NorA in complex with Fab36 (NorA-BRIL fusion)

2025-06-25 REL RCSB INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update RCSB RCSB 2024-03-19 2024-12-11 2024-12-11 2025-06-25 National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) R01AI165782 United States National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) AI108889 United States National Science Foundation (NSF, United States) MCB1902449 United States National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS) R01NS108151 United States National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) R01DK135088 United States NorA in complex with Fab36 (NorA-BRIL fusion) Xie P Li Y Kuang H Wang DN Traaseth NJ membrane protein, Staphylococcus aureus, antibiotic resistance, efflux pump, TRANSPORT PROTEIN, TRANSPORT PROTEIN-IMMUNE SYSTEM complex Xie P Li Y Lamon G Kuang H Wang DN Traaseth NJ A fiducial-assisted strategy compatible with resolving small MFS transporter structures in multiple conformations using cryo-EM. Nat Commun UK 16 7 7 2025 39746942 doi:10.1038/s41467-024-54986-5 2041-1723 9b3k FULLOVERLAP NorA-BRIL(3A)-Fab36-FabBRIL NorA-BRIL(3A)-Fab36-FabBRIL 0 1 2 3

FabBRIL was added but not built in model due to masking. Here is its sequence: Heavy chain: SEVQLVESGGGLVQPGGSLRLSCAASGFNVVDFSLHWVRQAPGKGLEWVAYISSSSGSTSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARWGYWPGEPWWKAFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS Light chain: DIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQYLYYSLVTFGQGTKVEIKRTVAAPSVFIFPPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG

Staphylococcus aureus NorA-BRIL(3A) fusion Staphylococcus aureus 0.053388516000000004

NorA-BRIL(3A) fusion details: M1 to R380 is NorA domain; A381 to A383 is the 3A linker; A384 to L490 is Bril domain (most residues for Bril domain were not built since a mask was added only around NorA domain during data processing)

1 Escherichia coli BL21(DE3) LEVO MNKQIFVLYFNIFLIFLGIGLVIPVLPVYLKDLGLTGSDLGLLVAAFALSQMIISPFGGTLADKLGKKLIICIGLILFSV SEFMFAVGHNFSVLMLSRVIGGMSAGMVMPGVTGLIADISPSHQKAKNFGYMSAIINSGFILGPGIGGFMAEVSHRMPFY FAGALGILAFIMSIVLIHDPKKSTTSGFQKLEPQLLTKINWKVFITPVILTLVLSFGLSAFETLYSLYTADKVNYSPKDI SIAITGGGIFGALFQIYFFDKFMKYFSELTFIAWSLLYSVVVLILLVFANDYWSIMLISFVVFIGFDMIRPAITNYFSNI AGERQGFAGGLNSTFTSMGNFIGPLIAGALFDVHIEAPIYMAIGVSLAGVVIVLIEKQHRAAAADLEDNWETLNDNLKVI EKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTT RNAYIQKYL Q53459 Fab36 heavy chain Homo sapiens 0.028044464999999998 1 Escherichia coli LEVO MKKNIAFLLASMFVFSIATNAYAEISEVQLVESGGGLVQPGGSLRLSCAASGFTFSSSSIHWVRQAPGKGLEWVASISSS SGSTSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARYSRYYYYAWRVGGYWGGLDYWGQGTLVTVFNQIKGP SVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVN HKPSNTKVDKKVEPKSCDKTHT Fab36 light chain Homo sapiens 0.025794859 1 Escherichia coli LEVO MKKNIAFLLASMFVFSIATNAYASDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYS GVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQSSSSLITFGQGTKVEIKRTVAAPSVFIFPPSDSQLKSGTASVVCLL NNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC singleParticle particle 7.5 400.0 NaCl Sodium Chloride 20.0 tris(hydroxymethyl)aminomethane

400 mM NaCl, 20 mM Tris

Quantifoil R1.2/1.3 GOLD 300 GOLD HOLEY GLOW DISCHARGE 25 OTHER

hold for 10 sec before 25sec glow discharging

ETHANE 100 281 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 100.0 2.7 1.0 1.8 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 77.0 77.0 GATAN K3 BIOQUANTUM (6k x 4k) 5760 4092 1.2 55.54 1 4031695

Topaz Training

cryoSPARC v3.3.1 Patch CTF estimation (multi) was used for CTF correction

Patch CTF estimation (multi) was used for CTF correction

PHASE FLIPPING AND AMPLITUDE CORRECTION

Ab-initio reconstruction

1 2.56 FSC 0.143 CUT-OFF cryoSPARC v3.3.1 298088 OTHER cryoSPARC v3.3.1

Branch-and-bound maximum likelihood

OTHER cryoSPARC v3.3.1

Branch-and-bound Maximum likelihood

3 103066.0 cryoSPARC v3.3.1

3 classes have 298088, 3733, and 7378 particles respectively

emd_44143.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 297.0 297.0 297.0 90.0 90.0 90.0 X Y Z -1.7745634 2.5826147 -0.00018061617 0.037735958 0.825 0.825 0.825 0.0788 AUTHOR ::::EMDATABANK.org::::EMD-44143:::: 7LO8 PDB experimental model RIGID BODY FIT REAL emd_44143_msk_1.map emd_44143_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 297.0 297.0 297.0 90.0 90.0 90.0 X Y Z -0.26606575 0.7386157 0.00031554134 0.01978463 0.825 0.825 0.825 AUTHOR ::::EMDATABANK.org::::EMD-44143:::: emd_44143_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 297.0 297.0 297.0 90.0 90.0 90.0 X Y Z -0.26580796 0.7468729 0.00030657367 0.019770365 0.825 0.825 0.825 AUTHOR ::::EMDATABANK.org::::EMD-44143::::