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 inward-open conformation (NorA-BRIL fusion) Xie P Li Y Kuang H Wang DN Traaseth NJ membrane protein, Staphylococcus aureus, antibiotic resistance, efflux pump, TRANSPORT PROTEIN 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 9b3m FULLOVERLAP NorA-BRIL(3A)-FabBRIL NorA-BRIL(3A)-FabBRIL 0 1
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 singleParticle particle 5.0 400.0 NaCl Sodium Chloride 50.0 Sodium Acetate
400 mM NaCl, 50 mM sodium acetate, pH 5.0
 Quantifoil R1.2/1.3 GOLD 300 GOLD HOLEY GLOW DISCHARGE 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 1812072
Topaz Training
 cryoSPARC v3.3.1 Patch CTF estimation
Patch CTF estimation (multi) was used for CTF correction
PHASE FLIPPING AND AMPLITUDE CORRECTION
Ab0initio reconstruction
 1 3.21 FSC 0.143 CUT-OFF cryoSPARC v3.3.1 159621 OTHER cryoSPARC v3.3.1
Branch-and-bound Maximum Likelihood
 OTHER cryoSPARC v3.3.1
Branch-and-bound Maximum Likelihood
 2 cryoSPARC v3.3.1
2 classes contain 53756 and 105865 particles respectively
 emd_44145.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 264.0 264.0 264.0 90.0 90.0 90.0 X Y Z -1.7279979 2.5843928 0.00005060106 0.0375483 0.825 0.825 0.825 0.0902 AUTHOR Other other
Alphafold2 prediction
 RIGID BODY FIT REAL emd_44145_msk_1.map emd_44145_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 264.0 264.0 264.0 90.0 90.0 90.0 X Y Z -0.45621547 0.9387956 0.0007622037 0.02994919 0.825 0.825 0.825 AUTHOR emd_44145_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 264.0 264.0 264.0 90.0 90.0 90.0 X Y Z -0.45338857 0.93087864 0.0007407988 0.030134065 0.825 0.825 0.825 AUTHOR