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- EMDB-12990: Cryo-EM structure of N. gonorhoeae LptDE in complex with ProMacro... -
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Basic information
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Title | Cryo-EM structure of N. gonorhoeae LptDE in complex with ProMacrobodies | |||||||||
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Function / homology | ![]() lipopolysaccharide transport / Gram-negative-bacterium-type cell outer membrane assembly / carbohydrate transmembrane transporter activity / : / cell outer membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
![]() | Botte M / Ni D / Schenck S / Zimmermann I / Chami M / Bocquet N / Egloff P / Bucher D / Trabuco M / Cheng RKY ...Botte M / Ni D / Schenck S / Zimmermann I / Chami M / Bocquet N / Egloff P / Bucher D / Trabuco M / Cheng RKY / Brunner JD / Seeger MA / Stahlberg H / Hennig M | |||||||||
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![]() | ![]() Title: Cryo-EM structures of a LptDE transporter in complex with Pro-macrobodies offer insight into lipopolysaccharide translocation. Authors: Mathieu Botte / Dongchun Ni / Stephan Schenck / Iwan Zimmermann / Mohamed Chami / Nicolas Bocquet / Pascal Egloff / Denis Bucher / Matilde Trabuco / Robert K Y Cheng / Janine D Brunner / ...Authors: Mathieu Botte / Dongchun Ni / Stephan Schenck / Iwan Zimmermann / Mohamed Chami / Nicolas Bocquet / Pascal Egloff / Denis Bucher / Matilde Trabuco / Robert K Y Cheng / Janine D Brunner / Markus A Seeger / Henning Stahlberg / Michael Hennig / ![]() ![]() Abstract: Lipopolysaccharides are major constituents of the extracellular leaflet in the bacterial outer membrane and form an effective physical barrier for environmental threats and for antibiotics in Gram- ...Lipopolysaccharides are major constituents of the extracellular leaflet in the bacterial outer membrane and form an effective physical barrier for environmental threats and for antibiotics in Gram-negative bacteria. The last step of LPS insertion via the Lpt pathway is mediated by the LptD/E protein complex. Detailed insights into the architecture of LptDE transporter complexes have been derived from X-ray crystallography. However, no structure of a laterally open LptD transporter, a transient state that occurs during LPS release, is available to date. Here, we report a cryo-EM structure of a partially opened LptDE transporter in complex with rigid chaperones derived from nanobodies, at 3.4 Å resolution. In addition, a subset of particles allows to model a structure of a laterally fully opened LptDE complex. Our work offers insights into the mechanism of LPS insertion, provides a structural framework for the development of antibiotics targeting LptD and describes a highly rigid chaperone scaffold to enable structural biology of challenging protein targets. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.9 KB 14.9 KB | Display Display | ![]() |
Images | ![]() | 89 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 308.9 KB | Display | ![]() |
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Full document | ![]() | 308.5 KB | Display | |
Data in XML | ![]() | 7.1 KB | Display | |
Data in CIF | ![]() | 8.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ommMC ![]() 7omtC 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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Voxel size | X=Y=Z: 0.88308 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
-Entire : Cryo-EM structure of N. gonorhoeae LptDE in complex with ProMacro...
Entire | Name: Cryo-EM structure of N. gonorhoeae LptDE in complex with ProMacrobodies |
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Components |
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-Supramolecule #1: Cryo-EM structure of N. gonorhoeae LptDE in complex with ProMacro...
Supramolecule | Name: Cryo-EM structure of N. gonorhoeae LptDE in complex with ProMacrobodies type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: LPS-assembly protein LptD
Macromolecule | Name: LPS-assembly protein LptD / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 87.65693 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MARLFSLKPL VLSLGFCFGT HCAADTVAAE EADGRVAEGG AQGASESAQA SDLTLGSTCL FCSNESGSPE RTEAAVQGSG EASVPEDYT RIVADRMEGQ SKVKVRAEGS VIIERDGAVL NTDWADYDQS GDTVTVGDRF ALQQDGTLIR GETLTYNLDQ Q TGEAHNVR ...String: MARLFSLKPL VLSLGFCFGT HCAADTVAAE EADGRVAEGG AQGASESAQA SDLTLGSTCL FCSNESGSPE RTEAAVQGSG EASVPEDYT RIVADRMEGQ SKVKVRAEGS VIIERDGAVL NTDWADYDQS GDTVTVGDRF ALQQDGTLIR GETLTYNLDQ Q TGEAHNVR METEQGGRRL QSVSRTAEML GEGRYKLTET QFNTCSAGDA GWYVKAASVE ADRGKGIGVA KHAAFVFGGV PL FYTPWAD FPLDGNRKSG LLVPSVSAGS DGVSLSVPYY FNLAPNFDAT FAPGIIGERG ATFDGQIRYL RPDYSGQTDL TWL PHDKKS GRNNRYQAKW QHRHDISDTL QAGVDFNQVS DSGYYRDFYG GEEIAGNVNL NRRVWLDYGG RAAGGSLNAG LSVQ KYQTL ANQSGYKDEP YAIMPRLSAD WHKNAGRAQI GVSAQFTRFS HDGRQDGSRL VVYPGIKWDF SNSWGYVRPK LGLHA TYYS LDSFGGKASR SVGRVLPVVN IDGGTTFERN TRLFGGGVVQ TIEPRLFYNY IPAKSQNDLP NFDSSESSFG YGQLFR ENL YYGNDRINAA NSLSTAVQSR ILDGATGEER FRAGIGQKFY FKDDAVMLDG SVGKNPRSRS DWVAFASGGI GGRFTLD SS IHYNQNDKRA EHYAVGAGYR PAPGKVLNAR YKYGRNEKIY LQADGSYFYD KLSQLDLSAQ WPLTRNLSAV VRYNYGFE A KKPIEMLAGA EYKSSCGCWG AGVYAQRYVT GENTYKNAVF FSLQLKDLSS VGRNPAGRMD VAVPGYIPAH SLSAGRNKR P |
-Macromolecule #2: LPS-assembly lipoprotein LptE
Macromolecule | Name: LPS-assembly lipoprotein LptE / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 18.499066 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MNKIFLTAAA LVLGACGFHL KGADGISPPL TYRSWHIEGG QALQFPLETA LYQASGRVDD AAGAQMTLRI DSVSQNKETY TVTRAAVIN EYLLILTVEA QVLKRGEPVG KPMTVSVRRI LDYADNEILG KQEEEETLWA EMRQDVAEQI VRRLTFLKAE H HHHHH |
-Macromolecule #3: ProMacrobody 21,Maltodextrin-binding protein
Macromolecule | Name: ProMacrobody 21,Maltodextrin-binding protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 56.714457 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GPSQVQLVES GGGLVQPGGS LRLSCAASGF PVKYEHMYWY RQAPGKEREW VAAINSAGNE THYADSVKGR FTISRDNAKN TVYLQMNSL KPEDTAVYYC NVKDIGWWAA YDYWGQGTQV TVPPLVIWIN GDKGYNGLAE VGKKFEKDTG IKVTVEHPDK L EEKFPQVA ...String: GPSQVQLVES GGGLVQPGGS LRLSCAASGF PVKYEHMYWY RQAPGKEREW VAAINSAGNE THYADSVKGR FTISRDNAKN TVYLQMNSL KPEDTAVYYC NVKDIGWWAA YDYWGQGTQV TVPPLVIWIN GDKGYNGLAE VGKKFEKDTG IKVTVEHPDK L EEKFPQVA ATGDGPDIIF WAHDRFGGYA QSGLLAEITP DKAFQDKLYP FTWDAVRYNG KLIAYPIAVE ALSLIYNKDL LP NPPKTWE EIPALDKELK AKGKSALMFN LQEPYFTWPL IAADGGYAFK YENGKYDIKD VGVDNAGAKA GLTFLVDLIK NKH MNADTD YSIAEAAFNK GETAMTINGP WAWSNIDTSK VNYGVTVLPT FKGQPSKPFV GVLSAGINAA SPNKELAKEF LENY LLTDE GLEAVNKDKP LGAVALKSYE EELAKDPRIA ATMENAQKGE IMPNIPQMSA FWYAVRTAVI NAASGRQTVD EALKD AQTP GSGGGSAWSH PQFEKGGGSG GGSGGSAWSH PQFEKA |
-Macromolecule #4: ProMacrobody 51,Maltodextrin-binding protein
Macromolecule | Name: ProMacrobody 51,Maltodextrin-binding protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 56.86159 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GPSQVQLVES GGGSVQAGGS LRLSCAASGS ISSITYLGWF RQAPGKEREG VAALATYYGH TYYADSVKGR FTVSLDNAKN TVYLQMNSL KPEDTALYYC AAAYSGIWTP LGVWATYEYW GQGTQVTVPP LVIWINGDKG YNGLAEVGKK FEKDTGIKVT V EHPDKLEE ...String: GPSQVQLVES GGGSVQAGGS LRLSCAASGS ISSITYLGWF RQAPGKEREG VAALATYYGH TYYADSVKGR FTVSLDNAKN TVYLQMNSL KPEDTALYYC AAAYSGIWTP LGVWATYEYW GQGTQVTVPP LVIWINGDKG YNGLAEVGKK FEKDTGIKVT V EHPDKLEE KFPQVAATGD GPDIIFWAHD RFGGYAQSGL LAEITPDKAF QDKLYPFTWD AVRYNGKLIA YPIAVEALSL IY NKDLLPN PPKTWEEIPA LDKELKAKGK SALMFNLQEP YFTWPLIAAD GGYAFKYENG KYDIKDVGVD NAGAKAGLTF LVD LIKNKH MNADTDYSIA EAAFNKGETA MTINGPWAWS NIDTSKVNYG VTVLPTFKGQ PSKPFVGVLS AGINAASPNK ELAK EFLEN YLLTDEGLEA VNKDKPLGAV ALKSYEEELA KDPRIAATME NAQKGEIMPN IPQMSAFWYA VRTAVINAAS GRQTV DEAL KDAQTPGSGG GSAWSHPQFE KGGGSGGGSG GSAWSHPQFE KA |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 184206 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |