9QEG | pdb_00009qeg

Cryo-EM structure of the 70S ribosome of a MLSb sensitive S. aureus strain "KES34" in complex with solithromycin


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.21 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural studies on ribosomes of differentially macrolide-resistant Staphylococcus aureus strains.

Rivalta, A.Fedorenko, A.Le Scornet, A.Thompson, S.Halfon, Y.Breiner Goldstein, E.Cavdaroglu, S.Melenitzky, T.Hiregange, D.G.Zimmerman, E.Bashan, A.Yap, M.F.Yonath, A.

(2025) Life Sci Alliance 8

  • DOI: https://doi.org/10.26508/lsa.202503325
  • Primary Citation of Related Structures:  
    9QEG, 9QEH

  • PubMed Abstract: 

    Antimicrobial resistance is a major global health challenge, diminishing the efficacy of many antibiotics, including macrolides. In Staphylococcus aureus , an opportunistic pathogen, macrolide resistance is primarily mediated by Erm-family methyltransferases, which mono- or dimethylate A2058 in the 23S ribosomal RNA, reducing drug binding. Although macrolide-ribosome interactions have been characterized in nonpathogenic species, their structural basis in clinically relevant pathogens remains limited. In this study, we investigate the impact of ermB -mediated resistance on drug binding by analyzing ribosomes from S. aureus strains with varying levels of ermB expression and activity. Using cryo-electron microscopy, we determined the high-resolution structures of solithromycin-bound ribosomes, including those with dimethylated A2058. Our structural analysis reveals the specific interactions that enable solithromycin binding despite double methylation and resistance, as corroborated by microbiological and biochemical data, suggesting that further optimization of ketolide-ribosome interactions could enhance macrolide efficacy against resistant S. aureus strains.


  • Organizational Affiliation
    • Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL33AA [auth 1]52Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL34B [auth 2]45Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL35C [auth 3]66Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL36D [auth 4]37Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL2F [auth C]277Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL3G [auth D]220Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL4H [auth E]207Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL6I [auth G]178Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL13J [auth H]145Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL14K [auth I]122Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL15L [auth J]146Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL16M [auth K]144Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL17N [auth L]122Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL18O [auth M]119Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL19P [auth N]116Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL20Q [auth O]118Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL21R [auth P]102Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL22S [auth Q]117Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL23T [auth R]91Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL24U [auth S]105Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25V [auth T]217Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL27W [auth U]94Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL28X [auth V]62Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL29Y [auth W]73Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL30Z [auth X]59Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL32AA [auth Z]57Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL5BA [auth F]179Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS5EA [auth Ae]166Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS6FA [auth Af]98Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS7GA [auth Ag]156Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS9HA [auth Ai]132Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS12IA [auth Al]137Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS15JA [auth Ao]89Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS16KA [auth Ap]91Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS17LA [auth Aq]87Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS18MA [auth Ar]80Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS20NA [auth At]83Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS10PA [auth Aj]102Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS3QA [auth Ac]217Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS13RA [auth Am]121Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS11SA [auth Ak]129Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS2TA [auth Ab]255Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS8UA [auth Ah]132Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS4VA [auth Ad]200Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS14BWA [auth An]61Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
UniProt
Find proteins for Q2FEQ2 (Staphylococcus aureus (strain USA300))
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UniProt GroupQ2FEQ2
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS19XA [auth As]92Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
UniProt
Find proteins for Q2FEP3 (Staphylococcus aureus (strain USA300))
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL31BBB [auth 13]84Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
UniProt
Find proteins for Q2FF08 (Staphylococcus aureus (strain USA300))
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Go to UniProtKB:  Q2FF08
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UniProt GroupQ2FF08
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Entity ID: 5
MoleculeChains LengthOrganismImage
5S ribosomal RNAE [auth B]115Staphylococcus aureus subsp. aureus USA300
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Entity ID: 29
MoleculeChains LengthOrganismImage
E-site tRNA moleculeCA [auth 11]15Staphylococcus aureus subsp. aureus USA300
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Entity ID: 30
MoleculeChains LengthOrganismImage
23S ribosomal RNADA [auth A]2,923Staphylococcus aureus subsp. aureus USA300
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Entity ID: 41
MoleculeChains LengthOrganismImage
16S ribosomal RNAOA [auth Aa]1,552Staphylococcus aureus subsp. aureus USA300
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Entity ID: 51
MoleculeChains LengthOrganismImage
mRNA moleculeYA [auth d]19Staphylococcus aureus subsp. aureus USA300
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Entity ID: 52
MoleculeChains LengthOrganismImage
P-site tRNA moleculeZA [auth 8]71Staphylococcus aureus subsp. aureus USA300
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Entity ID: 53
MoleculeChains LengthOrganismImage
A-site tRNA moleculeAB [auth 9]5Staphylococcus aureus subsp. aureus USA300
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EM1 (Subject of Investigation/LOI)
Query on EM1

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HB [auth A](3aS,4R,7S,9R,10R,11R,13R,15R,15aR)-1-{4-[4-(3-aminophenyl)-1H-1,2,3-triazol-1-yl]butyl}-4-ethyl-7-fluoro-11-methoxy-3a ,7,9,11,13,15-hexamethyl-2,6,8,14-tetraoxotetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-10-yl 3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranoside
C43 H65 F N6 O10
IXXFZUPTQVDPPK-ZAWHAJPISA-N
ZN
Query on ZN

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CB [auth 1],
DB [auth 4],
GB [auth Z],
VK [auth An]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

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AI [auth A]
BI [auth A]
CI [auth A]
DI [auth A]
EI [auth A]
AI [auth A],
BI [auth A],
CI [auth A],
DI [auth A],
EI [auth A],
FI [auth A],
GI [auth A],
HI [auth A],
II [auth A],
JI [auth A],
KI [auth A],
SK [auth Aa],
TK [auth Aa],
UK [auth Aa],
WH [auth A],
XH [auth A],
YH [auth A],
ZH [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

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AC [auth A]
AD [auth A]
AE [auth A]
AF [auth A]
AG [auth A]
AC [auth A],
AD [auth A],
AE [auth A],
AF [auth A],
AG [auth A],
AH [auth A],
AJ [auth Aa],
AK [auth Aa],
BC [auth A],
BD [auth A],
BE [auth A],
BF [auth A],
BG [auth A],
BH [auth A],
BJ [auth Aa],
BK [auth Aa],
CC [auth A],
CD [auth A],
CE [auth A],
CF [auth A],
CG [auth A],
CH [auth A],
CJ [auth Aa],
CK [auth Aa],
DC [auth A],
DD [auth A],
DE [auth A],
DF [auth A],
DG [auth A],
DH [auth A],
DJ [auth Aa],
DK [auth Aa],
EB [auth C],
EC [auth A],
ED [auth A],
EE [auth A],
EF [auth A],
EG [auth A],
EH [auth A],
EJ [auth Aa],
EK [auth Aa],
FB [auth D],
FC [auth A],
FD [auth A],
FE [auth A],
FF [auth A],
FG [auth A],
FH [auth A],
FJ [auth Aa],
FK [auth Aa],
GC [auth A],
GD [auth A],
GE [auth A],
GF [auth A],
GG [auth A],
GH [auth A],
GJ [auth Aa],
GK [auth Aa],
HC [auth A],
HD [auth A],
HE [auth A],
HF [auth A],
HG [auth A],
HH [auth A],
HJ [auth Aa],
HK [auth Aa],
IB [auth A],
IC [auth A],
ID [auth A],
IE [auth A],
IF [auth A],
IG [auth A],
IH [auth A],
IJ [auth Aa],
IK [auth Aa],
JB [auth A],
JC [auth A],
JD [auth A],
JE [auth A],
JF [auth A],
JG [auth A],
JH [auth A],
JJ [auth Aa],
JK [auth Aa],
KB [auth A],
KC [auth A],
KD [auth A],
KE [auth A],
KF [auth A],
KG [auth A],
KH [auth A],
KJ [auth Aa],
KK [auth Aa],
LB [auth A],
LC [auth A],
LD [auth A],
LE [auth A],
LF [auth A],
LG [auth A],
LH [auth A],
LI [auth Aa],
LJ [auth Aa],
LK [auth Aa],
MB [auth A],
MC [auth A],
MD [auth A],
ME [auth A],
MF [auth A],
MG [auth A],
MH [auth A],
MI [auth Aa],
MJ [auth Aa],
MK [auth Aa],
NB [auth A],
NC [auth A],
ND [auth A],
NE [auth A],
NF [auth A],
NG [auth A],
NH [auth A],
NI [auth Aa],
NJ [auth Aa],
NK [auth Aa],
OB [auth A],
OC [auth A],
OD [auth A],
OE [auth A],
OF [auth A],
OG [auth A],
OH [auth A],
OI [auth Aa],
OJ [auth Aa],
OK [auth Aa],
PB [auth A],
PC [auth A],
PD [auth A],
PE [auth A],
PF [auth A],
PG [auth A],
PH [auth A],
PI [auth Aa],
PJ [auth Aa],
PK [auth Aa],
QB [auth A],
QC [auth A],
QD [auth A],
QE [auth A],
QF [auth A],
QG [auth A],
QH [auth A],
QI [auth Aa],
QJ [auth Aa],
QK [auth Aa],
RB [auth A],
RC [auth A],
RD [auth A],
RE [auth A],
RF [auth A],
RG [auth A],
RH [auth A],
RI [auth Aa],
RJ [auth Aa],
RK [auth Aa],
SB [auth A],
SC [auth A],
SD [auth A],
SE [auth A],
SF [auth A],
SG [auth A],
SH [auth A],
SI [auth Aa],
SJ [auth Aa],
TB [auth A],
TC [auth A],
TD [auth A],
TE [auth A],
TF [auth A],
TG [auth A],
TH [auth A],
TI [auth Aa],
TJ [auth Aa],
UB [auth A],
UC [auth A],
UD [auth A],
UE [auth A],
UF [auth A],
UG [auth A],
UH [auth A],
UI [auth Aa],
UJ [auth Aa],
VB [auth A],
VC [auth A],
VD [auth A],
VE [auth A],
VF [auth A],
VG [auth A],
VH [auth A],
VI [auth Aa],
VJ [auth Aa],
WB [auth A],
WC [auth A],
WD [auth A],
WE [auth A],
WF [auth A],
WG [auth A],
WI [auth Aa],
WJ [auth Aa],
XB [auth A],
XC [auth A],
XD [auth A],
XE [auth A],
XF [auth A],
XG [auth A],
XI [auth Aa],
XJ [auth Aa],
YB [auth A],
YC [auth A],
YD [auth A],
YE [auth A],
YF [auth A],
YG [auth A],
YI [auth Aa],
YJ [auth Aa],
ZB [auth A],
ZC [auth A],
ZD [auth A],
ZE [auth A],
ZF [auth A],
ZG [auth A],
ZI [auth Aa],
ZJ [auth Aa]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.21 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


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Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-04
    Type: Initial release
  • Version 1.1: 2025-06-18
    Changes: Data collection, Database references
  • Version 1.2: 2025-07-02
    Changes: Data collection