00000108592 
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Entity ID: 43
MoleculeChains LengthOrganismImage
28S rRNAQA [auth 2]5,054Homo sapiens
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Entity ID: 44
MoleculeChains LengthOrganismImage
5.8S rRMARA [auth 8]156Homo sapiens
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Entity ID: 51
MoleculeChains LengthOrganismImage
5S RNAYA [auth W]120Homo sapiens
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 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