7QGG | pdb_00007qgg

Neuronal RNA granules are ribosome complexes stalled at the pre-translocation state

  • Classification: RIBOSOME
  • Organism(s): Rattus norvegicus
  • Mutation(s): No 

  • Deposited: 2021-12-08 Released: 2022-10-26 
  • Deposition Author(s): Pulk, A., Kipper, K., Mansour, A.
  • Funding Organization(s): European Molecular Biology Organization (EMBO), Estonian Research Council

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.86 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Neuronal RNA granules are ribosome complexes stalled at the pre-translocation state.

Kipper, K., Mansour, A., Pulk, A.

(2022) J Mol Biology 434: 167801-167801

  • DOI: https://doi.org/10.1016/j.jmb.2022.167801
  • Primary Citation of Related Structures:  
    7QGG

  • PubMed Abstract: 

    The polarized cell morphology of neurons dictates many neuronal processes, including the axodendridic transport of specific mRNAs and subsequent translation. mRNAs together with ribosomes and RNA-binding proteins form RNA granules that are targeted to axodendrites for localized translation in neurons. It has been established that localized protein synthesis in neurons is essential for long-term memory formation, synaptic plasticity, and neurodegeneration. We have used proteomics and electron microscopy to characterize neuronal RNA granules (nRNAg) isolated from rat brain tissues or human neuroblastoma. We show that ribosome-containing RNA granules are morula-like structures when visualized by electron microscopy. Crosslinking-coupled mass-spectrometry identified a potential G3BP2 binding site on the ribosome near the eIF3d-binding site on the 40S ribosomal subunit. We used cryo-EM to resolve the structure of the ribosome-component of nRNAg. The cryo-EM reveals that predominant particles in nRNAg are 80S ribosomes, resembling the pre-translocation state where tRNA's are in the hybrid A/P and P/E site. We also describe a new kind of principal motion of the ribosome, which we call the rocking motion.

    • Organizational Affiliation: 

    Structural Biology Unit, Institute of Technology, University of Tartu, Tartu 50411, Estonia.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein SAB [auth SA]295Rattus norvegicusMutation(s): 0 
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Find proteins for P38983 (Rattus norvegicus)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aC [auth SB]264Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for P49242 (Rattus norvegicus)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3D [auth SD]243Rattus norvegicusMutation(s): 0 
EC: 4.2.99.18
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Find proteins for P62909 (Rattus norvegicus)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4, X isoformE [auth SE]263Rattus norvegicusMutation(s): 0 
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Find proteins for P62703 (Rattus norvegicus)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5F [auth SF]204Rattus norvegicusMutation(s): 0 
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Find proteins for B0BN81 (Rattus norvegicus)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7G [auth SH]194Rattus norvegicusMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8H [auth SI]208Rattus norvegicusMutation(s): 0 
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Find proteins for P62243 (Rattus norvegicus)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S10I [auth SK]165Rattus norvegicusMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11J [auth SL]158Rattus norvegicusMutation(s): 0 
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Find proteins for A0A8B8VW69 (Balaenoptera musculus)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15K [auth SP]145Rattus norvegicusMutation(s): 0 
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Find proteins for A0A2K6QL61 (Rhinopithecus roxellana)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Rps16 proteinL [auth SQ]146Rattus norvegicusMutation(s): 0 
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Find proteins for Q5XFV9 (Rattus norvegicus)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17M [auth SR]135Rattus norvegicusMutation(s): 0 
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Find proteins for P04644 (Rattus norvegicus)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18N [auth SS]152Rattus norvegicusMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19O [auth ST]145Rattus norvegicusMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S20P [auth SU]119Rattus norvegicusMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21Q [auth SV]83Rattus norvegicusMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23R [auth SX]143Rattus norvegicusMutation(s): 0 
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Find proteins for A0A340WVW7 (Lipotes vexillifer)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26S [auth Sa]115Rattus norvegicusMutation(s): 0 
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Find proteins for A0A2K5LQY6 (Cercocebus atys)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28T [auth Sc]69Rattus norvegicusMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29U [auth Sd]56Rattus norvegicusMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor of activated protein C kinase 1V [auth Sg]317Rattus norvegicusMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2W [auth SC]293Rattus norvegicusMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6X [auth SG]249Rattus norvegicusMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9Y [auth SJ]194Rattus norvegicusMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12Z [auth SM]132Rattus norvegicusMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13AA [auth SN]151Rattus norvegicusMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14BA [auth SO]151Rattus norvegicusMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15aCA [auth SW]130Rattus norvegicusMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24DA [auth SY]133Rattus norvegicusMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25EA [auth SZ]125Rattus norvegicusMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27FA [auth Sb]84Rattus norvegicusMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-like domain-containing proteinGA [auth Se]59Rattus norvegicusMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S27aHA [auth Sf]156Rattus norvegicusMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8IA [auth A]257Rattus norvegicusMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3JA [auth B]403Rattus norvegicusMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4KA [auth C]421Rattus norvegicusMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5NA [auth F]297Rattus norvegicusMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6OA [auth G]298Rattus norvegicusMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7PA [auth H]260Rattus norvegicusMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7aQA [auth I]266Rattus norvegicusMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9RA [auth J]192Rattus norvegicusMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10SA [auth K]214Rattus norvegicusMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11TA [auth L]178Rattus norvegicusMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13UA [auth M]211Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for P41123 (Rattus norvegicus)
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14VA [auth N]214Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for Q63507 (Rattus norvegicus)
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L15WA [auth O]204Rattus norvegicusMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13aXA [auth P]203Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for Q5RK10 (Rattus norvegicus)
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17YA [auth Q]184Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for A0A8J4KQ25 (Eudyptes chrysocome)
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18ZA [auth R]188Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for P12001 (Rattus norvegicus)
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L19AB [auth S]196Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for A0A2J8KH59 (Pan troglodytes)
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aBB [auth T]176Rattus norvegicusMutation(s): 0 
UniProt
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21CB [auth U]160Rattus norvegicusMutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22DB [auth V]128Rattus norvegicusMutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23EB [auth W]140Rattus norvegicusMutation(s): 0 
UniProt
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L24FB [auth X]157Rattus norvegicusMutation(s): 0 
UniProt
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23aGB [auth Y]156Rattus norvegicusMutation(s): 0 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26HB [auth Z]145Rattus norvegicusMutation(s): 0 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27IB [auth a]136Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for A0A851LWS6 (Corythaeola cristata)
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27aJB [auth b]148Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for P18445 (Rattus norvegicus)
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29KB [auth c]156Rattus norvegicusMutation(s): 0 
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Find proteins for P25886 (Rattus norvegicus)
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30LB [auth d]115Rattus norvegicusMutation(s): 0 
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Find proteins for P62890 (Rattus norvegicus)
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31MB [auth e]125Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for G7NZE1 (Macaca fascicularis)
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32NB [auth f]135Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for P62912 (Rattus norvegicus)
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35aOB [auth g]110Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for P04646 (Rattus norvegicus)
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34PB [auth h]117Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for A6HVR9 (Rattus norvegicus)
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35QB [auth i]123Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for P17078 (Rattus norvegicus)
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36RB [auth j]105Rattus norvegicusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y3U8 (Homo sapiens)
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PHAROS:  Q9Y3U8
GTEx:  ENSG00000130255 
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L37SB [auth k]97Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for A0A2Y9RW09 (Trichechus manatus latirostris)
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38TB [auth l]70Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for A0A1A7W9T9 (Iconisemion striatum)
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39UB [auth m]51Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for A0A7N4PFJ2 (Sarcophilus harrisii)
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-60S ribosomal protein L40VB [auth n]128Rattus norvegicusMutation(s): 0 
UniProt
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41WB [auth o]25Rattus norvegicusMutation(s): 0 
UniProt
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L36aXB [auth p]106Rattus norvegicusMutation(s): 0 
UniProt
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37aYB [auth q]92Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for A0A6J2LF66 (Phyllostomus discolor)
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28ZB [auth r]137Rattus norvegicusMutation(s): 0 
UniProt
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Entity ID: 83
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10aEC [auth Cz]217Rattus norvegicusMutation(s): 0 
UniProt
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Entity ID: 84
MoleculeChains Sequence LengthOrganismDetailsImage
ALA-ALA-LYS-ALAFC [auth y]4Rattus norvegicusMutation(s): 0 
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
DD [auth k]
ED [auth p]
FD [auth q]
HC [auth S2]
KC [auth Sa]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
AD [auth E]
BD [auth E]
CD [auth Z]
GC [auth S2]
GD [auth t]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.86 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
MODEL REFINEMENTCoot
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Molecular Biology Organization (EMBO)EstoniaIG 3911
Estonian Research CouncilEstoniaPSG87
Estonian Research CouncilEstoniaMOBTP44

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-26
    Type: Initial release
  • Version 1.1: 2023-05-10
    Changes: Database references, Refinement description
  • Version 1.2: 2024-04-24
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Data collection, Structure summary