7NHN

VgaL, an antibiotic resistance ABCF, in complex with 70S ribosome from Listeria monocytogenes

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: 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 ...

    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. Daniel.Wilson@chemie.uni-hamburg.de.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lmo0919 proteinA [auth 0]567Listeria monocytogenes EGD-eMutation(s): 2 
Gene Names: lmo0919
UniProt
Find proteins for Q8Y8I3 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2F [auth G]277Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: rplB, lmo2629
UniProt
Find proteins for P60426 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3G [auth H]209Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: rplC, lmo2632
UniProt
Find proteins for Q8Y440 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
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Entity ID: 8
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50S ribosomal protein L4H [auth I]207Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: rplD, lmo2631
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Find proteins for P61055 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
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Entity ID: 9
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50S ribosomal protein L5I [auth J]179Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: rplE, lmo2620
UniProt
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Entity ID: 10
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50S ribosomal protein L6J [auth K]178Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: rplF, lmo2617
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Entity ID: 11
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50S ribosomal protein L13K [auth M]145Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: rplM, lmo2597
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Entity ID: 12
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50S ribosomal protein L14L [auth N]122Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: rplN, lmo2622
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Entity ID: 13
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50S ribosomal protein L15M [auth O]146Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: rplO, lmo2613
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Entity ID: 14
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50S ribosomal protein L16N [auth P]144Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: rplP, lmo2625
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Entity ID: 15
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50S ribosomal protein L17O [auth Q]135Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: rplQ, lmo2605
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Entity ID: 16
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50S ribosomal protein L18P [auth R]119Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: rplR, lmo2616
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Entity ID: 17
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50S ribosomal protein L19Q [auth S]114Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: rplS, lmo1787
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Find proteins for O53083 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
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Entity ID: 18
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50S ribosomal protein L20R [auth T]119Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: rplT, lmo1783
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Entity ID: 19
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50S ribosomal protein L21S [auth U]102Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: rplU, lmo1542
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Entity ID: 20
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50S ribosomal protein L22T [auth V]118Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: rplV, lmo2627
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Entity ID: 21
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50S ribosomal protein L23U [auth W]94Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: rplW, lmo2630
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Entity ID: 22
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50S ribosomal protein L24V [auth X]103Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: rplX, lmo2621
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Entity ID: 23
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50S ribosomal protein L27W [auth Z]96Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: rpmA, lmo1540
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Entity ID: 24
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50S ribosomal protein L28X [auth 1]62Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: rpmB, lmo1816
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Entity ID: 25
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50S ribosomal protein L29Y [auth 2]63Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: rpmC, lmo2624
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Entity ID: 26
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50S ribosomal protein L30Z [auth 3]59Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: rpmD, lmo2614
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Entity ID: 27
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50S ribosomal protein L32-2AA [auth 5]57Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: rpmF2, lmo2047
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50S ribosomal protein L33 1BA [auth 6]49Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: rpmG1, lmo1335
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50S ribosomal protein L34CA [auth 7]44Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: rpmH, lmo2856
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Entity ID: 30
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50S ribosomal protein L35DA [auth 8]66Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: rpmI, lmo1784
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Find proteins for P0A491 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
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Entity ID: 31
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50S ribosomal protein L36EA [auth 9]37Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: rpmJ, lmo2609
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Entity ID: 33
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30S ribosomal protein S2GA [auth c]249Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: rpsB, lmo1658
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Entity ID: 34
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30S ribosomal protein S3HA [auth d]218Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: rpsC, lmo2626
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30S ribosomal protein S4IA [auth e]200Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: rpsD, lmo1596
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30S ribosomal protein S5JA [auth f]167Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: rpsE, lmo2615
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Entity ID: 37
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30S ribosomal protein S6KA [auth g]97Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: rpsF, lmo0044
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Entity ID: 38
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30S ribosomal protein S7LA [auth h]156Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: rpsG, lmo2655
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30S ribosomal protein S8MA [auth i]132Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: rpsH, lmo2618
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30S ribosomal protein S9NA [auth j]130Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: rpsI, lmo2596
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Entity ID: 41
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30S ribosomal protein S10OA [auth k]102Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: rpsJ, lmo2633
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30S ribosomal protein S11PA [auth l]129Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: rpsK, lmo2607
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S12QA [auth m]137Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: rpsL, lmo2656
UniProt
Find proteins for P66372 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S13RA [auth n]121Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: rpsM, lmo2608
UniProt
Find proteins for P66383 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZSA [auth o]61Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: rpsZ, rpsN1, lmo2619
UniProt
Find proteins for P66401 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S15TA [auth p]89Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: rpsO, lmo1330
UniProt
Find proteins for Q92C24 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S16UA [auth q]90Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: rpsP, lmo1797
UniProt
Find proteins for Q8Y699 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S17VA [auth r]87Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: rpsQ, lmo2623
UniProt
Find proteins for Q927L6 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S18WA [auth s]79Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: rpsR, lmo0046
UniProt
Find proteins for P66461 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19XA [auth t]92Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: rpsS, lmo2628
UniProt
Find proteins for P66484 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
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Entity ID: 51
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30S ribosomal protein S20YA [auth u]84Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: rpsT, lmo1480
UniProt
Find proteins for P66503 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L31 type BZA [auth 4]81Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: rpmE2, rpmE, lmo2548
UniProt
Find proteins for P0A485 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
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Entity ID: 2
MoleculeChainsLengthOrganismImage
tRNA-fMetB [auth D]77Listeria monocytogenes EGD-e
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Entity ID: 3
MoleculeChainsLengthOrganismImage
RNA (5'-R(P*GP*AP*GP*GP*UP*NP*NP*NP*NP*NP*NP*AP*UP*G)-3')C [auth b]14Listeria monocytogenes EGD-e
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Entity ID: 4
MoleculeChainsLengthOrganismImage
23S rRNAD [auth A]2928Listeria monocytogenes EGD-e
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Entity ID: 5
MoleculeChainsLengthOrganismImage
16S rRNAE [auth a]1542Listeria monocytogenes EGD-e
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Entity ID: 32
MoleculeChainsLengthOrganismImage
5S rRNAFA [auth B]114Listeria monocytogenes EGD-e
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Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP
Download Ideal Coordinates CCD File 
AB [auth 0],
BB [auth 0]		ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N		 Ligand Interaction
SPD
Query on SPD
Download Ideal Coordinates CCD File 
GB [auth A],
IG [auth a]		SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
LH [auth 5],
MH [auth 9],
OH [auth o]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
K
Query on K
Download Ideal Coordinates CCD File 
EC [auth A],
GD [auth A],
JC [auth A],
JE [auth A],
KC [auth A],
EC [auth A],
GD [auth A],
JC [auth A],
JE [auth A],
KC [auth A],
KH [auth P],
LD [auth A],
NC [auth A],
OC [auth A],
OE [auth A],
OG [auth a],
PE [auth A],
PF [auth A],
SF [auth A],
TE [auth A],
TF [auth A],
TG [auth a],
UD [auth A],
WG [auth a],
YC [auth A],
ZE [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
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],
BC [auth A],
BD [auth A],
BE [auth A],
BF [auth A],
BG [auth A],
BH [auth a],
CB [auth 0],
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],
EB [auth D],
ED [auth A],
EE [auth A],
EF [auth A],
EG [auth A],
EH [auth a],
FB [auth b],
FC [auth A],
FD [auth A],
FE [auth A],
FF [auth A],
FG [auth A],
FH [auth a],
GC [auth A],
GE [auth A],
GF [auth A],
GG [auth A],
GH [auth a],
HB [auth A],
HC [auth A],
HD [auth A],
HE [auth A],
HF [auth A],
HG [auth A],
HH [auth G],
IB [auth A],
IC [auth A],
ID [auth A],
IE [auth A],
IF [auth A],
IH [auth H],
JB [auth A],
JD [auth A],
JF [auth A],
JG [auth a],
JH [auth O],
KB [auth A],
KD [auth A],
KE [auth A],
KF [auth A],
KG [auth a],
LB [auth A],
LC [auth A],
LE [auth A],
LF [auth A],
LG [auth a],
MB [auth A],
MC [auth A],
MD [auth A],
ME [auth A],
MF [auth A],
MG [auth a],
NB [auth A],
ND [auth A],
NE [auth A],
NF [auth A],
NG [auth a],
NH [auth o],
OB [auth A],
OD [auth A],
OF [auth A],
PB [auth A],
PC [auth A],
PD [auth A],
PG [auth a],
QB [auth A],
QC [auth A],
QD [auth A],
QE [auth A],
QF [auth A],
QG [auth a],
RB [auth A],
RC [auth A],
RD [auth A],
RE [auth A],
RF [auth A],
RG [auth a],
SB [auth A],
SC [auth A],
SD [auth A],
SE [auth A],
SG [auth a],
TB [auth A],
TC [auth A],
TD [auth A],
UB [auth A],
UC [auth A],
UE [auth A],
UF [auth A],
UG [auth a],
VB [auth A],
VC [auth A],
VD [auth A],
VE [auth A],
VF [auth A],
VG [auth a],
WB [auth A],
WC [auth A],
WD [auth A],
WE [auth A],
WF [auth A],
XB [auth A],
XC [auth A],
XD [auth A],
XE [auth A],
XF [auth A],
XG [auth a],
YB [auth A],
YD [auth A],
YE [auth A],
YF [auth A],
YG [auth a],
ZB [auth A],
ZC [auth A],
ZD [auth A],
ZF [auth A],
ZG [auth a]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

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

Structure Validation

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View more in-depth experimental data

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