Core SusCD transporter units from the inactive levan utilisome in the presence of levan fructo-oligosaccharides DP 15-25

2024-10-23 REL PDBe PDBe PDBe 2022-06-29 2023-06-07 2023-06-07 2024-10-23 Wellcome Trust 215064/Z/18/Z United Kingdom Wellcome Trust 214222/Z/18/Z United Kingdom Wellcome Trust 108466/Z/15/Z United Kingdom Core SusCD transporter units from the inactive levan utilisome in the presence of levan fructo-oligosaccharides DP 15-25 White JBR Silale A Ranson NA van den Berg B Membrane protein transporter, glycan transporter, SusCD, utilisome, TonB dependent transporter, TBDT, levan, TRANSPORT PROTEIN White JBR Silale A Feasey M Heunis T Zhu Y Zheng H Gajbhiye A Firbank S Basle A Trost M Bolam DN van den Berg B Ranson NA Outer membrane utilisomes mediate glycan uptake in gut Bacteroidetes. Nature UK 618 583 589 2023 37286596 doi:10.1038/s41586-023-06146-w 1476-4687 0006 NATUAS EMD-15288 other EM volume

Substrate-free levan utilisome

EMD-15289 other EM volume

Levan utilisome with levan FOS DP 8-12

EMD-15290 other EM volume

SusCD core transporter units from the levan utilisome in the presence of levan fructo-oligosaccharides DP 8-12

EMD-15291 other EM volume

Inactive levan utilisation machinery (utilisome) with in the presence of levan fructo-oligosaccharides DP 15-25

8aa3 FULLOVERLAP Inactive levan utilisation machinery (utilisome) in the presence of fructo-oligosaccharides DP 15-25 Inactive levan utilisation machinery (utilisome) in the presence of fructo-oligosaccharides DP 15-25 0 1 2

Sample for EM experiments was the purified levan utilisome (Bt1760-Bt1763). Particle subtraction and focused refinement were used to generate a map of the core SusC2D2 transport unit with bound fructo-oligosaccharides.

Bacteroides thetaiotaomicron SusD homolog Bacteroides thetaiotaomicron VPI-5482 ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 0.065029414 2 LEVO MKKIIYIATIGITLLTTSCDDFLDRQVPQGIVTGDQIASPEYVDNLVISAYAIWATGDDINSSFSLWNYDVRSDDCYKGG SGTEDGGVFNALEISKGINTTDWNINDIWKRLYQCITRANTALQSLDQMDEKTYPLKNQRIAEMRFLRGHAHFMLKQLFK KIVIVNDENMEPDAYNELSNTTYTNDEQWQKIADDFQFAYDNLPEVQIEKGRPAQAAAAAYLAKTYLYKAYRQDGADNAL TGINEEDLKQVVKYTDPLIMAKGGYGLETDYSMNFLPQYENGAESVWAIQYSINDGTYNGNLNWGMGLTTPQILGCCDFH KPSQNLVNAFKTDSQGKPLFSTYDNENYEVATDNVDPRLFHTVGMPGFPYKYNEGYIIQKNDDWSRSKGLYGYYVSLKEN VDPDCDCLKKGSYWASSLNHIVIRYADVLLMRAEALIQLNDGRITDAISLINEVRSRAAGSTMLIFNYKEDYGVNFKVTP YDLKAYAQDEAMKMLKWERRVEFGMESSRFFDLVRWGEAKDVINAYYVTEASRCSIYKNAGFTENKNEYLPVPFEQISAS NGNYTQNFGW Q8A6W4 SusC homolog Bacteroides thetaiotaomicron VPI-5482 ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 0.11548360199999999 2 LEVO MPGIMKNKKLLCSVCFLFAFMSALWGQNITVKGNVTSKTDGQPIIGASVVETTATTNGTITDFDGNFTLSVPVNSTLKIT YIGYKPVTVKAAAIVNVLLEEDTQMVDEVVVTGYTTQRKADLTGAVSVVKVDEIQKQGENNPVKALQGRVPGMNITADGN PSGSATVRIRGIGTLNNNDPLYIIDGVPTKAGMHELNGNDIESIQVLKDAASASIYGSRAANGVIIITTKQGKKGQIKIN FDASVSASMYQSKMNVLNTEQYGRAMWQAYVNDGENPNGNALGYAYNWGYNADGNPVLYGMTLSKYLDSKNTMPVADTDW FDEITRTGVIQQYNLSVSNGSEKGSSFFSLGYYKNLGVIKDTDFDRFSARMNSDYKLIDDILTIGQHFTLNRTSEVQAPG GIIETALDIPSAIPVYASDGSWGGPVGGWPDRRNPRAVLEYNKDNRYTYWRMFGDAYVNLTPFKGFNLRSTFGLDYANKQ ARYFTYPYQEGTQTNNGKSAVEAKQEHWTKWMWNAIATYQLEVGKHRGDVMIGMELNREDDSHFSGYKEDFSILTPDYMW PDAGSGTAQAYGAGEGYSLVSFFGKMNYSYADRYLLSLTLRRDGSSRFGKNHRYATFPSVSLGWRITQENFMKELTWLDD LKLRASWGQTGNQEISNLARYTIYAPNYGTTDSFGGQSYGTAYDITGSNGGGVLPSGFKRNQIGNDNIKWETTTQTNVGI DFSLFKQSLYGSLEYYYKKATDILTEMAGVGVLGEGGSRWINSGAMKNQGFEFNLGYRNKTAFGLTYDLNGNISTYRNEI LELPETVAANGKFGGNGVKSVVGHTYGAQVGYIADGIFKSQDEVDNHATQEGAAVGRIRYRDIDHNGVIDERDQNWIYDP TPSFSYGLNIYLEYKNFDLTMFWQGVQGVDIISDVKKKSDFWSASNVGFLNKGTRLLNAWSPTNPNSDIPALTRSDTNNE QRVSTYFVENGSFLKLRNIQLGYTVPAVISKKMRMDRLRFYCSAQNLLTIKSKNFTGEDPENPNFSYPIPVNITFGLNIG F Q8A6W3 MAGNESIUM ION 2.4305e-05 4 MG singleParticle particle 3 7.5 10.0 HEPES 100.0 NaCl Sodium Chloride 0.03 DDM

Supplemented with 0.5 mM levan fructo-oligosaccharides DP 15-25

Quantifoil R1.2/1.3 COPPER 300 CARBON HOLEY GLOW DISCHARGE 60 OTHER

30 mA current

ETHANE 100 277.15 FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.5 3.0 FEI FALCON III (4k x 4k) COUNTING 37.8 1 C2 2.7 FSC 0.143 CUT-OFF RELION 3.1 120957 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_15292.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 319.50003 319.50003 319.50003 90.0 90.0 90.0 X Y Z -0.09410892 0.23825604 0.00068592123 0.006688675 1.065 1.065 1.065 0.057 AUTHOR ::::EMDATABANK.org::::EMD-15292:::: Sharpened map from post-processing with an ad-hoc low-pass filter of 2.8 A emd_15292_msk_1.map emd_15292_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 319.50003 319.50003 319.50003 90.0 90.0 90.0 X Y Z -0.023361336 0.12775822 0.00029093714 0.0051562623 1.065 1.065 1.065 AUTHOR ::::EMDATABANK.org::::EMD-15292:::: Unsharpened map from 3D refinement emd_15292_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 319.50003 319.50003 319.50003 90.0 90.0 90.0 X Y Z -0.023361336 0.12775822 0.00029093714 0.0051562623 1.065 1.065 1.065 AUTHOR ::::EMDATABANK.org::::EMD-15292:::: Unsharpened map from 3D refinement emd_15292_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 319.50003 319.50003 319.50003 90.0 90.0 90.0 X Y Z -0.023067348 0.13636996 0.00030008634 0.0054810587 1.065 1.065 1.065 AUTHOR ::::EMDATABANK.org::::EMD-15292:::: emd_15292_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 319.50003 319.50003 319.50003 90.0 90.0 90.0 X Y Z -0.0247124 0.1360179 0.00028180744 0.005474611 1.065 1.065 1.065 AUTHOR ::::EMDATABANK.org::::EMD-15292::::