+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11273 | ||||||||||||||||||
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Title | Open-open state of the Bt1762-Bt1763 levan transport system | ||||||||||||||||||
Map data | Map filtered by local resolution | ||||||||||||||||||
Sample |
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Function / homology | Function and homology information | ||||||||||||||||||
Biological species | Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||||||||||||||
Authors | White JBR / van den Berg B / Ranson NA | ||||||||||||||||||
Funding support | United Kingdom, Switzerland, 5 items
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Citation | Journal: Nat Commun / Year: 2021 Title: Insights into SusCD-mediated glycan import by a prominent gut symbiont. Authors: Declan A Gray / Joshua B R White / Abraham O Oluwole / Parthasarathi Rath / Amy J Glenwright / Adam Mazur / Michael Zahn / Arnaud Baslé / Carl Morland / Sasha L Evans / Alan Cartmell / ...Authors: Declan A Gray / Joshua B R White / Abraham O Oluwole / Parthasarathi Rath / Amy J Glenwright / Adam Mazur / Michael Zahn / Arnaud Baslé / Carl Morland / Sasha L Evans / Alan Cartmell / Carol V Robinson / Sebastian Hiller / Neil A Ranson / David N Bolam / Bert van den Berg / Abstract: In Bacteroidetes, one of the dominant phyla of the mammalian gut, active uptake of large nutrients across the outer membrane is mediated by SusCD protein complexes via a "pedal bin" transport ...In Bacteroidetes, one of the dominant phyla of the mammalian gut, active uptake of large nutrients across the outer membrane is mediated by SusCD protein complexes via a "pedal bin" transport mechanism. However, many features of SusCD function in glycan uptake remain unclear, including ligand binding, the role of the SusD lid and the size limit for substrate transport. Here we characterise the β2,6 fructo-oligosaccharide (FOS) importing SusCD from Bacteroides thetaiotaomicron (Bt1762-Bt1763) to shed light on SusCD function. Co-crystal structures reveal residues involved in glycan recognition and suggest that the large binding cavity can accommodate several substrate molecules, each up to ~2.5 kDa in size, a finding supported by native mass spectrometry and isothermal titration calorimetry. Mutational studies in vivo provide functional insights into the key structural features of the SusCD apparatus and cryo-EM of the intact dimeric SusCD complex reveals several distinct states of the transporter, directly visualising the dynamics of the pedal bin transport mechanism. | ||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11273.map.gz | 42.7 MB | EMDB map data format | |
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Header (meta data) | emd-11273-v30.xml emd-11273.xml | 20.2 KB 20.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11273_fsc.xml | 9.5 KB | Display | FSC data file |
Images | emd_11273.png | 46 KB | ||
Masks | emd_11273_msk_1.map | 70.2 MB | Mask map | |
Others | emd_11273_additional_1.map.gz emd_11273_additional_2.map.gz | 7 MB 53.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11273 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11273 | HTTPS FTP |
-Related structure data
Related structure data | 6zltMC 6ytcC 6z8iC 6z9aC 6zazC 6zluC 6zm1C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_11273.map.gz / Format: CCP4 / Size: 70.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Map filtered by local resolution | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_11273_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Post-processed map output from RELION
File | emd_11273_additional_1.map | ||||||||||||
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Annotation | Post-processed map output from RELION | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 3D refine map output from RELION
File | emd_11273_additional_2.map | ||||||||||||
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Annotation | 3D refine map output from RELION | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Dimeric Bt1762-Bt1763 levan transporter complex
Entire | Name: Dimeric Bt1762-Bt1763 levan transporter complex |
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Components |
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-Supramolecule #1: Dimeric Bt1762-Bt1763 levan transporter complex
Supramolecule | Name: Dimeric Bt1762-Bt1763 levan transporter complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Molecular weight | Theoretical: 360 KDa |
-Supramolecule #2: SusD homolog
Supramolecule | Name: SusD homolog / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria) |
Recombinant expression | Organism: Bacteroides thetaiotaomicron (bacteria) |
-Supramolecule #3: SusC homolog
Supramolecule | Name: SusC homolog / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria) |
-Macromolecule #1: SusD homolog
Macromolecule | Name: SusD homolog / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria) |
Molecular weight | Theoretical: 64.17816 KDa |
Recombinant expression | Organism: Bacteroides thetaiotaomicron (bacteria) |
Sequence | String: CDDFLDRQVP QGIVTGDQIA SPEYVDNLVI SAYAIWATGD DINSSFSLWN YDVRSDDCYK GGSGTEDGGV FNALEISKGI NTTDWNIND IWKRLYQCIT RANTALQSLD QMDEKTYPLK NQRIAEMRFL RGHAHFMLKQ LFKKIVIVND ENMEPDAYNE L SNTTYTND ...String: CDDFLDRQVP QGIVTGDQIA SPEYVDNLVI SAYAIWATGD DINSSFSLWN YDVRSDDCYK GGSGTEDGGV FNALEISKGI NTTDWNIND IWKRLYQCIT RANTALQSLD QMDEKTYPLK NQRIAEMRFL RGHAHFMLKQ LFKKIVIVND ENMEPDAYNE L SNTTYTND EQWQKIADDF QFAYDNLPEV QIEKGRPAQA AAAAYLAKTY LYKAYRQDGA DNALTGINEE DLKQVVKYTD PL IMAKGGY GLETDYSMNF LPQYENGAES VWAIQYSIND GTYNGNLNWG MGLTTPQILG CCDFHKPSQN LVNAFKTDSQ GKP LFSTYD NENYEVATDN VDPRLFHTVG MPGFPYKYNE GYIIQKNDDW SRSKGLYGYY VSLKENVDPD CDCLKKGSYW ASSL NHIVI RYADVLLMRA EALIQLNDGR ITDAISLINE VRSRAAGSTM LIFNYKEDYG VNFKVTPYDL KAYAQDEAMK MLKWE RRVE FGMESSRFFD LVRWGEAKDV INAYYVTEAS RCSIYKNAGF TENKNEYLPV PFEQISASNG NYTQNFGWAA AAHHHH HH |
-Macromolecule #2: SusC homolog
Macromolecule | Name: SusC homolog / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria) |
Molecular weight | Theoretical: 103.915227 KDa |
Sequence | String: VVVTGYTTQR KADLTGAVSV VKVDEIQKQG ENNPVKALQG RVPGMNITAD GNPSGSATVR IRGIGTLNNN DPLYIIDGVP TKAGMHELN GNDIESIQVL KDAASASIYG SRAANGVIII TTKQGKKGQI KINFDASVSA SMYQSKMNVL NTEQYGRAMW Q AYVNDGEN ...String: VVVTGYTTQR KADLTGAVSV VKVDEIQKQG ENNPVKALQG RVPGMNITAD GNPSGSATVR IRGIGTLNNN DPLYIIDGVP TKAGMHELN GNDIESIQVL KDAASASIYG SRAANGVIII TTKQGKKGQI KINFDASVSA SMYQSKMNVL NTEQYGRAMW Q AYVNDGEN PNGNALGYAY NWGYNADGNP VLYGMTLSKY LDSKNTMPVA DTDWFDEITR TGVIQQYNLS VSNGSEKGSS FF SLGYYKN LGVIKDTDFD RFSARMNSDY KLIDDILTIG QHFTLNRTSE VQAPGGIIET ALDIPSAIPV YASDGSWGGP VGG WPDRRN PRAVLEYNKD NRYTYWRMFG DAYVNLTPFK GFNLRSTFGL DYANKQARYF TYPYQEGTQT NNGKSAVEAK QEHW TKWMW NAIATYQLEV GKHRGDVMIG MELNREDDSH FSGYKEDFSI LTPDYMWPDA GSGTAQAYGA GEGYSLVSFF GKMNY SYAD RYLLSLTLRR DGSSRFGKNH RYATFPSVSL GWRITQENFM KELTWLDDLK LRASWGQTGN QEISNLARYT IYAPNY GTT DSFGGQSYGT AYDITGSNGG GVLPSGFKRN QIGNDNIKWE TTTQTNVGID FSLFKQSLYG SLEYYYKKAT DILTEMA GV GVLGEGGSRW INSGAMKNQG FEFNLGYRNK TAFGLTYDLN GNISTYRNEI LELPETVAAN GKFGGNGVKS VVGHTYGA Q VGYIADGIFK SQDEVDNHAT QEGAAVGRIR YRDIDHNGVI DERDQNWIYD PTPSFSYGLN IYLEYKNFDL TMFWQGVQG VDIISDVKKK SDFWSASNVG FLNKGTRLLN AWSPTNPNSD IPALTRSDTN NEQRVSTYFV ENGSFLKLRN IQLGYTVPAV ISKKMRMDR LRFYCSAQNL LTIKSKNFTG EDPENPNFSY PIPVNITFGL NIGF |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.02 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 63.84 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |