2024-01-31 REL RCSB RCSB RCSB 2023-10-04 2024-01-03 2024-01-03 2024-01-31 National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) AI149778 United States National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) AI081059 United States National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) AI153358 United States National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) AI158028 United States Howard Hughes Medical Institute (HHMI) Hanna Gray Fellowship United States Acinetobacter baylyi LptB2FG bound to Acinetobacter baylyi lipopolysaccharide and a macrocyclic peptide Pahil KS Gilman MSA Baidin V Kruse AC Kahne D lipopolysaccharide, ABC, ATPase, antibiotic, macrocyclic peptide, gram-negative bacteria, ESKAPE, Lipid transport Pahil KS Gilman MSA Baidin V Clairfeuille T Mattei P Bieniossek C Dey F Muri D Baettig R Lobritz M Bradley K Kruse AC Kahne D A new antibiotic traps lipopolysaccharide in its intermembrane transporter. Nature UK 625 572 577 2024 38172635 doi:10.1038/s41586-023-06799-7 1476-4687 0006 NATUAS EMD-42206 other EM volume 8ufh FULLOVERLAP Inner membrane lipopolysaccharide transporter composed of LptF, LptG, and two molecules of LptB in complex with lipopolysaccharide and a macrocyclic peptide Inner membrane lipopolysaccharide transporter composed of LptF, LptG, and two molecules of LptB in complex with lipopolysaccharide and a macrocyclic peptide 0 1 2 3 Acinetobacter baylyi ADP1 0.139483 Lipopolysaccharide export system ATP-binding protein LptB Acinetobacter baylyi ADP1 0.029032343999999998 2 Acinetobacter baylyi ADP1 LEVO MHHHHHHHMEQIAQQQPQTLCIKHLAKNYSKRWVVKDVSFEMQSGQIVGLLGPNGAGKTTSFYMVVGLVRMDKGEIHLDN LDLSDLAMHERARKGIGYLPQEASIFRKLTIAENIMAILETRKDLNKQQRQQRLQELLNDFKITHIKDSLGMSVSGGERR RAEIARALAADPKFMLLDEPFAGVDPISVGDIKDIIRNLKDRGIGVLITDHNVRETLAICEHAYIVSEGAVIAEGSPQDI LENEQVRKVYLGDDFTV Q6FC66 Lipopolysaccharide export system permease protein LptF Acinetobacter baylyi ADP1 0.041564273 1 Acinetobacter baylyi ADP1 LEVO MIIRRYLVKQVVSTSLVVIALLTLIMMGGRLIKYFGVAAQGRLDAGVLFSIIGYRMPEFLTLILPLGFFIGLMLVFGRLY VDHEMAVLNGSGISRIRLGQLLIPLALVFLVIQGILMLWMTPWGLRQFDQLSSSQAVRTGFDLVRPKEFISSGPYTIYAG DLSEDRKNLKDIFFYQRAQKEGKPDVMILAKEATRVVMENETANVVDLIQGRRYEIYPGKAKYSQAEFQRYRLRLENDKS ATFETDKVEALPSSKLWNKWNDPVIASEMGWRVFGPFTIVIALMMAVALCEVSPRQGRYYRLIPAIFIFASLIVLLIAIR TRISRDELGVWAYPAALAVYGIAAALFSRKQKLAPKIKKQIKRVRA Q6FFD7 LPS export ABC transporter permease LptG Acinetobacter baylyi ADP1 0.040080621 1 Acinetobacter baylyi ADP1 LEVO MLARRIVAKHVTKTTALAMLGTTIVLVILQVLFTYLGELSNLKADYSAWQAFLYVLWGAPRYLYEILPISALIGAILGLG TLASNSELIVMRSVGISLWRIVGWVIRSALVLVLLSFALSEWVVPYTNERANSVKSHQSVAALGEVRGYWSREGQRFIYV DYANSQGQLKRIQVVDFDDNYRLKSVTNAEQGQFVKDGQWLLNHSQQMAIQGQGDAVLANAAKQPFSLALQPKYVHMVTI DPEDLSFSQLVSFMNYMREYSQVPKTYQLAFWKKVASPFALITLVLVACSFIFGPLRQQSMGFRLVIALFIGLGFYYLQD FLGYASLVYNPSPAWFVLGPIVLMFVAGSYLLYRAR Q6FFD6 (2~{R},4~{R},5~{R},6~{R})-2-[(2~{R},4~{R},5~{R},6~{R})-5-[(2~{S},4~{R},5~{R},6~{R})-4-[(2~{R},3~{R},4~{R},5~{S},6~{S})-3-acetamido-6-carboxy-4,5-bis(oxidanyl)oxan-2-yl]oxy-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-carboxy-5-oxidanyl-oxan-2-yl]oxy-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-carboxy-2-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-4-[(3~{S})-3-dodecanoyloxydodecanoyl]oxy-6-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-5-[[(3~{R})-3-heptanoyloxynonanoyl]amino]-3-oxidanyl-4-[(3~{R})-3-oxidanyloctanoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-5-[[(3~{S})-3-[(3~{R})-3-oxidanyldodecanoyl]oxydecanoyl]amino]-3-phosphonooxy-oxan-2-yl]methoxy]oxan-4-yl]oxy-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-4,5-bis(oxidanyl)oxane-2-carboxylic acid 0.002537735 1 WJW (7S,10S,13S,17P)-10-(4-aminobutyl)-7-(3-aminopropyl)-17-(6-aminopyridin-3-yl)-20-chloro-13-[(1H-indol-3-yl)methyl]-12-methyl-6,7,9,10,12,13,15,16-octahydropyrido[2,3-b][1,5,8,11,14]benzothiatetraazacycloheptadecine-8,11,14(5H)-trione 0.0007974109999999999 1 Y75 singleParticle particle 7 7.4 300.0 NaCl Sodium chloride 20.0 NH2C(CH2OH)3 Tris pH 7.4 0.02 C56H92O25 glyco-diosgenin
300 mM NaCl, 20 mM Tris [pH 7.4], 0.02% GDN, 0.25 mM tris(hydroxypropyl)phosphine, 8 mM imidazole
 ETHANE 100 277 FEI VITROBOT MARK IV
This sample was monodisperse as determined by SEC.
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.1 2.4 GATAN K3 BIOQUANTUM (6k x 4k) 57.3 1 1900000
Ab initio model generated based on the data using cryoSPARC
 3.2 FSC 0.143 CUT-OFF cryoSPARC 503695 RANDOM ASSIGNMENT cryoSPARC MAXIMUM LIKELIHOOD cryoSPARC cryoSPARC emd_42207.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 231.0 231.0 231.0 90.0 90.0 90.0 X Y Z -2.7695599 4.457256 0.0036356798 0.12349392 0.825 0.825 0.825 0.65 AUTHOR Acinetobacter baylyi LptB2FG bound to Acinetobacter baylyi LPS and a macrocyclic peptide. emd_42207_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 231.0 231.0 231.0 90.0 90.0 90.0 X Y Z -1.4449644 2.10236 0.0039999685 0.064533174 0.825 0.825 0.825 AUTHOR Acinetobacter baylyi LptB2FG bound to Acinetobacter baylyi LPS and a macrocyclic peptide. Non-uniform refinement post 3D classification showing variation in macrocyclic peptide conformation. emd_42207_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 231.0 231.0 231.0 90.0 90.0 90.0 X Y Z -1.36218 1.8383484 0.0038026085 0.060423765 0.825 0.825 0.825 AUTHOR Acinetobacter baylyi LptB2FG bound to Acinetobacter baylyi LPS and a macrocyclic peptide. Non-uniform refinement post 3D classification showing variation in macrocyclic peptide conformation. emd_42207_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 231.0 231.0 231.0 90.0 90.0 90.0 X Y Z -2.6504235 4.19521 0.0038272196 0.12756439 0.825 0.825 0.825 AUTHOR Acinetobacter baylyi LptB2FG bound to Acinetobacter baylyi LPS and a macrocyclic peptide. Local refinement with a mask excluding the detergent micelle. emd_42207_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 231.0 231.0 231.0 90.0 90.0 90.0 X Y Z -0.4632908 0.9506351 0.002943334 0.048934538 0.825 0.825 0.825 AUTHOR Acinetobacter baylyi LptB2FG bound to Acinetobacter baylyi LPS and a macrocyclic peptide. Half map B. emd_42207_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 231.0 231.0 231.0 90.0 90.0 90.0 X Y Z -0.4609226 0.977981 0.002939726 0.048939414 0.825 0.825 0.825 AUTHOR Acinetobacter baylyi LptB2FG bound to Acinetobacter baylyi LPS and a macrocyclic peptide. Half map A.