7NHK

LsaA, an antibiotic resistance ABCF, in complex with 70S ribosome from Enterococcus faecalis


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis of ABCF-mediated resistance to pleuromutilin, lincosamide, and streptogramin A antibiotics in Gram-positive pathogens.

Crowe-McAuliffe, C.Murina, V.Turnbull, K.J.Kasari, M.Mohamad, M.Polte, C.Takada, H.Vaitkevicius, K.Johansson, J.Ignatova, Z.Atkinson, G.C.O'Neill, A.J.Hauryliuk, V.Wilson, D.N.

(2021) Nat Commun 12: 3577-3577

  • DOI: https://doi.org/10.1038/s41467-021-23753-1
  • Primary Citation of Related Structures:  
    7NHK, 7NHL, 7NHM, 7NHN

  • PubMed Abstract: 

    Target protection proteins confer resistance to the host organism by directly binding to the antibiotic target. One class of such proteins are the antibiotic resistance (ARE) ATP-binding cassette (ABC) proteins of the F-subtype (ARE-ABCFs), which are widely distributed throughout Gram-positive bacteria and bind the ribosome to alleviate translational inhibition from antibiotics that target the large ribosomal subunit. Here, we present single-particle cryo-EM structures of ARE-ABCF-ribosome complexes from three Gram-positive pathogens: Enterococcus faecalis LsaA, Staphylococcus haemolyticus VgaA LC and Listeria monocytogenes VgaL. Supported by extensive mutagenesis analysis, these structures enable a general model for antibiotic resistance mediated by these ARE-ABCFs to be proposed. In this model, ABCF binding to the antibiotic-stalled ribosome mediates antibiotic release via mechanistically diverse long-range conformational relays that converge on a few conserved ribosomal RNA nucleotides located at the peptidyltransferase center. These insights are important for the future development of antibiotics that overcome such target protection resistance mechanisms.


  • Organizational Affiliation

    Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ABC-F type ribosomal protection protein Lsa(A)A [auth 0]541Enterococcus faecalisMutation(s): 2 
Gene Names: DVW78_08325
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29B [auth 1]62Enterococcus faecalisMutation(s): 0 
UniProt
Find proteins for A0A1B4XKV0 (Enterococcus faecalis)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30C [auth 2]59Enterococcus faecalisMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32D [auth 4]59Enterococcus faecalisMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33E [auth 5]49Enterococcus faecalisMutation(s): 0 
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Find proteins for A0A1B4XR98 (Enterococcus faecalis)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34F [auth 6]44Enterococcus faecalisMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35G [auth 7]66Enterococcus faecalisMutation(s): 0 
UniProt
Find proteins for A0A1B4XM73 (Enterococcus faecalis)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36H [auth 8]38Enterococcus faecalisMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2K [auth G]276Enterococcus faecalisMutation(s): 0 
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Find proteins for A0A1B4XKR6 (Enterococcus faecalis)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3L [auth H]209Enterococcus faecalisMutation(s): 0 
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Find proteins for A0A1B4XKR3 (Enterococcus faecalis)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4M [auth I]207Enterococcus faecalisMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5N [auth J]179Enterococcus faecalisMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6O [auth K]178Enterococcus faecalisMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13P [auth M]147Enterococcus faecalisMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14Q [auth N]122Enterococcus faecalisMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15R [auth O]146Enterococcus faecalisMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16S [auth P]144Enterococcus faecalisMutation(s): 0 
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Find proteins for A0A1B4XKU1 (Enterococcus faecalis)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17T [auth Q]127Enterococcus faecalisMutation(s): 0 
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Find proteins for A0A1B4XKX1 (Enterococcus faecalis)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18U [auth R]118Enterococcus faecalisMutation(s): 0 
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Find proteins for A0A1B4XKS7 (Enterococcus faecalis)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19V [auth S]115Enterococcus faecalisMutation(s): 0 
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Find proteins for A0A1B4XPL8 (Enterococcus faecalis)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20W [auth T]119Enterococcus faecalisMutation(s): 0 
UniProt
Find proteins for A0A1B4XM76 (Enterococcus faecalis)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21X [auth U]102Enterococcus faecalisMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22Y [auth V]115Enterococcus faecalisMutation(s): 0 
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Find proteins for A0A1B4XKT6 (Enterococcus faecalis)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23Z [auth W]96Enterococcus faecalisMutation(s): 0 
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Find proteins for A0A1B4XKR7 (Enterococcus faecalis)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24AA [auth X]103Enterococcus faecalisMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27BA [auth Y]95Enterococcus faecalisMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28CA [auth Z]62Enterococcus faecalisMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2EA [auth c]261Enterococcus faecalisMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3FA [auth d]218Enterococcus faecalisMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4GA [auth e]203Enterococcus faecalisMutation(s): 0 
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Find proteins for A0A1B4XRV7 (Enterococcus faecalis)
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5HA [auth f]166Enterococcus faecalisMutation(s): 0 
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Find proteins for A0A1B4XKW0 (Enterococcus faecalis)
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6IA [auth g]100Enterococcus faecalisMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7JA [auth h]156Enterococcus faecalisMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8KA [auth i]132Enterococcus faecalisMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9LA [auth j]130Enterococcus faecalisMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10MA [auth k]102Enterococcus faecalisMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11NA [auth l]129Enterococcus faecalisMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12OA [auth m]137Enterococcus faecalisMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13PA [auth n]121Enterococcus faecalisMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZQA [auth o]61Enterococcus faecalisMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15RA [auth p]89Enterococcus faecalisMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16SA [auth q]91Enterococcus faecalisMutation(s): 0 
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Find proteins for A0A1B4XP69 (Enterococcus faecalis)
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17TA [auth r]88Enterococcus faecalisMutation(s): 0 
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Find proteins for A0A1B4XKS3 (Enterococcus faecalis)
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UniProt GroupA0A1B4XKS3
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18UA [auth s]79Enterococcus faecalisMutation(s): 0 
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UniProt GroupA0A1B4XKB3
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19VA [auth t]92Enterococcus faecalisMutation(s): 0 
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UniProt GroupA0A1B4XKS0
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20WA [auth u]83Enterococcus faecalisMutation(s): 0 
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Find proteins for A0A1B4XQJ7 (Enterococcus faecalis)
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UniProt GroupA0A1B4XQJ7
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L1ZA [auth F]229Enterococcus faecalisMutation(s): 0 
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Find proteins for A0A1B4XR48 (Enterococcus faecalis)
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UniProt GroupA0A1B4XR48
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31 type BAB [auth 3]89Enterococcus faecalisMutation(s): 0 
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Find proteins for A0A1B4XMV6 (Enterococcus faecalis)
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Entity ID: 9
MoleculeChains LengthOrganismImage
23S rRNAI [auth A]2,912Enterococcus faecalis
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Entity ID: 10
MoleculeChains LengthOrganismImage
5S rRNAJ [auth B]116Enterococcus faecalis
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Entity ID: 30
MoleculeChains LengthOrganismImage
16S rRNADA [auth a]1,558Enterococcus faecalis
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Entity ID: 50
MoleculeChains LengthOrganismImage
tRNA-fMETiXA [auth D]77Enterococcus faecalis
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Entity ID: 51
MoleculeChains LengthOrganismImage
RNA (5'-R(P*GP*GP*AP*GP*GP*UP*AP*UP*GP*AP*CP*AP*A)-3')YA [auth b]20Enterococcus faecalis
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Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

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BB [auth 0],
CB [auth 0]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
PUT
Query on PUT

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AI [auth a],
BI [auth a],
OG [auth A],
PG [auth A]
1,4-DIAMINOBUTANE
C4 H12 N2
KIDHWZJUCRJVML-UHFFFAOYSA-N
ZN
Query on ZN

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CI [auth o],
FB [auth 4],
GB [auth 8]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

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AG [auth A]
BD [auth A]
BE [auth A]
BH [auth a]
EC [auth A]
AG [auth A],
BD [auth A],
BE [auth A],
BH [auth a],
EC [auth A],
EE [auth A],
EH [auth a],
GC [auth A],
HC [auth A],
HD [auth A],
KB [auth A],
KF [auth A],
MH [auth a],
OE [auth A],
PE [auth A],
QD [auth A],
QG [auth A],
RB [auth A],
SC [auth A],
TG [auth P],
VE [auth A],
WH [auth a],
XB [auth A],
XG [auth a],
YB [auth A],
YG [auth a],
ZE [auth A],
ZF [auth A],
ZG [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]
AH [auth a]
AC [auth A],
AD [auth A],
AE [auth A],
AF [auth A],
AH [auth a],
BC [auth A],
BF [auth A],
BG [auth A],
CC [auth A],
CD [auth A],
CE [auth A],
CF [auth A],
CG [auth A],
CH [auth a],
DB [auth 0],
DC [auth A],
DD [auth A],
DE [auth A],
DF [auth A],
DG [auth A],
DH [auth a],
DI [auth D],
EB [auth 0],
ED [auth A],
EF [auth A],
EG [auth A],
FC [auth A],
FD [auth A],
FE [auth A],
FF [auth A],
FG [auth A],
FH [auth a],
GD [auth A],
GE [auth A],
GF [auth A],
GG [auth A],
GH [auth a],
HB [auth A],
HE [auth A],
HF [auth A],
HG [auth A],
HH [auth a],
IB [auth A],
IC [auth A],
ID [auth A],
IE [auth A],
IF [auth A],
IG [auth A],
IH [auth a],
JB [auth A],
JC [auth A],
JD [auth A],
JE [auth A],
JF [auth A],
JG [auth A],
JH [auth a],
KC [auth A],
KD [auth A],
KE [auth A],
KG [auth A],
KH [auth a],
LB [auth A],
LC [auth A],
LD [auth A],
LE [auth A],
LF [auth A],
LG [auth A],
LH [auth a],
MB [auth A],
MC [auth A],
MD [auth A],
ME [auth A],
MF [auth A],
MG [auth A],
NB [auth A],
NC [auth A],
ND [auth A],
NE [auth A],
NF [auth A],
NG [auth A],
NH [auth a],
OB [auth A],
OC [auth A],
OD [auth A],
OF [auth A],
OH [auth a],
PB [auth A],
PC [auth A],
PD [auth A],
PF [auth A],
PH [auth a],
QB [auth A],
QC [auth A],
QE [auth A],
QF [auth A],
QH [auth a],
RC [auth A],
RD [auth A],
RE [auth A],
RF [auth A],
RG [auth B],
RH [auth a],
SB [auth A],
SD [auth A],
SE [auth A],
SF [auth A],
SG [auth O],
SH [auth a],
TB [auth A],
TC [auth A],
TD [auth A],
TE [auth A],
TF [auth A],
TH [auth a],
UB [auth A],
UC [auth A],
UD [auth A],
UE [auth A],
UF [auth A],
UG [auth a],
UH [auth a],
VB [auth A],
VC [auth A],
VD [auth A],
VF [auth A],
VG [auth a],
VH [auth a],
WB [auth A],
WC [auth A],
WD [auth A],
WE [auth A],
WF [auth A],
WG [auth a],
XC [auth A],
XD [auth A],
XE [auth A],
XF [auth A],
XH [auth a],
YC [auth A],
YD [auth A],
YE [auth A],
YF [auth A],
YH [auth a],
ZB [auth A],
ZC [auth A],
ZD [auth A],
ZH [auth a]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyWI3285/8-1
Swedish Research CouncilSweden2017-03783
Swedish Research CouncilSweden2019-01085
European Regional Development FundSweden2014-2020.4.01.15-0013
Estonian Research CouncilEstoniaPRG335
Swedish Research CouncilSweden2018-00956

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-05
    Type: Initial release
  • Version 1.1: 2021-06-23
    Changes: Database references