8JDJ

Structure of the Human cytoplasmic Ribosome with human tRNA Asp(Q34) and mRNA(GAU)

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

  • Deposited: 2023-05-14 Released: 2023-12-06 
  • Deposition Author(s): Ishiguro, K., Yokoyama, T., Shirouzu, M., Suzuki, T.
  • Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan), Japan Society for the Promotion of Science (JSPS), Japan Science and Technology

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Glycosylated queuosines in tRNAs optimize translational rate and post-embryonic growth.

Zhao, X., Ma, D., Ishiguro, K., Saito, H., Akichika, S., Matsuzawa, I., Mito, M., Irie, T., Ishibashi, K., Wakabayashi, K., Sakaguchi, Y., Yokoyama, T., Mishima, Y., Shirouzu, M., Iwasaki, S., Suzuki, T., Suzuki, T.

(2023) Cell 186: 5517

  • DOI: https://doi.org/10.1016/j.cell.2023.10.026
  • Primary Citation of Related Structures:  
    7Y7C, 7Y7D, 7Y7E, 7Y7F, 7Y7G, 7Y7H, 8JDJ, 8JDK, 8JDL, 8JDM

  • PubMed Abstract: 

    Transfer RNA (tRNA) modifications are critical for protein synthesis. Queuosine (Q), a 7-deaza-guanosine derivative, is present in tRNA anticodons. In vertebrate tRNAs for Tyr and Asp, Q is further glycosylated with galactose and mannose to generate galQ and manQ, respectively. However, biogenesis and physiological relevance of Q-glycosylation remain poorly understood. Here, we biochemically identified two RNA glycosylases, QTGAL and QTMAN, and successfully reconstituted Q-glycosylation of tRNAs using nucleotide diphosphate sugars. Ribosome profiling of knockout cells revealed that Q-glycosylation slowed down elongation at cognate codons, UAC and GAC (GAU), respectively. We also found that galactosylation of Q suppresses stop codon readthrough. Moreover, protein aggregates increased in cells lacking Q-glycosylation, indicating that Q-glycosylation contributes to proteostasis. Cryo-EM of human ribosome-tRNA complex revealed the molecular basis of codon recognition regulated by Q-glycosylations. Furthermore, zebrafish qtgal and qtman knockout lines displayed shortened body length, implying that Q-glycosylation is required for post-embryonic growth in vertebrates.

    • Organizational Affiliation: 

    Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan.


Macromolecules

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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8257Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161016 
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UniProt GroupP62917
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3403Homo sapiensMutation(s): 0 
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PHAROS:  P39023
GTEx:  ENSG00000100316 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4427Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174444 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5297Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000122406 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6288Homo sapiensMutation(s): 0 
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PHAROS:  Q02878
GTEx:  ENSG00000089009 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7248Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000147604 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7a266Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000148303 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9192Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163682 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10-like214Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000165496 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11178Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142676 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13211Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167526 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14215Homo sapiensMutation(s): 0 
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PHAROS:  P50914
GTEx:  ENSG00000188846 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15204Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174748 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13a203Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142541 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17184Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000265681 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18188Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000063177 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19196Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108298 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18a176Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105640 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21160Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000122026 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000116251 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23AA [auth a]140Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125691 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L24BA [auth b]157Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000114391 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23aCA [auth c]156Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198242 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26DA [auth d]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161970 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27EA [auth e]136Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000131469 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27aFA [auth f]148Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000166441 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29GA [auth g]159Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000162244 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30HA [auth h]115Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000156482 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31IA [auth i]125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000071082 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32JA [auth j]135Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000144713 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35aKA [auth k]110Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182899 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34LA [auth l]117Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000109475 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35MA [auth m]123Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136942 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36NA [auth n]105Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000130255 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37OA [auth o]97Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145592 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38PA [auth p]70Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000172809 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39QA [auth q]51Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198918 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-60S ribosomal protein L40RA [auth r]128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000221983 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41SA [auth s]25Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000229117 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36aTA [auth t]106Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000241343 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37aUA [auth u]92Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197756 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28VA [auth v]137Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108107 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein SAXA [auth x]295Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000168028 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aYA [auth y]264Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145425 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2ZA [auth z]293Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000140988 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3AB [auth 0]243Homo sapiensMutation(s): 0 
EC: 4.2.99.18
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GTEx:  ENSG00000149273 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4, X isoformBB [auth 1]263Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198034 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5CB [auth 2]204Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000083845 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6DB [auth 3]249Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137154 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7EB [auth 4]194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171863 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8FB [auth 5]208Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142937 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9GB [auth 6]194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000170889 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S10HB [auth 7]165Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000124614 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11IB [auth 8]158Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142534 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13JB [auth 9]151Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000110700 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14KB [auth AA]151Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000164587 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15LB [auth AB]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115268 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16MB [auth AC]146Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105193 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17NB [auth AD]135Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182774 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18OB [auth AE]152Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000231500 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19PB [auth AF]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105372 
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S20QB [auth AG]119Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000008988 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21RB [auth AH]83Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171858 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15aSB [auth AI]130Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000134419 
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23TB [auth AJ]143Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000186468 
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24UB [auth AK]133Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000138326 
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25VB [auth AL]125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000118181 
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26WB [auth AM]115Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197728 
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27XB [auth AN]84Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000177954 
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28YB [auth AO]69Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000233927 
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29ZB [auth AP]56Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000213741 
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30AC [auth AQ]59Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000149806 
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor of activated protein C kinase 1BC [auth AR]317Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204628 
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Entity ID: 1
MoleculeChains LengthOrganismImage
mRNA14Homo sapiens
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Entity ID: 2
MoleculeChains LengthOrganismImage
tRNA(Asp)
B, C
75Homo sapiens
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Entity ID: 3
MoleculeChains LengthOrganismImage
28S ribosomal RNA5,070Homo sapiens
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Entity ID: 4
MoleculeChains LengthOrganismImage
5S ribosomal RNA120Homo sapiens
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Entity ID: 5
MoleculeChains LengthOrganismImage
5.8S ribosomal RNA156Homo sapiens
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Entity ID: 48
MoleculeChains LengthOrganismImage
18S ribosomal RNAWA [auth w]1,869Homo sapiens
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
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AX [auth AP]
TS [auth o]
US [auth r]
VS [auth t]
XS [auth u]
AX [auth AP],
TS [auth o],
US [auth r],
VS [auth t],
XS [auth u],
ZW [auth AM]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
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AD [auth D]
AE [auth D]
AF [auth D]
AG [auth D]
AH [auth D]
AD [auth D],
AE [auth D],
AF [auth D],
AG [auth D],
AH [auth D],
AI [auth D],
AJ [auth D],
AK [auth D],
AL [auth D],
AM [auth D],
AN [auth D],
AO [auth D],
AP [auth D],
AQ [auth D],
AR [auth D],
AS [auth F],
AT [auth w],
AU [auth w],
AV [auth w],
AW [auth w],
BD [auth D],
BE [auth D],
BF [auth D],
BG [auth D],
BH [auth D],
BI [auth D],
BJ [auth D],
BK [auth D],
BL [auth D],
BM [auth D],
BN [auth D],
BO [auth D],
BP [auth D],
BQ [auth D],
BR [auth D],
BS [auth G],
BT [auth w],
BU [auth w],
BV [auth w],
BW [auth w],
CC [auth A],
CD [auth D],
CE [auth D],
CF [auth D],
CG [auth D],
CH [auth D],
CI [auth D],
CJ [auth D],
CK [auth D],
CL [auth D],
CM [auth D],
CN [auth D],
CO [auth D],
CP [auth D],
CQ [auth D],
CR [auth D],
CS [auth G],
CT [auth w],
CU [auth w],
CV [auth w],
CW [auth w],
DC [auth D],
DD [auth D],
DE [auth D],
DF [auth D],
DG [auth D],
DH [auth D],
DI [auth D],
DJ [auth D],
DK [auth D],
DL [auth D],
DM [auth D],
DN [auth D],
DO [auth D],
DP [auth D],
DQ [auth D],
DR [auth D],
DS [auth H],
DT [auth w],
DU [auth w],
DV [auth w],
DW [auth w],
EC [auth D],
ED [auth D],
EE [auth D],
EF [auth D],
EG [auth D],
EH [auth D],
EI [auth D],
EJ [auth D],
EK [auth D],
EL [auth D],
EM [auth D],
EN [auth D],
EO [auth D],
EP [auth D],
EQ [auth D],
ER [auth D],
ES [auth I],
ET [auth w],
EU [auth w],
EV [auth w],
EW [auth w],
FC [auth D],
FD [auth D],
FE [auth D],
FF [auth D],
FG [auth D],
FH [auth D],
FI [auth D],
FJ [auth D],
FK [auth D],
FL [auth D],
FM [auth D],
FN [auth D],
FO [auth D],
FP [auth D],
FQ [auth D],
FR [auth D],
FS [auth N],
FT [auth w],
FU [auth w],
FV [auth w],
FW [auth w],
GC [auth D],
GD [auth D],
GE [auth D],
GF [auth D],
GG [auth D],
GH [auth D],
GI [auth D],
GJ [auth D],
GK [auth D],
GL [auth D],
GM [auth D],
GN [auth D],
GO [auth D],
GP [auth D],
GQ [auth D],
GR [auth D],
GS [auth O],
GT [auth w],
GU [auth w],
GV [auth w],
GW [auth w],
HC [auth D],
HD [auth D],
HE [auth D],
HF [auth D],
HG [auth D],
HH [auth D],
HI [auth D],
HJ [auth D],
HK [auth D],
HL [auth D],
HM [auth D],
HN [auth D],
HO [auth D],
HP [auth D],
HQ [auth D],
HR [auth D],
HS [auth O],
HT [auth w],
HU [auth w],
HV [auth w],
HW [auth w],
IC [auth D],
ID [auth D],
IE [auth D],
IF [auth D],
IG [auth D],
IH [auth D],
II [auth D],
IJ [auth D],
IK [auth D],
IL [auth D],
IM [auth D],
IN [auth D],
IO [auth D],
IP [auth D],
IQ [auth D],
IR [auth D],
IS [auth S],
IT [auth w],
IU [auth w],
IV [auth w],
IW [auth w],
JC [auth D],
JD [auth D],
JE [auth D],
JF [auth D],
JG [auth D],
JH [auth D],
JI [auth D],
JJ [auth D],
JK [auth D],
JL [auth D],
JM [auth D],
JN [auth D],
JO [auth D],
JP [auth D],
JQ [auth D],
JR [auth D],
JS [auth U],
JT [auth w],
JU [auth w],
JV [auth w],
JW [auth w],
KC [auth D],
KD [auth D],
KE [auth D],
KF [auth D],
KG [auth D],
KH [auth D],
KI [auth D],
KJ [auth D],
KK [auth D],
KL [auth D],
KM [auth D],
KN [auth D],
KO [auth D],
KP [auth D],
KQ [auth D],
KR [auth D],
KS [auth U],
KT [auth w],
KU [auth w],
KV [auth w],
KW [auth w],
LC [auth D],
LD [auth D],
LE [auth D],
LF [auth D],
LG [auth D],
LH [auth D],
LI [auth D],
LJ [auth D],
LK [auth D],
LL [auth D],
LM [auth D],
LN [auth D],
LO [auth D],
LP [auth D],
LQ [auth D],
LR [auth E],
LS [auth V],
LT [auth w],
LU [auth w],
LV [auth w],
LW [auth w],
MC [auth D],
MD [auth D],
ME [auth D],
MF [auth D],
MG [auth D],
MH [auth D],
MI [auth D],
MJ [auth D],
MK [auth D],
ML [auth D],
MM [auth D],
MN [auth D],
MO [auth D],
MP [auth D],
MQ [auth D],
MR [auth E],
MS [auth V],
MT [auth w],
MU [auth w],
MV [auth w],
MW [auth w],
NC [auth D],
ND [auth D],
NE [auth D],
NF [auth D],
NG [auth D],
NH [auth D],
NI [auth D],
NJ [auth D],
NK [auth D],
NL [auth D],
NM [auth D],
NN [auth D],
NO [auth D],
NP [auth D],
NQ [auth D],
NR [auth E],
NS [auth X],
NT [auth w],
NU [auth w],
NV [auth w],
NW [auth w],
OC [auth D],
OD [auth D],
OE [auth D],
OF [auth D],
OG [auth D],
OH [auth D],
OI [auth D],
OJ [auth D],
OK [auth D],
OL [auth D],
OM [auth D],
ON [auth D],
OO [auth D],
OP [auth D],
OQ [auth D],
OR [auth E],
OS [auth a],
OT [auth w],
OU [auth w],
OV [auth w],
OW [auth w],
PC [auth D],
PD [auth D],
PE [auth D],
PF [auth D],
PG [auth D],
PH [auth D],
PI [auth D],
PJ [auth D],
PK [auth D],
PL [auth D],
PM [auth D],
PN [auth D],
PO [auth D],
PP [auth D],
PQ [auth D],
PR [auth E],
PS [auth g],
PT [auth w],
PU [auth w],
PV [auth w],
PW [auth w],
QC [auth D],
QD [auth D],
QE [auth D],
QF [auth D],
QG [auth D],
QH [auth D],
QI [auth D],
QJ [auth D],
QK [auth D],
QL [auth D],
QM [auth D],
QN [auth D],
QO [auth D],
QP [auth D],
QQ [auth D],
QR [auth E],
QS [auth j],
QT [auth w],
QU [auth w],
QV [auth w],
QW [auth w],
RC [auth D],
RD [auth D],
RE [auth D],
RF [auth D],
RG [auth D],
RH [auth D],
RI [auth D],
RJ [auth D],
RK [auth D],
RL [auth D],
RM [auth D],
RN [auth D],
RO [auth D],
RP [auth D],
RQ [auth D],
RR [auth E],
RS [auth k],
RT [auth w],
RU [auth w],
RV [auth w],
RW [auth w],
SC [auth D],
SD [auth D],
SE [auth D],
SF [auth D],
SG [auth D],
SH [auth D],
SI [auth D],
SJ [auth D],
SK [auth D],
SL [auth D],
SM [auth D],
SN [auth D],
SO [auth D],
SP [auth D],
SQ [auth D],
SR [auth E],
SS [auth l],
ST [auth w],
SU [auth w],
SV [auth w],
SW [auth w],
TC [auth D],
TD [auth D],
TE [auth D],
TF [auth D],
TG [auth D],
TH [auth D],
TI [auth D],
TJ [auth D],
TK [auth D],
TL [auth D],
TM [auth D],
TN [auth D],
TO [auth D],
TP [auth D],
TQ [auth D],
TR [auth E],
TT [auth w],
TU [auth w],
TV [auth w],
TW [auth w],
UC [auth D],
UD [auth D],
UE [auth D],
UF [auth D],
UG [auth D],
UH [auth D],
UI [auth D],
UJ [auth D],
UK [auth D],
UL [auth D],
UM [auth D],
UN [auth D],
UO [auth D],
UP [auth D],
UQ [auth D],
UR [auth E],
UT [auth w],
UU [auth w],
UV [auth w],
UW [auth w],
VC [auth D],
VD [auth D],
VE [auth D],
VF [auth D],
VG [auth D],
VH [auth D],
VI [auth D],
VJ [auth D],
VK [auth D],
VL [auth D],
VM [auth D],
VN [auth D],
VO [auth D],
VP [auth D],
VQ [auth D],
VR [auth F],
VT [auth w],
VU [auth w],
VV [auth w],
VW [auth w],
WC [auth D],
WD [auth D],
WE [auth D],
WF [auth D],
WG [auth D],
WH [auth D],
WI [auth D],
WJ [auth D],
WK [auth D],
WL [auth D],
WM [auth D],
WN [auth D],
WO [auth D],
WP [auth D],
WQ [auth D],
WR [auth F],
WS [auth u],
WT [auth w],
WU [auth w],
WV [auth w],
WW [auth w],
XC [auth D],
XD [auth D],
XE [auth D],
XF [auth D],
XG [auth D],
XH [auth D],
XI [auth D],
XJ [auth D],
XK [auth D],
XL [auth D],
XM [auth D],
XN [auth D],
XO [auth D],
XP [auth D],
XQ [auth D],
XR [auth F],
XT [auth w],
XU [auth w],
XV [auth w],
XW [auth AA],
YC [auth D],
YD [auth D],
YE [auth D],
YF [auth D],
YG [auth D],
YH [auth D],
YI [auth D],
YJ [auth D],
YK [auth D],
YL [auth D],
YM [auth D],
YN [auth D],
YO [auth D],
YP [auth D],
YQ [auth D],
YR [auth F],
YS [auth w],
YT [auth w],
YU [auth w],
YV [auth w],
YW [auth AF],
ZC [auth D],
ZD [auth D],
ZE [auth D],
ZF [auth D],
ZG [auth D],
ZH [auth D],
ZI [auth D],
ZJ [auth D],
ZK [auth D],
ZL [auth D],
ZM [auth D],
ZN [auth D],
ZO [auth D],
ZP [auth D],
ZQ [auth D],
ZR [auth F],
ZS [auth w],
ZT [auth w],
ZU [auth w],
ZV [auth w]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18
MODEL REFINEMENTCoot0.9.5
RECONSTRUCTIONRELION3.1.3

Structure Validation

View Full Validation Report



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

Deposition Data

Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan--
Japan Society for the Promotion of Science (JSPS)Japan26113003, 26220205 and 18H05272
Japan Science and TechnologyJapanJPMJER2002

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-06
    Type: Initial release
  • Version 1.1: 2023-12-27
    Changes: Database references