+Open data
-Basic information
Entry | Database: PDB / ID: 7lo8 | |||||||||||||||||||||||||||
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Title | NorA in complex with Fab36 | |||||||||||||||||||||||||||
Components |
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Keywords | TRANSPORT PROTEIN / efflux pump / antibiotic resistance | |||||||||||||||||||||||||||
Function / homology | Function and homology information | |||||||||||||||||||||||||||
Biological species | Staphylococcus aureus (bacteria) Homo sapiens (human) | |||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.16 Å | |||||||||||||||||||||||||||
Authors | Brawley, D.N. / Sauer, D.B. / Song, J.M. / Koide, A. / Koide, S. / Traaseth, N.J. / Wang, D.N. | |||||||||||||||||||||||||||
Funding support | United States, 8items
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Citation | Journal: Nat Chem Biol / Year: 2022 Title: Structural basis for inhibition of the drug efflux pump NorA from Staphylococcus aureus. Authors: Douglas N Brawley / David B Sauer / Jianping Li / Xuhui Zheng / Akiko Koide / Ganesh S Jedhe / Tiffany Suwatthee / Jinmei Song / Zheng Liu / Paramjit S Arora / Shohei Koide / Victor J Torres ...Authors: Douglas N Brawley / David B Sauer / Jianping Li / Xuhui Zheng / Akiko Koide / Ganesh S Jedhe / Tiffany Suwatthee / Jinmei Song / Zheng Liu / Paramjit S Arora / Shohei Koide / Victor J Torres / Da-Neng Wang / Nathaniel J Traaseth / Abstract: Membrane protein efflux pumps confer antibiotic resistance by extruding structurally distinct compounds and lowering their intracellular concentration. Yet, there are no clinically approved drugs to ...Membrane protein efflux pumps confer antibiotic resistance by extruding structurally distinct compounds and lowering their intracellular concentration. Yet, there are no clinically approved drugs to inhibit efflux pumps, which would potentiate the efficacy of existing antibiotics rendered ineffective by drug efflux. Here we identified synthetic antigen-binding fragments (Fabs) that inhibit the quinolone transporter NorA from methicillin-resistant Staphylococcus aureus (MRSA). Structures of two NorA-Fab complexes determined using cryo-electron microscopy reveal a Fab loop deeply inserted in the substrate-binding pocket of NorA. An arginine residue on this loop interacts with two neighboring aspartate and glutamate residues essential for NorA-mediated antibiotic resistance in MRSA. Peptide mimics of the Fab loop inhibit NorA with submicromolar potency and ablate MRSA growth in combination with the antibiotic norfloxacin. These findings establish a class of peptide inhibitors that block antibiotic efflux in MRSA by targeting indispensable residues in NorA without the need for membrane permeability. | |||||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7lo8.cif.gz | 154.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lo8.ent.gz | 123.2 KB | Display | PDB format |
PDBx/mmJSON format | 7lo8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7lo8_validation.pdf.gz | 748.9 KB | Display | wwPDB validaton report |
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Full document | 7lo8_full_validation.pdf.gz | 756.5 KB | Display | |
Data in XML | 7lo8_validation.xml.gz | 28.2 KB | Display | |
Data in CIF | 7lo8_validation.cif.gz | 41.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lo/7lo8 ftp://data.pdbj.org/pub/pdb/validation_reports/lo/7lo8 | HTTPS FTP |
-Related structure data
Related structure data | 23464MC 7lo7C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 42353.238 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) Gene: norA, tetA, tetA_2, BTN44_09105, DD547_00670, DQV53_04080, EP54_04170, EQ90_03440, FA040_06730, G0V24_03995, G0X12_10865, G0Z18_04370, G6Y10_04720, GO746_14090, GO803_07545, GO805_01365, GO821_ ...Gene: norA, tetA, tetA_2, BTN44_09105, DD547_00670, DQV53_04080, EP54_04170, EQ90_03440, FA040_06730, G0V24_03995, G0X12_10865, G0Z18_04370, G6Y10_04720, GO746_14090, GO803_07545, GO805_01365, GO821_08105, GO894_15090, GO942_03500, HMPREF2819_04810, HMPREF3211_00604, NCTC10654_00801, NCTC10702_01167, NCTC10988_00893, NCTC9944_00776, RK64_04180, SAMEA1029528_00668, SAMEA1029547_01044, SAMEA1029553_00751, SAMEA1964876_01266, SAMEA1965205_01031, SAMEA1966505_00819, SAMEA1969349_01052, SAMEA1969845_01011, SAMEA1971706_01410, SAMEA1972827_00559, SAMEA2076212_00937, SAMEA2076218_00794, SAMEA2076220_00416, SAMEA2076226_00094, SAMEA2076463_00402, SAMEA2076464_00402, SAMEA2076470_00989, SAMEA2076472_00906, SAMEA2076478_00948, SAMEA2076480_00403, SAMEA2076481_00754, SAMEA2076743_00851, SAMEA2076745_01198, SAMEA2076746_00709, SAMEA2076747_00402, SAMEA2076749_01092, SAMEA2076751_00767, SAMEA2076752_01693, SAMEA2076755_01477, SAMEA2076756_01730, SAMEA2076758_01750, SAMEA2076759_01476, SAMEA2076761_01673, SAMEA2076762_01568, SAMEA2076763_01005, SAMEA2076764_01192, SAMEA2076765_00813, SAMEA2077023_01193, SAMEA2077025_00963, SAMEA2077027_00992, SAMEA2077029_00946, SAMEA2077031_00749, SAMEA2077034_01532, SAMEA2077035_00441, SAMEA2077039_00933, SAMEA2077040_00402, SAMEA2077041_01231, SAMEA2077044_01041, SAMEA2077045_01087, SAMEA2077046_01075, SAMEA2077293_01085, SAMEA2077294_01001, SAMEA2077295_01088, SAMEA2077297_00893, SAMEA2077300_01388, SAMEA2077301_01079, SAMEA2077302_01294, SAMEA2077303_01165, SAMEA2077307_01110, SAMEA2077832_01179, SAMEA2078252_00991, SAMEA2078256_00442, SAMEA2078307_00767, SAMEA2078308_00437, SAMEA2078553_00705, SAMEA2078558_00440, SAMEA2078560_00441, SAMEA2078569_01033, SAMEA2078570_00726, SAMEA2078572_00766, SAMEA2078824_00440, SAMEA2078837_00724, SAMEA2079048_01019, SAMEA2079051_00890, SAMEA2079277_00570, SAMEA2079291_00132, SAMEA2079503_00716, SAMEA2079507_01569, SAMEA2079512_00399, SAMEA2079517_00401, SAMEA2079724_00193, SAMEA2079727_00743, SAMEA2079728_01205, SAMEA2079732_00659, SAMEA2079742_00929, SAMEA2079946_00528, SAMEA2079949_00512, SAMEA2079951_00193, SAMEA2079952_00660, SAMEA2079957_00881, SAMEA2079958_00559, SAMEA2079960_00657, SAMEA2079961_00193, SAMEA2079968_00614, SAMEA2080329_00094, SAMEA2080330_00193, SAMEA2080334_00929, SAMEA2080433_00981, SAMEA2080812_00715, SAMEA2080898_00727, SAMEA2080900_00662, SAMEA2080904_00710, SAMEA2080913_00729, SAMEA2081043_01808, SAMEA2081053_01006, SAMEA2081054_00654, SAMEA2081055_00993, SAMEA2081060_00553, SAMEA2081211_01079, SAMEA2081213_00399, SAMEA2081218_00473, SAMEA2081341_00094, SAMEA2081342_00612, SAMEA2081349_00936, SAMEA2081359_00094, SAMEA2081362_00860, SAMEA2081468_00628, SAMEA2081474_00441, SAMEA2081475_00651, SAMEA2081476_01465, SAMEA2081479_01707, SAMEA2081480_01854, SAMEA2081560_01571, SAMEA2081561_01009, SAMEA2081564_00963, SAMEA2081567_00976, SAMEA2081568_01004, SAMEA2081569_00706, SAMEA2081570_00962, SAMEA2081571_00711, SAMEA2081572_00947, SAMEA2081573_00955, SAMEA2081575_01082, SAMEA2081577_00891, SAMEA2081578_00766, SAMEA2081579_01168, SAMEA2081581_01073, SAMEA2081582_01166, SAMEA2081673_00935, SAMEA2081674_00934, SAMEA958766_00618, SAMEA958770_01028, SAMEA958772_00649, SAMEA958778_01022, SAMEA958779_00094, SAMEA958785_00651, SAMEA958793_00683, SAMEA958798_00328, SAMEA958804_01063, SAMEA958810_00661, SAMEA958836_01276, SAMEA958838_00069, SAMEA958845_00683, SAMEA958846_00694, SAMEA958848_01177, SAMEA958855_00578, SAMEA958858_00913, SAMEA958870_01324, SAMEA958898_01209, SAMEA958906_00445, SAMEA958925_01036, SAMEA958951_01582, SAMEA958953_00694, SAMEA958961_00691, SAMEA958979_00607, SAMEA958987_00401, SAMEA958995_00511 Plasmid: pET28a / Details (production host): C-term 10 His tag / Cell (production host): E. coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: Q53459 |
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#2: Antibody | Mass: 28044.465 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
#3: Antibody | Mass: 25794.859 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: NorA:Fab36 complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Staphylococcus aureus (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 55.54 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 311335 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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