9HL9 | pdb_00009hl9

CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME WITH P/E-site tRNA AND mRNA : LM14Cs1H3 sKO STRAIN


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

p -Alkoxy-Substituted Anisomycins with Potent Anti-Trypanosomiasis Activity and Expanded Modes of Action.

Bora Bhowal, K.Nguyen, A.M.T.Ibarra-Meneses, A.V.Brito Lira, A.Rajan, K.S.Castano, J.D.Beaudry, F.Bashan, A.Fernandez-Prada, C.Olivier, M.Yonath, A.Lubell, W.D.

(2025) J Med Chem 68: 20264-20282

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c01291
  • Primary Citation of Related Structures:  
    9HL9

  • PubMed Abstract: 

    Neglected tropical diseases caused by trypanosomatid parasites present a major public healthcare issue, partly due to emerging resistance. Attachment of ω-alkynyl chains characteristic of the lipid tails of antiparasitic peptides to the p -position of anisomycin gave ethers exhibiting potent activity, rivalling that of the parent ribosomal inhibitor, especially against resistant Leishmania strains. Single-particle cryoelectron microscopy analysis revealed that O -propargyl anisomycin binds to the highly conserved peptidyl transferase center of the ribosome similar to the parent inhibitor. Thermal proteomic profiling and gene ontology analysis demonstrated that O -propargyl anisomycin exhibited a broader mode of action, including activity against glycosome-associated proteins. Alkynyl substituents improved antiparasitic activity against resistant strains, likely by enlarging the mode of action, offering a novel path toward therapy against trypanosomatid infections.


  • Organizational Affiliation
    • Department of Chemistry, Université de Montréal, 1375 Avenue Thérèse-Lavoie-Roux, Montréal, Quebec H2 V 0B3, Canada.

Macromolecules

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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L2I [auth LA]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 LB]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 LC]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 LD]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 LE]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 LF]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 LG]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 LH]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 LI]220Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for E9AEA8 (Leishmania major)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L23R [auth LJ]139Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein L14S [auth LK]175Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4QBJ1 (Leishmania major)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L27A/L29T [auth LL]145Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L15U [auth LM]204Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L10V [auth LN]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 LO]305Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for E9AF09 (Leishmania major)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18X [auth LP]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 LQ]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 LR]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 LS]159Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4QEX4 (Leishmania major)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L17BA [auth LT]166Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L22CA [auth LU]129Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q0X2 (Leishmania major)
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L23aDA [auth LV]145Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4QJ20 (Leishmania major)
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L26EA [auth LW]143Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal protein L24FA [auth LX]124Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q1W6 (Leishmania major)
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27GA [auth LY]134Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q504 (Leishmania major)
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L28HA [auth LZ]147Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L35IA [auth La]127Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29JA [auth Lb]70Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q178 (Leishmania major)
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L7KA [auth Lc]252Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30LA [auth Ld]104Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal subunit protein L31MA [auth Le]188Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32NA [auth Lf]133Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal protein l35aOA [auth Lg]144Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L34PA [auth Lh]168Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S Ribosomal protein L36QA [auth Li]105Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L37RA [auth Lj]83Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal protein L38SA [auth Lk]83Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L39TA [auth Ll]51Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-60S ribosomal protein L40UA [auth Lm]128Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L41VA [auth Ln]34Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37aWA [auth Lo]92Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L44XA [auth Lp]106Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS1BB [auth SA]264Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein SACB [auth SB]246Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S3DB [auth SC]219Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S9EB [auth SD]190Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4FB [auth SE]273Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2GB [auth SF]265Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6HB [auth SG]249Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5IB [auth SH]190Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7JB [auth SI]200Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S15AKB [auth SJ]130Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8LB [auth SK]220Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S16MB [auth SL]149Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal protein S20NB [auth SM]116Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S10OB [auth SN]168Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14PB [auth SO]144Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S23QB [auth SP]143Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12RB [auth SQ]141Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S18SB [auth SR]153Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal protein S29TB [auth SS]57Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S13UB [auth ST]151Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S17 family proteinVB [auth SU]173Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S17WB [auth SV]143Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S15XB [auth SW]152Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19-like proteinYB [auth SX]161Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S21ZB [auth SY]164Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24AC [auth SZ]137Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25BC [auth Sa]120Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26CC [auth Sb]112Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S27-1DC [auth Sc]86Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 83
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S33EC [auth Sd]87Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 84
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30FC [auth Se]66Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 85
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-60S ribosomal protein L40GC [auth Sf]152Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 86
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein subunit beta-like proteinHC [auth Sg]312Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 87
MoleculeChains Sequence LengthOrganismDetailsImage
Putative RNA binding proteinIC [auth Sh]235Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
LSUa_rRNAA [auth L1]1,782Leishmania major strain Friedlin
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Entity ID: 2
MoleculeChains LengthOrganismImage
LSUb_rRNAB [auth L2]1,526Leishmania major strain Friedlin
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Entity ID: 3
MoleculeChains LengthOrganismImage
SR1_rRNAC [auth L3]216Leishmania major strain Friedlin
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Entity ID: 4
MoleculeChains LengthOrganismImage
SR2_rRNAD [auth L4]184Leishmania major strain Friedlin
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Entity ID: 5
MoleculeChains LengthOrganismImage
SR4_rRNAE [auth L5]135Leishmania major strain Friedlin
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Entity ID: 6
MoleculeChains LengthOrganismImage
SR6_rRNAF [auth L6]73Leishmania major strain Friedlin
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Entity ID: 7
MoleculeChains LengthOrganismImage
5.8S_rRNAG [auth L7]171Leishmania major strain Friedlin
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Entity ID: 8
MoleculeChains LengthOrganismImage
5S_rRNAH [auth L8]124Leishmania major strain Friedlin
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Entity ID: 51
MoleculeChains LengthOrganismImage
P-site_tRNAYA [auth S3]78Leishmania major strain Friedlin
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Entity ID: 52
MoleculeChains LengthOrganismImage
E-site_tRNAZA [auth S4]76Leishmania major strain Friedlin
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Entity ID: 53
MoleculeChains LengthOrganismImage
mRNAAB [auth S5]13Leishmania major strain Friedlin
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Entity ID: 88
MoleculeChains LengthOrganismImage
SSU_rRNAJC [auth S1]2,204Leishmania major strain Friedlin
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Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IWA (Subject of Investigation/LOI)
Query on A1IWA

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KO [auth L2][(2R,3S,4S)-4-oxidanyl-2-[(4-prop-2-ynoxyphenyl)methyl]pyrrolidin-3-yl] ethanoate
C16 H19 N O4
ZCMDJPGGPUGBJT-PMPSAXMXSA-N
ZN
Query on ZN

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PP [auth Lj],
QP [auth Lm],
SP [auth Lo],
TP [auth Lp],
ZP [auth SS]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

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AP [auth LA]
BP [auth LA]
BQ [auth S1]
CQ [auth S1]
DQ [auth S1]
AP [auth LA],
BP [auth LA],
BQ [auth S1],
CQ [auth S1],
DQ [auth S1],
EQ [auth S1],
FQ [auth S1],
GP [auth LN],
GQ [auth S1],
HK [auth L2],
HQ [auth S1],
IK [auth L2],
JK [auth L2],
KC [auth L1],
KK [auth L2],
LC [auth L1],
MC [auth L1],
MO [auth L4],
NC [auth L1],
NO [auth L4],
OC [auth L1],
OO [auth L4],
PC [auth L1],
QC [auth L1],
RC [auth L1],
SC [auth L1],
VP [auth S5],
YP [auth SO]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

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AE [auth L1]
AF [auth L1]
AG [auth L1]
AH [auth L1]
AI [auth L1]
AE [auth L1],
AF [auth L1],
AG [auth L1],
AH [auth L1],
AI [auth L1],
AJ [auth L1],
AK [auth L1],
AL [auth L2],
AM [auth L2],
AN [auth L2],
AO [auth L2],
AQ [auth SW],
AR [auth S1],
AS [auth S1],
AT [auth S1],
AU [auth S1],
AV [auth S1],
BE [auth L1],
BF [auth L1],
BG [auth L1],
BH [auth L1],
BI [auth L1],
BJ [auth L1],
BK [auth L1],
BL [auth L2],
BM [auth L2],
BN [auth L2],
BO [auth L2],
BR [auth S1],
BS [auth S1],
BT [auth S1],
BU [auth S1],
BV [auth S1],
CD [auth L1],
CE [auth L1],
CF [auth L1],
CG [auth L1],
CH [auth L1],
CI [auth L1],
CJ [auth L1],
CK [auth L1],
CL [auth L2],
CM [auth L2],
CN [auth L2],
CO [auth L2],
CP [auth LB],
CR [auth S1],
CS [auth S1],
CT [auth S1],
CU [auth S1],
CV [auth S1],
DD [auth L1],
DE [auth L1],
DF [auth L1],
DG [auth L1],
DH [auth L1],
DI [auth L1],
DJ [auth L1],
DK [auth L1],
DL [auth L2],
DM [auth L2],
DN [auth L2],
DO [auth L2],
DP [auth LG],
DR [auth S1],
DS [auth S1],
DT [auth S1],
DU [auth S1],
DV [auth S1],
ED [auth L1],
EE [auth L1],
EF [auth L1],
EG [auth L1],
EH [auth L1],
EI [auth L1],
EJ [auth L1],
EK [auth L1],
EL [auth L2],
EM [auth L2],
EN [auth L2],
EO [auth L2],
EP [auth LJ],
ER [auth S1],
ES [auth S1],
ET [auth S1],
EU [auth S1],
EV [auth S1],
FD [auth L1],
FE [auth L1],
FF [auth L1],
FG [auth L1],
FH [auth L1],
FI [auth L1],
FJ [auth L1],
FK [auth L1],
FL [auth L2],
FM [auth L2],
FN [auth L2],
FO [auth L2],
FP [auth LM],
FR [auth S1],
FS [auth S1],
FT [auth S1],
FU [auth S1],
FV [auth S1],
GD [auth L1],
GE [auth L1],
GF [auth L1],
GG [auth L1],
GH [auth L1],
GI [auth L1],
GJ [auth L1],
GK [auth L1],
GL [auth L2],
GM [auth L2],
GN [auth L2],
GO [auth L2],
GR [auth S1],
GS [auth S1],
GT [auth S1],
GU [auth S1],
GV [auth S1],
HD [auth L1],
HE [auth L1],
HF [auth L1],
HG [auth L1],
HH [auth L1],
HI [auth L1],
HJ [auth L1],
HL [auth L2],
HM [auth L2],
HN [auth L2],
HO [auth L2],
HP [auth LN],
HR [auth S1],
HS [auth S1],
HT [auth S1],
HU [auth S1],
HV [auth S1],
ID [auth L1],
IE [auth L1],
IF [auth L1],
IG [auth L1],
IH [auth L1],
II [auth L1],
IJ [auth L1],
IL [auth L2],
IM [auth L2],
IN [auth L2],
IO [auth L2],
IP [auth LS],
IR [auth S1],
IS [auth S1],
IT [auth S1],
IU [auth S1],
IV [auth S1],
JD [auth L1],
JE [auth L1],
JF [auth L1],
JG [auth L1],
JH [auth L1],
JI [auth L1],
JJ [auth L1],
JL [auth L2],
JM [auth L2],
JN [auth L2],
JO [auth L2],
JP [auth LT],
JR [auth S1],
JS [auth S1],
JT [auth S1],
JU [auth S1],
JV [auth S1],
KD [auth L1],
KE [auth L1],
KF [auth L1],
KG [auth L1],
KH [auth L1],
KI [auth L1],
KJ [auth L1],
KL [auth L2],
KM [auth L2],
KN [auth L2],
KP [auth LT],
KR [auth S1],
KS [auth S1],
KT [auth S1],
KU [auth S1],
KV [auth S1],
LD [auth L1],
LE [auth L1],
LF [auth L1],
LG [auth L1],
LH [auth L1],
LI [auth L1],
LJ [auth L1],
LL [auth L2],
LM [auth L2],
LN [auth L2],
LO [auth L3],
LP [auth LV],
LR [auth S1],
LS [auth S1],
LT [auth S1],
LU [auth S1],
LV [auth S1],
MD [auth L1],
ME [auth L1],
MF [auth L1],
MG [auth L1],
MH [auth L1],
MI [auth L1],
MJ [auth L1],
ML [auth L2],
MM [auth L2],
MN [auth L2],
MP [auth Lf],
MR [auth S1],
MS [auth S1],
MT [auth S1],
MU [auth S1],
ND [auth L1],
NE [auth L1],
NF [auth L1],
NG [auth L1],
NH [auth L1],
NI [auth L1],
NJ [auth L1],
NL [auth L2],
NM [auth L2],
NN [auth L2],
NP [auth Lh],
NR [auth S1],
NS [auth S1],
NT [auth S1],
NU [auth S1],
OD [auth L1],
OE [auth L1],
OF [auth L1],
OG [auth L1],
OH [auth L1],
OI [auth L1],
OJ [auth L1],
OL [auth L2],
OM [auth L2],
ON [auth L2],
OP [auth Lh],
OR [auth S1],
OS [auth S1],
OT [auth S1],
OU [auth S1],
PD [auth L1],
PE [auth L1],
PF [auth L1],
PG [auth L1],
PH [auth L1],
PI [auth L1],
PJ [auth L1],
PL [auth L2],
PM [auth L2],
PN [auth L2],
PQ [auth S1],
PR [auth S1],
PS [auth S1],
PT [auth S1],
PU [auth S1],
QD [auth L1],
QE [auth L1],
QF [auth L1],
QG [auth L1],
QH [auth L1],
QI [auth L1],
QJ [auth L1],
QL [auth L2],
QM [auth L2],
QN [auth L2],
QO [auth L4],
QQ [auth S1],
QR [auth S1],
QS [auth S1],
QT [auth S1],
QU [auth S1],
RD [auth L1],
RE [auth L1],
RF [auth L1],
RG [auth L1],
RH [auth L1],
RI [auth L1],
RJ [auth L1],
RL [auth L2],
RM [auth L2],
RN [auth L2],
RO [auth L4],
RP [auth Ln],
RQ [auth S1],
RR [auth S1],
RS [auth S1],
RT [auth S1],
RU [auth S1],
SD [auth L1],
SE [auth L1],
SF [auth L1],
SG [auth L1],
SH [auth L1],
SI [auth L1],
SJ [auth L1],
SK [auth L2],
SL [auth L2],
SM [auth L2],
SN [auth L2],
SO [auth L7],
SQ [auth S1],
SR [auth S1],
SS [auth S1],
ST [auth S1],
SU [auth S1],
TD [auth L1],
TE [auth L1],
TF [auth L1],
TG [auth L1],
TH [auth L1],
TI [auth L1],
TJ [auth L1],
TK [auth L2],
TL [auth L2],
TM [auth L2],
TN [auth L2],
TO [auth L7],
TQ [auth S1],
TR [auth S1],
TS [auth S1],
TT [auth S1],
TU [auth S1],
UD [auth L1],
UE [auth L1],
UF [auth L1],
UG [auth L1],
UH [auth L1],
UI [auth L1],
UJ [auth L1],
UK [auth L2],
UL [auth L2],
UM [auth L2],
UN [auth L2],
UO [auth L7],
UP [auth S3],
UQ [auth S1],
UR [auth S1],
US [auth S1],
UT [auth S1],
UU [auth S1],
VD [auth L1],
VE [auth L1],
VF [auth L1],
VG [auth L1],
VH [auth L1],
VI [auth L1],
VJ [auth L1],
VK [auth L2],
VL [auth L2],
VM [auth L2],
VN [auth L2],
VO [auth L7],
VQ [auth S1],
VR [auth S1],
VS [auth S1],
VT [auth S1],
VU [auth S1],
WD [auth L1],
WE [auth L1],
WF [auth L1],
WG [auth L1],
WH [auth L1],
WI [auth L1],
WJ [auth L1],
WK [auth L2],
WL [auth L2],
WM [auth L2],
WN [auth L2],
WO [auth L7],
WP [auth SG],
WQ [auth S1],
WR [auth S1],
WS [auth S1],
WT [auth S1],
WU [auth S1],
XD [auth L1],
XE [auth L1],
XF [auth L1],
XG [auth L1],
XH [auth L1],
XI [auth L1],
XJ [auth L1],
XK [auth L2],
XL [auth L2],
XM [auth L2],
XN [auth L2],
XO [auth L8],
XQ [auth S1],
XR [auth S1],
XS [auth S1],
XT [auth S1],
XU [auth S1],
YD [auth L1],
YE [auth L1],
YF [auth L1],
YG [auth L1],
YH [auth L1],
YI [auth L1],
YJ [auth L1],
YK [auth L2],
YL [auth L2],
YM [auth L2],
YN [auth L2],
YO [auth L8],
YQ [auth S1],
YR [auth S1],
YS [auth S1],
YT [auth S1],
YU [auth S1],
ZD [auth L1],
ZE [auth L1],
ZF [auth L1],
ZG [auth L1],
ZH [auth L1],
ZI [auth L1],
ZJ [auth L1],
ZK [auth L2],
ZL [auth L2],
ZM [auth L2],
ZN [auth L2],
ZO [auth L8],
ZQ [auth S1],
ZR [auth S1],
ZS [auth S1],
ZT [auth S1],
ZU [auth S1]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
AD [auth L1]
BD [auth L1]
IQ [auth S1]
JQ [auth S1]
KQ [auth S1]
AD [auth L1],
BD [auth L1],
IQ [auth S1],
JQ [auth S1],
KQ [auth S1],
LK [auth L2],
LQ [auth S1],
MK [auth L2],
MQ [auth S1],
NK [auth L2],
NQ [auth S1],
OK [auth L2],
OQ [auth S1],
PK [auth L2],
PO [auth L4],
QK [auth L2],
RK [auth L2],
TC [auth L1],
UC [auth L1],
VC [auth L1],
WC [auth L1],
XC [auth L1],
XP [auth SL],
YC [auth L1],
ZC [auth L1]
SODIUM ION
Na
FKNQFGJONOIPTF-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 REFINEMENTPHENIX1.20.1_4487
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Israel Science FoundationIsrael--
European Research Council (ERC)European Union--

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-15
    Type: Initial release
  • Version 1.1: 2025-10-22
    Changes: Data collection, Database references
  • Version 2.0: 2025-11-19
    Type: Coordinate replacement
    Reason: Model completeness
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary