9GHH | pdb_00009ghh

Staphylococcus aureus FusB bound to the large subunit of the S. aureus 70S ribosome (FusB-Sa70S:LSU)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 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 mechanism of FusB-mediated rescue from fusidic acid inhibition of protein synthesis.

Gonzalez-Lopez, A.Ge, X.Larsson, D.S.D.Sihlbom Wallem, C.Sanyal, S.Selmer, M.

(2025) Nat Commun 16: 3693-3693

  • DOI: https://doi.org/10.1038/s41467-025-58902-3
  • Primary Citation of Related Structures:  
    9GHA, 9GHB, 9GHC, 9GHD, 9GHE, 9GHF, 9GHG, 9GHH

  • PubMed Abstract: 

    The antibiotic resistance protein FusB rescues protein synthesis from inhibition by fusidic acid (FA), which locks elongation factor G (EF-G) to the ribosome after GTP hydrolysis. Here, we present time-resolved single-particle cryo-EM structures explaining the mechanism of FusB-mediated rescue. FusB binds to the FA-trapped EF-G on the ribosome, causing large-scale conformational changes of EF-G that break interactions with the ribosome, tRNA, and mRNA. This leads to dissociation of EF-G from the ribosome, followed by FA release. We also observe two independent binding sites of FusB on the classical-state ribosome, overlapping with the binding site of EF-G to each of the ribosomal subunits, yet not inhibiting tRNA delivery. The affinity of FusB to the ribosome and the concentration of FusB in S. aureus during FusB-mediated resistance support that direct binding of FusB to ribosomes could occur in the cell. Our results reveal an intricate resistance mechanism involving specific interactions of FusB with both EF-G and the ribosome, and a non-canonical release pathway of EF-G.


  • Organizational Affiliation

    Department of Cell and Molecular Biology, Uppsala University, BMC, Uppsala, Sweden.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28A [auth 1]62Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29B [auth 2]69Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30C [auth 3]59Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31 type BD [auth 4]84Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL32E [auth 5]57Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL33AF [auth 6]49Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34G [auth 7]45Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35H [auth 8]66Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36I [auth 9]37Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Far1L [auth C]213Staphylococcus aureusMutation(s): 0 
Gene Names: far1fusB
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Find proteins for Q8GNY5 (Staphylococcus aureus)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2O [auth G]277Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3P [auth H]220Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4Q [auth I]207Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5R [auth J]179Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6S [auth K]178Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13T [auth M]145Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14U [auth N]122Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15V [auth O]146Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16W [auth P]144Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17X [auth Q]122Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18Y [auth R]119Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19Z [auth S]116Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20AA [auth T]118Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21BA [auth U]102Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22CA [auth V]117Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23DA [auth W]91Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24EA [auth X]105Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25FA [auth Y]217Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27GA [auth Z]94Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2JA [auth c]255Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3KA [auth d]217Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4LA [auth e]200Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5MA [auth f]166Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6NA [auth g]98Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7OA [auth h]156Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8PA [auth i]132Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9QA [auth j]132Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS10RA [auth k]102Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11SA [auth l]129Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12TA [auth m]137Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13UA [auth n]121Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZVA [auth o]61Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15WA [auth p]89Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16XA [auth q]91Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for Q2FZ45 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FZ45 
Go to UniProtKB:  Q2FZ45
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UniProt GroupQ2FZ45
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17YA [auth r]87Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for Q2FW15 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FW15 
Go to UniProtKB:  Q2FW15
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UniProt GroupQ2FW15
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18ZA [auth s]80Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for Q2G111 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2G111 
Go to UniProtKB:  Q2G111
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UniProt GroupQ2G111
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19AB [auth t]92Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for Q2FW10 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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UniProt GroupQ2FW10
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20BB [auth u]83Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for Q2FXY6 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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UniProt GroupQ2FXY6
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21CB [auth v]58Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for Q2FXZ7 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Go to UniProtKB:  Q2FXZ7
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UniProt GroupQ2FXZ7
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Entity ID: 10
MoleculeChains LengthOrganismImage
23S rRNAJ [auth A]2,923Staphylococcus aureus subsp. aureus NCTC 8325
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Entity ID: 11
MoleculeChains LengthOrganismImage
5S rRNAK [auth B]115Staphylococcus aureus subsp. aureus NCTC 8325
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Entity ID: 13
MoleculeChains LengthOrganismImage
E-site tRNAM [auth D],
N [auth F]
77Escherichia coli K-12
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Entity ID: 33
MoleculeChains LengthOrganismImage
16S rRNAHA [auth a]1,555Staphylococcus aureus subsp. aureus NCTC 8325
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Entity ID: 34
MoleculeChains LengthOrganismImage
mRNAIA [auth b]24Escherichia coli K-12
Sequence Annotations
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PUT
Query on PUT

Download Ideal Coordinates CCD File 
BF [auth A],
CF [auth A]
1,4-DIAMINOBUTANE
C4 H12 N2
KIDHWZJUCRJVML-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
DB [auth 5],
EB [auth 9],
WF [auth C],
XG [auth o]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
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],
BC [auth A],
BD [auth A],
BE [auth A],
BG [auth a],
CC [auth A],
CD [auth A],
CE [auth A],
CG [auth a],
DC [auth A],
DD [auth A],
DE [auth A],
DF [auth A],
DG [auth a],
EC [auth A],
ED [auth A],
EE [auth A],
EF [auth A],
EG [auth a],
FB [auth A],
FC [auth A],
FD [auth A],
FE [auth A],
FF [auth A],
FG [auth a],
GB [auth A],
GC [auth A],
GD [auth A],
GE [auth A],
GF [auth A],
GG [auth a],
HB [auth A],
HC [auth A],
HD [auth A],
HE [auth A],
HF [auth A],
HG [auth a],
IB [auth A],
IC [auth A],
ID [auth A],
IE [auth A],
IF [auth A],
IG [auth a],
JB [auth A],
JC [auth A],
JD [auth A],
JE [auth A],
JF [auth A],
JG [auth a],
KB [auth A],
KC [auth A],
KD [auth A],
KE [auth A],
KF [auth A],
KG [auth a],
LB [auth A],
LC [auth A],
LD [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],
NC [auth A],
ND [auth A],
NE [auth A],
NF [auth A],
NG [auth a],
OB [auth A],
OC [auth A],
OD [auth A],
OE [auth A],
OF [auth A],
OG [auth a],
PB [auth A],
PC [auth A],
PD [auth A],
PE [auth A],
PF [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],
SF [auth A],
SG [auth a],
TB [auth A],
TC [auth A],
TD [auth A],
TE [auth A],
TF [auth A],
TG [auth a],
UB [auth A],
UC [auth A],
UD [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],
WG [auth a],
XB [auth A],
XC [auth A],
XD [auth A],
XE [auth A],
XF [auth F],
YB [auth A],
YC [auth A],
YD [auth A],
YE [auth A],
YF [auth G],
ZB [auth A],
ZC [auth A],
ZD [auth A],
ZE [auth A],
ZF [auth a]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.4.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sven och Lilly Lawskis fond for naturvetenskaplig forskningSweden--
Uppsala Antibiotic CenterSweden--
Swedish Research CouncilSweden2016-06264
Swedish Research CouncilSweden2022-04511

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-26
    Type: Initial release
  • Version 1.1: 2025-04-30
    Changes: Data collection, Database references
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