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Open data
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Basic information
Entry | ![]() | ||||||||||||
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Title | LolCDE-apo in nanodiscs | ||||||||||||
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![]() | membrane protein / ABC transporter | ||||||||||||
Function / homology | ![]() lipoprotein releasing activity / protein localization to outer membrane / lipoprotein localization to outer membrane / plasma membrane protein complex / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / lipoprotein transport / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / transmembrane transport / outer membrane-bounded periplasmic space ...lipoprotein releasing activity / protein localization to outer membrane / lipoprotein localization to outer membrane / plasma membrane protein complex / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / lipoprotein transport / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / transmembrane transport / outer membrane-bounded periplasmic space / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | ||||||||||||
![]() | Luo QS / Bei WW / Shi HG | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structures of LolCDE reveal the molecular mechanism of bacterial lipoprotein sorting in Escherichia coli. Authors: Weiwei Bei / Qingshan Luo / Huigang Shi / Haizhen Zhou / Min Zhou / Xinzheng Zhang / Yihua Huang / ![]() Abstract: Bacterial lipoproteins perform a diverse array of functions including bacterial envelope biogenesis and microbe-host interactions. Lipoproteins in gram-negative bacteria are sorted to the outer ...Bacterial lipoproteins perform a diverse array of functions including bacterial envelope biogenesis and microbe-host interactions. Lipoproteins in gram-negative bacteria are sorted to the outer membrane (OM) via the localization of lipoproteins (Lol) export pathway. The ATP-binding cassette (ABC) transporter LolCDE initiates the Lol pathway by selectively extracting and transporting lipoproteins for trafficking. Here, we report cryo-EM structures of LolCDE in apo, lipoprotein-bound, and AMPPNP-bound states at a resolution of 3.5 to 4.2 Å. Structure-based disulfide crosslinking, photo-crosslinking, and functional complementation assay verify the apo-state structure and reveal the molecular details regarding substrate selectivity and substrate entry route. Our studies snapshot 3 functional states of LolCDE in a transport cycle, providing deep insights into the mechanisms that underlie LolCDE-mediated lipoprotein sorting in E. coli. | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 25.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.2 KB 13.2 KB | Display Display | ![]() |
Images | ![]() | 110.2 KB | ||
Filedesc metadata | ![]() | 5.8 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 590.4 KB | Display | ![]() |
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Full document | ![]() | 590.1 KB | Display | |
Data in XML | ![]() | 5.6 KB | Display | |
Data in CIF | ![]() | 6.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7v8mMC ![]() 7v8iC ![]() 7v8lC C: citing same article ( M: atomic model generated by this map |
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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: 1.36 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 : LolCDE-apo in nanodiscs
Entire | Name: LolCDE-apo in nanodiscs |
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Components |
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-Supramolecule #1: LolCDE-apo in nanodiscs
Supramolecule | Name: LolCDE-apo in nanodiscs / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Lipoprotein-releasing system transmembrane protein LolC
Macromolecule | Name: Lipoprotein-releasing system transmembrane protein LolC type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 43.295516 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MYQPVALFIG LRYMRGRAAD RFGRFVSWLS TIGITLGVMA LVTVLSVMNG FERELQNNIL GLMPQAILSS EHGSLNPQQL PETAVKLDG VNRVAPITTG DVVLQSARSV AVGVMLGIDP AQKDPLTPYL VNVKQTDLEP GKYNVILGEQ LASQLGVNRG D QIRVMVPS ...String: MYQPVALFIG LRYMRGRAAD RFGRFVSWLS TIGITLGVMA LVTVLSVMNG FERELQNNIL GLMPQAILSS EHGSLNPQQL PETAVKLDG VNRVAPITTG DVVLQSARSV AVGVMLGIDP AQKDPLTPYL VNVKQTDLEP GKYNVILGEQ LASQLGVNRG D QIRVMVPS ASQFTPMGRI PSQRLFNVIG TFAANSEVDG YEMLVNIEDA SRLMRYPAGN ITGWRLWLDE PLKVDSLSQQ KL PEGSKWQ DWRDRKGELF QAVRMEKNMM GLLLSLIVAV AAFNIITSLG LMVMEKQGEV AILQTQGLTP RQIMMVFMVQ GAS AGIIGA ILGAALGALL ASQLNNLMPI IGVLLDGAAL PVAIEPLQVI VIALVAMAIA LLSTLYPSWR AAATQPAEAL RYE UniProtKB: Lipoprotein-releasing system transmembrane protein LolC |
-Macromolecule #2: Lipoprotein-releasing system ATP-binding protein LolD
Macromolecule | Name: Lipoprotein-releasing system ATP-binding protein LolD / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO EC number: Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 25.471291 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MNKILLQCDN LCKRYQEGSV QTDVLHNVSF SVGEGEMMAI VGSSGSGKST LLHLLGGLDT PTSGDVIFNG QPMSKLSSAA KAELRNQKL GFIYQFHHLL PDFTALENVA MPLLIGKKKP AEINSRALEM LKAVGLDHRA NHRPSELSGG ERQRVAIARA L VNNPRLVL ...String: MNKILLQCDN LCKRYQEGSV QTDVLHNVSF SVGEGEMMAI VGSSGSGKST LLHLLGGLDT PTSGDVIFNG QPMSKLSSAA KAELRNQKL GFIYQFHHLL PDFTALENVA MPLLIGKKKP AEINSRALEM LKAVGLDHRA NHRPSELSGG ERQRVAIARA L VNNPRLVL ADEPTGNLDA RNADSIFQLL GELNRLQGTA FLVVTHDLQL AKRMSRQLEM RDGRLTAELS LMGAE UniProtKB: Lipoprotein-releasing system ATP-binding protein LolD |
-Macromolecule #3: Lipoprotein-releasing system transmembrane protein LolE
Macromolecule | Name: Lipoprotein-releasing system transmembrane protein LolE type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 45.385977 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MAMPLSLLIG LRFSRGRRRG GMVSLISVIS TIGIALGVAV LIVGLSAMNG FERELNNRIL AVVPHGEIEA VDQPWTNWQE ALDHVQKVP GIAAAAPYIN FTGLVESGAN LRAIQVKGVN PQQEQRLSAL PSFVQGDAWR NFKAGEQQII IGKGVADALK V KQGDWVSI ...String: MAMPLSLLIG LRFSRGRRRG GMVSLISVIS TIGIALGVAV LIVGLSAMNG FERELNNRIL AVVPHGEIEA VDQPWTNWQE ALDHVQKVP GIAAAAPYIN FTGLVESGAN LRAIQVKGVN PQQEQRLSAL PSFVQGDAWR NFKAGEQQII IGKGVADALK V KQGDWVSI MIPNSNPEHK LMQPKRVRLH VAGILQLSGQ LDHSFAMIPL ADAQQYLDMG SSVSGIALKM TDVFNANKLV RD AGEVTNS YVYIKSWIGT YGYMYRDIQM IRAIMYLAMV LVIGVACFNI VSTLVMAVKD KSGDIAVLRT LGAKDGLIRA IFV WYGLLA GLFGSLCGVI IGVVVSLQLT PIIEWIEKLI GHQFLSSDIY FIDFLPSELH WLDVFYVLVT ALLLSLLASW YPAR RASNI DPARVLSGQ UniProtKB: Lipoprotein-releasing system transmembrane protein LolE |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Grid | Model: Quantifoil R2/2 / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: NITROGEN / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: LEICA EM GP |
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Electron microscopy
Microscope | FEI TITAN |
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Image recording | Film or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
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Image processing
Startup model | Type of model: PDB ENTRY |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 137445 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |