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Open data
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Basic information
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Title | Substrate-free levan utilisation machinery (utilisome) | ||||||||||||
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![]() | Membrane protein transporter / glycan transporter / SusCD / utilisome / TonB dependent transporter / TBDT / TRANSPORT PROTEIN / levan | ||||||||||||
Function / homology | ![]() beta-fructofuranosidase / hydrolase activity, hydrolyzing O-glycosyl compounds / cell outer membrane / carbohydrate metabolic process / metal ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||||||||
![]() | White JBR / Silale A / Ranson NA / van den Berg B | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Outer membrane utilisomes mediate glycan uptake in gut Bacteroidetes. Authors: Joshua B R White / Augustinas Silale / Matthew Feasey / Tiaan Heunis / Yiling Zhu / Hong Zheng / Akshada Gajbhiye / Susan Firbank / Arnaud Baslé / Matthias Trost / David N Bolam / Bert van ...Authors: Joshua B R White / Augustinas Silale / Matthew Feasey / Tiaan Heunis / Yiling Zhu / Hong Zheng / Akshada Gajbhiye / Susan Firbank / Arnaud Baslé / Matthias Trost / David N Bolam / Bert van den Berg / Neil A Ranson / ![]() Abstract: Bacteroidetes are abundant members of the human microbiota, utilizing a myriad of diet- and host-derived glycans in the distal gut. Glycan uptake across the bacterial outer membrane of these bacteria ...Bacteroidetes are abundant members of the human microbiota, utilizing a myriad of diet- and host-derived glycans in the distal gut. Glycan uptake across the bacterial outer membrane of these bacteria is mediated by SusCD protein complexes, comprising a membrane-embedded barrel and a lipoprotein lid, which is thought to open and close to facilitate substrate binding and transport. However, surface-exposed glycan-binding proteins and glycoside hydrolases also play critical roles in the capture, processing and transport of large glycan chains. The interactions between these components in the outer membrane are poorly understood, despite being crucial for nutrient acquisition by our colonic microbiota. Here we show that for both the levan and dextran utilization systems of Bacteroides thetaiotaomicron, the additional outer membrane components assemble on the core SusCD transporter, forming stable glycan-utilizing machines that we term utilisomes. Single-particle cryogenic electron microscopy structures in the absence and presence of substrate reveal concerted conformational changes that demonstrate the mechanism of substrate capture, and rationalize the role of each component in the utilisome. | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 9.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 22.4 KB 22.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.7 KB | Display | ![]() |
Images | ![]() | 64.7 KB | ||
Masks | ![]() | 103 MB | ![]() | |
Others | ![]() ![]() ![]() | 78.6 MB 78.7 MB 78.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 691.4 KB | Display | ![]() |
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Full document | ![]() | 690.9 KB | Display | |
Data in XML | ![]() | 18 KB | Display | |
Data in CIF | ![]() | 23.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8a9yMC ![]() 7znrC ![]() 7znsC ![]() 8aa0C ![]() 8aa1C ![]() 8aa2C ![]() 8aa3C ![]() 8aa4C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.065 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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-Additional map: Unsharpened map from masked 3D refinement
File | emd_15288_additional_1.map | ||||||||||||
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Annotation | Unsharpened map from masked 3D refinement | ||||||||||||
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-Half map: Post-processed map with ad-hoc lowpass filter of 3.6 A
File | emd_15288_half_map_1.map | ||||||||||||
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Annotation | Post-processed map with ad-hoc lowpass filter of 3.6 A | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_15288_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Substrate-free levan utilisation machinery (utilisome)
Entire | Name: Substrate-free levan utilisation machinery (utilisome) |
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Components |
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-Supramolecule #1: Substrate-free levan utilisation machinery (utilisome)
Supramolecule | Name: Substrate-free levan utilisation machinery (utilisome) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 Details: Sample for EM experiments was the purified levan utilisome composed of Bt1760-Bt1763. Bt1762 lipoprotein subunits were masked out in refinement and are therefore not present in the associated assembly. |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Glycoside hydrolase family 32
Macromolecule | Name: Glycoside hydrolase family 32 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() Strain: ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50 |
Molecular weight | Theoretical: 59.299926 KDa |
Sequence | String: MMKNMILPIA FTALIASMTA CSDETDPILT QKNWDGTATY FQSSDEHGFS MYYKPQVGFV GDPMPFYDPV AKDFKVMYLQ DYRPNPEAT YHPIFGVATK DGATYESLGE LISCGGRDEQ DAAIGTGGTI YNPADKLYYT FYTGNKFKPS SDQNAQVVMV A TSPDFKTW ...String: MMKNMILPIA FTALIASMTA CSDETDPILT QKNWDGTATY FQSSDEHGFS MYYKPQVGFV GDPMPFYDPV AKDFKVMYLQ DYRPNPEAT YHPIFGVATK DGATYESLGE LISCGGRDEQ DAAIGTGGTI YNPADKLYYT FYTGNKFKPS SDQNAQVVMV A TSPDFKTW TKNRTFYLKG DTYGYDKNDF RDPFLFQTED GVYHMLIATR KNGKGHIAEF TSADLKEWES AGTFMTMMWD RF YECPDVF KMGDWWYLIY SEQASFMRKV QYFKGRTLED LKATTANDAG IWPDNREGML DSRAFYAGKT ASDGTNRYIW GWC PTRAGN DNGNVGDVEP EWAGNLVAQR LIQHEDGTLT LGVPDAIDRK YTSAQEVKVM AKDGNMIESG KTYTLGEGAS VIFN RLKVH NKISFTVKTA SNTDRFGISF VRGTDSASWY SIHVNADEGK ANFEKDGDDA KYLFDNKFNI PADNEYRVTI YSDQS VCVT YINDQLSFTN RIYQMQKNPW SLCCYKGEIT VSDVQVSTY |
-Macromolecule #2: DUF4960 domain-containing protein
Macromolecule | Name: DUF4960 domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() Strain: ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50 |
Molecular weight | Theoretical: 50.429227 KDa |
Sequence | String: MKSIIKQLYT ILLVTVACLT VTGCSDDFKS GLRLDGDVWV NSIRLDEYAG TVDYQNKAIV VGVPYDYDIT RMVVTEMNLS EGAKASIAI GETIDFSLPV SLTVKNGDVQ MSYTITVKRD EAKILTFKLN DTYVGKVDQL SKTISVVVPL TVDITQLKGT F TVTDGATV ...String: MKSIIKQLYT ILLVTVACLT VTGCSDDFKS GLRLDGDVWV NSIRLDEYAG TVDYQNKAIV VGVPYDYDIT RMVVTEMNLS EGAKASIAI GETIDFSLPV SLTVKNGDVQ MSYTITVKRD EAKILTFKLN DTYVGKVDQL SKTISVVVPL TVDITQLKGT F TVTDGATV TPASGSIQDF TNPVTYTATY RSAVTPYVVT VTQGNVIPTA FVGTASSVSL LTSPEEKAAA QWMMDNVSMS EY ISFKDVV DGKVDLGKYT AIWWHFHADN GDNPPLPDDA KAAAEKFKVY YQNGGNLLLT RYATFYIANL GIAKDERVPN NSW GGNEDS PEITSAPWSF LITGSESHPL FQDLRWKDGD KSTVYTCDAG YAITNSTAQW HIGTDWGGYD DLNAWRNLTG GIDL AHGGD GAVVIAEFEP RSNSGRTLCI GSGCYDWYGK GVDASADYYH YNVEQMTLNA INYLCK |
-Macromolecule #3: SusC homolog
Macromolecule | Name: SusC homolog / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() Strain: ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50 |
Molecular weight | Theoretical: 115.483602 KDa |
Sequence | String: MPGIMKNKKL LCSVCFLFAF MSALWGQNIT VKGNVTSKTD GQPIIGASVV ETTATTNGTI TDFDGNFTLS VPVNSTLKIT YIGYKPVTV KAAAIVNVLL EEDTQMVDEV VVTGYTTQRK ADLTGAVSVV KVDEIQKQGE NNPVKALQGR VPGMNITADG N PSGSATVR ...String: MPGIMKNKKL LCSVCFLFAF MSALWGQNIT VKGNVTSKTD GQPIIGASVV ETTATTNGTI TDFDGNFTLS VPVNSTLKIT YIGYKPVTV KAAAIVNVLL EEDTQMVDEV VVTGYTTQRK ADLTGAVSVV KVDEIQKQGE NNPVKALQGR VPGMNITADG N PSGSATVR IRGIGTLNNN DPLYIIDGVP TKAGMHELNG NDIESIQVLK DAASASIYGS RAANGVIIIT TKQGKKGQIK IN FDASVSA SMYQSKMNVL NTEQYGRAMW QAYVNDGENP NGNALGYAYN WGYNADGNPV LYGMTLSKYL DSKNTMPVAD TDW FDEITR TGVIQQYNLS VSNGSEKGSS FFSLGYYKNL GVIKDTDFDR FSARMNSDYK LIDDILTIGQ HFTLNRTSEV QAPG GIIET ALDIPSAIPV YASDGSWGGP VGGWPDRRNP RAVLEYNKDN RYTYWRMFGD AYVNLTPFKG FNLRSTFGLD YANKQ ARYF TYPYQEGTQT NNGKSAVEAK QEHWTKWMWN AIATYQLEVG KHRGDVMIGM ELNREDDSHF SGYKEDFSIL TPDYMW PDA GSGTAQAYGA GEGYSLVSFF GKMNYSYADR YLLSLTLRRD GSSRFGKNHR YATFPSVSLG WRITQENFMK ELTWLDD LK LRASWGQTGN QEISNLARYT IYAPNYGTTD SFGGQSYGTA YDITGSNGGG VLPSGFKRNQ IGNDNIKWET TTQTNVGI D FSLFKQSLYG SLEYYYKKAT DILTEMAGVG VLGEGGSRWI NSGAMKNQGF EFNLGYRNKT AFGLTYDLNG NISTYRNEI LELPETVAAN GKFGGNGVKS VVGHTYGAQV GYIADGIFKS QDEVDNHATQ EGAAVGRIRY RDIDHNGVID ERDQNWIYDP TPSFSYGLN IYLEYKNFDL TMFWQGVQGV DIISDVKKKS DFWSASNVGF LNKGTRLLNA WSPTNPNSDI PALTRSDTNN E QRVSTYFV ENGSFLKLRN IQLGYTVPAV ISKKMRMDRL RFYCSAQNLL TIKSKNFTGE DPENPNFSYP IPVNITFGLN IG F |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 3 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 |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 35.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.3000000000000003 µm / Nominal defocus min: 1.5 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |