8QIE | pdb_00008qie

CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME : LM32Cs1C1 mutant snoRNA overexpression, class 4


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.43 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.1 of the entry. See complete history

Literature

A small nucleolar RNA dictates the structure and function of translating ribosomes in Leishmania.

Rajan, K.S.Aryal, S.Murugeshan, S.Zhu, Y.Bashan, A.Olami, M.Madmoni, H.Nobe, Y.Doniger, T.Cohen-Chalamish, S.Prina, E.Pescher, P.Beneke, T.Taoka, M.Holley, C.L.Unger, R.Spath, G.F.Yonath, A.Michaeli, S.

(2026) Nat Commun 

  • DOI: https://doi.org/10.1038/s41467-026-75486-8
  • Primary Citation Related Structures: 
    8QHU, 8QIE, 9FXO

  • PubMed Abstract: 

    The most common rRNA modification is 2'-O-methylation. Here, we determine the landscape of 2'-O-methylation in Leishmania, a parasite that cycles between two different hosts, insect and mammalian. We find two 2'-O-methylated positions that are differentially modified during the parasite's two life stages. The deposition of these modifications is guided by snoRNAs. When we perform cytosine base-editing of the snoRNA responsible for guiding one of the two stage-regulated modifications, Am479, we fail to detect ribosomes lacking this modification, suggesting that it is essential. To better understand the role of the snoRNA and its guided modification, we determine the cryo-EM structures of ribosomes from cells overexpressing the guiding snoRNA and compare them to ribosomes from the parental strain. We do not find structural changes around Am479 or in the small subunit rRNA, but observe a difference in H68 of the large subunit rRNA due to a second base-pairing interaction, suggesting a potential chaperone activity for the snoRNA. Based on these results, translatome and tRNA analysis, we propose a mechanism whereby changes in ribosome structure affect the release of specific tRNAs, which correlate with changes in translation of only a subset of mRNAs.


  • Organizational Affiliation
    • Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel. rajanks@iisc.ac.in.

Macromolecule Content 

  • Total Structure Weight: 3,564.83 kDa 
  • Atom Count: 206,527 
  • Modeled Residue Count: 16,717 
  • Deposited Residue Count: 19,416 
  • Unique protein chains: 76
  • Unique nucleic acid chains: 10

Macromolecules


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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L2I [auth A]260Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4FWX5 (Leishmania major)
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative ribosomal protein L3J [auth B]419Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q2Q6 (Leishmania major)
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative ribosomal protein L1aK [auth C]373Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for E9ADW5 (Leishmania major)
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L11L [auth D]188Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for P48157 (Leishmania major)
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L9M [auth E]190Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4QC91 (Leishmania major)
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L6N [auth F]195Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q4D3 (Leishmania major)
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L7aO [auth G]264Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4QIP1 (Leishmania major)
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L13aP [auth H]222Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4QFG2 (Leishmania major)
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L13Q [auth I]220Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L23R [auth J]139Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein L14S [auth K]175Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L27A/L29T [auth L]145Leishmania major strain FriedlinMutation(s): 0 
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Find proteins for E9AFK0 (Leishmania major)
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribosomal protein L15U [auth M]204Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L10V [auth N]213Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for O97213 (Leishmania major)
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L5W [auth O]305Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for E9AF10 (Leishmania major)
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L18X [auth P]198Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4QG98 (Leishmania major)
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L19Y [auth Q]254Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4QJ37 (Leishmania major)
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aZ [auth R]179Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q5J4 (Leishmania major)
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L21AA [auth S]159Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aDA [auth SA]264Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein SAEA [auth SB]246Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q0Q0 (Leishmania major)
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Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S3FA [auth SC]219Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S9GA [auth SD]190Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S4HA [auth SE]273Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4QG31 (Leishmania major)
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Entity ID: 35
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S2IA [auth SF]265Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S6JA [auth SG]249Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q9NE83 (Leishmania major)
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Entity ID: 37
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S5KA [auth SH]190Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q868B1 (Leishmania major)
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Entity ID: 38
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S7LA [auth SI]200Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for E9AC32 (Leishmania major)
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Entity ID: 39
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S15AMA [auth SJ]130Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 40
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S8NA [auth SK]220Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 41
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S16OA [auth SL]149Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative ribosomal protein S20PA [auth SM]116Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S10QA [auth SN]168Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S14RA [auth SO]144Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S23SA [auth SP]143Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 46
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S12TA [auth SQ]141Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 47
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S18UA [auth SR]153Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 48
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative ribosomal protein S29VA [auth SS]57Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 49
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S13WA [auth ST]151Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S11XA [auth SU]173Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 51
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S17YA [auth SV]143Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 52
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S15ZA [auth SW]152Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 53
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S19-like proteinAB [auth SX]161Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 54
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S21BB [auth SY]164Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 55
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S24CB [auth SZ]137Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 56
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S25DB [auth Sa]120Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 57
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S26EB [auth Sb]112Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 58
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S27-1FB [auth Sc]86Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 59
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S33GB [auth Sd]87Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 60
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S30HB [auth Se]66Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 61
MoleculeChains  Sequence LengthOrganismDetailsImage
Ubiquitin-60S ribosomal protein L40IB [auth Sf]152Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 62
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein subunit beta-like proteinJB [auth Sg]312Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 63
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative RNA binding proteinKB [auth Sh]235Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 64
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L17LB [auth T]166Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 65
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L22MB [auth U]129Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 66
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L23aNB [auth V]145Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 67
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L26OB [auth W]143Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 68
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative ribosomal protein L24PB [auth X]124Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 69
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L27QB [auth Y]134Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 70
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L28RB [auth Z]147Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 71
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L35SB [auth a]127Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 72
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L29TB [auth b]70Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 73
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L7UB [auth c]252Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 74
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L30VB [auth d]104Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 75
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative 60S ribosomal subunit protein L31WB [auth e]188Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 76
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L32XB [auth f]133Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 77
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative ribosomal protein l35aYB [auth g]144Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 78
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L34ZB [auth h]168Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 79
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative 60S Ribosomal protein L36AC [auth i]105Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 80
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribosomal protein L37BC [auth j]83Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 81
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative ribosomal protein L38CC [auth k]83Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 82
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L39DC [auth l]51Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 83
MoleculeChains  Sequence LengthOrganismDetailsImage
Ubiquitin-60S ribosomal protein L40EC [auth m]128Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for P69201 (Leishmania major)
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Entity ID: 84
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L41FC [auth n]34Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 85
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L37aGC [auth o]92Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 86
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L44HC [auth p]106Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
LSUa_rRNA_chain_1A [auth 1]1,782Leishmania major strain Friedlin
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Entity ID: 2
MoleculeChains LengthOrganismImage
LSUb_rRNA_chain_2B [auth 2]1,526Leishmania major strain Friedlin
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Entity ID: 3
MoleculeChains LengthOrganismImage
SR1_chain_3C [auth 3]216Leishmania major strain Friedlin
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Entity ID: 4
MoleculeChains LengthOrganismImage
SR2_chain_4D [auth 4]184Leishmania major strain Friedlin
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Entity ID: 5
MoleculeChains LengthOrganismImage
SR4_chain_5E [auth 5]135Leishmania major strain Friedlin
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Entity ID: 6
MoleculeChains LengthOrganismImage
SR6_chain_6F [auth 6]73Leishmania major strain Friedlin
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Entity ID: 7
MoleculeChains LengthOrganismImage
5.8S_rRNA_chain_7G [auth 7]171Leishmania major strain Friedlin
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Entity ID: 8
MoleculeChains LengthOrganismImage
5S_rRNA_chain_8H [auth 8]123Leishmania major strain Friedlin
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Entity ID: 28
MoleculeChains LengthOrganismImage
SSU_rRNA_chain_S1BA [auth S1]2,204Leishmania major strain Friedlin
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Entity ID: 29
MoleculeChains LengthOrganismImage
E-site_tRNA_chain_S4CA [auth S4]76Leishmania major strain Friedlin
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN

Query on ZN



Download:Ideal Coordinates CCD File
RM [auth p]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K

Query on K



Download:Ideal Coordinates CCD File
BM [auth S1]
CM [auth S1]
HF [auth 1]
LG [auth 2]
LM [auth S1]
BM [auth S1],
CM [auth S1],
HF [auth 1],
LG [auth 2],
LM [auth S1],
SE [auth 1],
TE [auth 1],
UE [auth 1],
VE [auth 1],
WE [auth 1],
WH [auth 2],
XE [auth 1],
XH [auth 2],
YE [auth 1],
ZE [auth 1],
ZK [auth S1]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
AE [auth 1]
AH [auth 2]
AI [auth 2]
AJ [auth S1]
AK [auth S1]
AE [auth 1],
AH [auth 2],
AI [auth 2],
AJ [auth S1],
AK [auth S1],
AL [auth S1],
BE [auth 1],
BF [auth 1],
BH [auth 2],
BI [auth 2],
BJ [auth S1],
BK [auth S1],
BL [auth S1],
CE [auth 1],
CF [auth 1],
CH [auth 2],
CI [auth 2],
CJ [auth S1],
CK [auth S1],
CL [auth S1],
DE [auth 1],
DF [auth 1],
DH [auth 2],
DI [auth 2],
DJ [auth S1],
DK [auth S1],
DL [auth S1],
EE [auth 1],
EF [auth 1],
EG [auth 2],
EH [auth 2],
EI [auth 2],
EJ [auth S1],
EK [auth S1],
EL [auth S1],
EM [auth S1],
FE [auth 1],
FF [auth 1],
FG [auth 2],
FH [auth 2],
FI [auth 2],
FJ [auth S1],
FK [auth S1],
FL [auth S1],
FM [auth S1],
GD [auth 1],
GE [auth 1],
GF [auth 1],
GG [auth 2],
GH [auth 2],
GI [auth 2],
GJ [auth S1],
GK [auth S1],
GL [auth S1],
GM [auth S1],
HD [auth 1],
HE [auth 1],
HG [auth 2],
HH [auth 2],
HI [auth 2],
HJ [auth S1],
HK [auth S1],
HL [auth S1],
HM [auth S1],
IC [auth 1],
ID [auth 1],
IE [auth 1],
IF [auth 2],
IG [auth 2],
IH [auth 2],
II [auth 2],
IJ [auth S1],
IK [auth S1],
IL [auth S1],
IM [auth S1],
JC [auth 1],
JD [auth 1],
JE [auth 1],
JF [auth 2],
JG [auth 2],
JH [auth 2],
JI [auth 4],
JJ [auth S1],
JK [auth S1],
JL [auth S1],
JM [auth S1],
KC [auth 1],
KD [auth 1],
KE [auth 1],
KF [auth 2],
KG [auth 2],
KH [auth 2],
KI [auth 4],
KK [auth S1],
KL [auth S1],
KM [auth S1],
LC [auth 1],
LD [auth 1],
LE [auth 1],
LF [auth 2],
LH [auth 2],
LK [auth S1],
LL [auth S1],
MC [auth 1],
MD [auth 1],
ME [auth 1],
MF [auth 2],
MG [auth 2],
MH [auth 2],
MK [auth S1],
ML [auth S1],
MM [auth S1],
NC [auth 1],
ND [auth 1],
NE [auth 1],
NF [auth 2],
NG [auth 2],
NH [auth 2],
NI [auth 4],
NK [auth S1],
NL [auth S1],
NM [auth S1],
OC [auth 1],
OD [auth 1],
OE [auth 1],
OF [auth 2],
OG [auth 2],
OH [auth 2],
OK [auth S1],
OL [auth S1],
PC [auth 1],
PD [auth 1],
PF [auth 2],
PG [auth 2],
PH [auth 2],
PI [auth 5],
PK [auth S1],
PL [auth S1],
PM [auth SX],
QC [auth 1],
QD [auth 1],
QF [auth 2],
QG [auth 2],
QH [auth 2],
QI [auth 5],
QK [auth S1],
QL [auth S1],
QM [auth Sb],
RC [auth 1],
RD [auth 1],
RF [auth 2],
RG [auth 2],
RH [auth 2],
RI [auth 5],
RJ [auth S1],
RK [auth S1],
RL [auth S1],
SC [auth 1],
SD [auth 1],
SF [auth 2],
SG [auth 2],
SH [auth 2],
SI [auth 6],
SJ [auth S1],
SK [auth S1],
SL [auth S1],
TC [auth 1],
TD [auth 1],
TF [auth 2],
TG [auth 2],
TI [auth 7],
TJ [auth S1],
TK [auth S1],
TL [auth S1],
UC [auth 1],
UD [auth 1],
UF [auth 2],
UG [auth 2],
UI [auth 7],
UJ [auth S1],
UK [auth S1],
UL [auth S1],
VC [auth 1],
VD [auth 1],
VF [auth 2],
VG [auth 2],
VI [auth 8],
VJ [auth S1],
VK [auth S1],
VL [auth S1],
WC [auth 1],
WD [auth 1],
WF [auth 2],
WG [auth 2],
WI [auth A],
WJ [auth S1],
WK [auth S1],
WL [auth S1],
XC [auth 1],
XD [auth 1],
XF [auth 2],
XG [auth 2],
XI [auth A],
XJ [auth S1],
XK [auth S1],
XL [auth S1],
YC [auth 1],
YD [auth 1],
YG [auth 2],
YI [auth J],
YJ [auth S1],
YK [auth S1],
YL [auth S1],
ZD [auth 1],
ZG [auth 2],
ZH [auth 2],
ZI [auth S],
ZJ [auth S1],
ZL [auth S1]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
AD [auth 1]
AF [auth 1]
AG [auth 2]
AM [auth S1]
BD [auth 1]
AD [auth 1],
AF [auth 1],
AG [auth 2],
AM [auth S1],
BD [auth 1],
BG [auth 2],
CD [auth 1],
CG [auth 2],
DD [auth 1],
DG [auth 2],
DM [auth S1],
ED [auth 1],
FD [auth 1],
KJ [auth S1],
LI [auth 4],
LJ [auth S1],
MI [auth 4],
MJ [auth S1],
NJ [auth S1],
OI [auth 4],
OJ [auth S1],
OM [auth S4],
PE [auth 1],
PJ [auth S1],
QE [auth 1],
QJ [auth S1],
RE [auth 1],
TH [auth 2],
UH [auth 2],
VH [auth 2],
YF [auth 2],
YH [auth 2],
ZC [auth 1],
ZF [auth 2]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.43 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union--

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-01
    Type: Initial release
  • Version 1.1: 2026-07-22
    Changes: Data collection, Database references