2026-09-02 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update REMEDIATION REPOSITORY Metalloprotein remediation STRUCTURE_SUMMARY chem_comp em_admin pdbx_entry_details pdbx_nonpoly_atom_coordination pdbx_nonpoly_atom_coordination_sphere pdbx_nonpoly_atom_coordination_sphere_order _chem_comp.formula _em_admin.last_update _pdbx_entry_details.has_protein_modification PDBe PDBe 2023-06-05 2023-08-16 2023-08-16 2026-09-02 Wellcome Trust 214222/Z/18/Z United Kingdom BtuB3G3 bound to cyanocobalamin with disordered EL8 Silale A Abellon-Ruiz J van den Berg B Cyanocobalamin, transporter, lipoprotein, complex, MEMBRANE PROTEIN Abellon-Ruiz J Jana K Silale A Frey AM Basle A Trost M Kleinekathofer U van den Berg B BtuB TonB-dependent transporters and BtuG surface lipoproteins form stable complexes for vitamin B 12 uptake in gut Bacteroides. Nat Commun UK 14 4714 4714 2023 37543597 doi:10.1038/s41467-023-40427-2 2041-1723 8p97 FULLOVERLAP EMDB EMD-17574 associated EM volume
BtuB3G3 bound to cyanocobalamin with disordered EL8
 Complex of TonB-dependent transporter BtuB3 with surface lipoprotein BtuG3 bound to cyanocobalamin (state 2) Complex of TonB-dependent transporter BtuB3 with surface lipoprotein BtuG3 bound to cyanocobalamin (state 2) 0 1 2 Bacteroides thetaiotaomicron VPI-5482 0.122 TonB-dependent receptor Bacteroides thetaiotaomicron VPI-5482 0.07889060899999999 1 Bacteroides thetaiotaomicron VPI-5482 LEVO MSGQQHSSDNKNWAEKGIVIREVEILGKRPMKDIGVQQTRFDSLVLKENIALSMADILTFNSSIFVKSYGRATLSTVSFR GTSASHTQVTWNGMRINNPMLGMTDFSMIPSYFIDDASLLHGTSSVNMAGGGLGGLVKLSTVPAHQEGFGMQYVQGIGSF STFDEFLQLKYGDKHWQISTRAVYQSSPNDYKYRNHDKKENIYDDKYNIIEQYYPIERNRSGAYKDLHILQEVYYNTGKG DRFGLNAWYTDSNRELALLTTDQGDLMDFENRQREHTLRSVLSWDHTRENWKVSARGGYVHTWLAYDYKRDLGNGIMATM TRSRSKVNTFYGQLDGEYFFSDKLLLTAGVSAHQHLVNSLDKDLNKDDNKNDKYGQGRKNDSIVYFDKGRIELSGNVSLK WQPVNRLGMSLVLRGEMFGTKWAPVIPAFFVDYVLSKRGNIMAKASITRNYRFPTLNDLYFLPGGNPALNNESGFTYETG LSFSVDKDNVYTLSGSASWFDQHINDWIIWLPTSKGFYSPVNLKKVHAYGVEVQADYAVAIDKAWKLGLNGTFAWTPSIN EGEPTSKADQSVGKQLPYIPEYSATLSGRLTYRSWGLLYKWCYYSERYTMTSNAVSYTGHLPPYLMSNVTLEKGFSLRWA DLSLKGTVNNLFDEEYLSVLSRPMPGINFEFFIGITPKWGKKKKGGGHHHHHH Q8A5Z2 Putative surface layer protein Bacteroides thetaiotaomicron VPI-5482 0.041165793 1 LEVO MKRILLSVLFIVFCLTAFVGCMKWDYGKMEPFRATGDGLFIMNEGNFQYGNATLSYYDPETKKVENEIFYRANAMKLGDV AQSMIVRDTIGWVVVNNSHVIFAISTNTFKEVGRITGLTSPRYIHFISDEKAYITQIWDYRIFIVNPKTYQITGYIECPD MTMETGSTEQMVQYGKYVYVNCWSYQNRILKIDTTTDKVVDQLTVGIQPTSLVMDKNFKMWTITDGGYKGSPYGYEEPSL YRIDAETFKIEKQFKFQLGDAPSEVQLNGAGDELYWINKDIWRMSVDEERVPVRPFLKYRDTKYYGLTVSPKNGDVYVAD AIDYQQQGMIYRYTEDGELVDEFYVGIIPGAFCWK Q8A5Z1 CYANOCOBALAMIN 0.001356373 1 CNC singleParticle particle 4 7.5 10.0 HEPES 100.0 NaCl sodium chloride ETHANE 100 277 FEI VITROBOT MARK IV
The protein complex was purified in lauryl maltose neopentyl glycol (LMNG). Prior to making grids, the sample was subjected to size exclusion chromatography without LMNG in the mobile phase to separate protein-LMNG complexes from free LMNG.
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.8 2.3000000000000003 165000.0 FEI TITAN KRIOS AUTOGRID HOLDER TFS Selectris X 10 FEI FALCON IV (4k x 4k) 1 9826 35.6 1 3311038 cryoSPARC 4.1.2 PHASE FLIPPING AND AMPLITUDE CORRECTION 2.75 FSC 0.143 CUT-OFF cryoSPARC 4.1.2 91067 MAXIMUM LIKELIHOOD cryoSPARC 4.1.2 MAXIMUM LIKELIHOOD cryoSPARC 4.1.2 emd_17574.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 378.88 378.88 378.88 90.0 90.0 90.0 X Y Z -0.59504086 0.9735194 0.00005422337 0.022464411 0.74 0.74 0.74 0.163 AUTHOR Sharpened final map 8OKV B PDB experimental model A AlphaFold in silico model RIGID BODY FIT REAL emd_17574_msk_1.map emd_17574_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 378.88 378.88 378.88 90.0 90.0 90.0 X Y Z -1.4366385 1.61277 0.00015601359 0.18661281 0.74 0.74 0.74 AUTHOR Half map A emd_17574_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 378.88 378.88 378.88 90.0 90.0 90.0 X Y Z -1.7832851 1.5950967 0.00015342944 0.18673524 0.74 0.74 0.74 AUTHOR Half map B