+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11883 | |||||||||
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Title | LolCDE apo structure | |||||||||
Map data | ||||||||||
Sample |
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Keywords | LolCDE / lipoprotein / lipoprotein transporter / lipoprotein sorting and transport / PROTEIN TRANSPORT | |||||||||
Function / homology | Function and homology information lipoprotein releasing activity / protein localization to outer membrane / lipoprotein localization to outer membrane / lipoprotein transport / plasma membrane protein complex / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / transmembrane transport / membrane => GO:0016020 ...lipoprotein releasing activity / protein localization to outer membrane / lipoprotein localization to outer membrane / lipoprotein transport / plasma membrane protein complex / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / transmembrane transport / membrane => GO:0016020 / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) / Escherichia coli (strain K12) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Tang XD / Chang SH | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2021 Title: Structural basis for bacterial lipoprotein relocation by the transporter LolCDE. Authors: Xiaodi Tang / Shenghai Chang / Ke Zhang / Qinghua Luo / Zhengyu Zhang / Ting Wang / Wen Qiao / Chen Wang / Chongrong Shen / Zhibo Zhang / Xiaofeng Zhu / Xiawei Wei / Changjiang Dong / Xing ...Authors: Xiaodi Tang / Shenghai Chang / Ke Zhang / Qinghua Luo / Zhengyu Zhang / Ting Wang / Wen Qiao / Chen Wang / Chongrong Shen / Zhibo Zhang / Xiaofeng Zhu / Xiawei Wei / Changjiang Dong / Xing Zhang / Haohao Dong / Abstract: Lipoproteins in the outer membrane of Gram-negative bacteria are involved in various vital physiological activities, including multidrug resistance. Synthesized in the cytoplasm and matured in the ...Lipoproteins in the outer membrane of Gram-negative bacteria are involved in various vital physiological activities, including multidrug resistance. Synthesized in the cytoplasm and matured in the inner membrane, lipoproteins must be transported to the outer membrane through the Lol pathway mediated by the ATP-binding cassette transporter LolCDE in the inner membrane via an unknown mechanism. Here, we report cryo-EM structures of Escherichia coli LolCDE in apo, lipoprotein-bound, LolA-bound, ADP-bound and AMP-PNP-bound states at a resolution of 3.2-3.8 Å, covering the complete lipoprotein transport cycle. Mutagenesis and in vivo viability assays verify features of the structures and reveal functional residues and structural characteristics of LolCDE. The results provide insights into the mechanisms of sorting and transport of outer-membrane lipoproteins and may guide the development of novel therapies against multidrug-resistant Gram-negative bacteria. | |||||||||
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_11883.map.gz | 3.3 MB | EMDB map data format | |
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Header (meta data) | emd-11883-v30.xml emd-11883.xml | 15.7 KB 15.7 KB | Display Display | EMDB header |
Images | emd_11883.png | 49.7 KB | ||
Filedesc metadata | emd-11883.cif.gz | 6.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11883 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11883 | HTTPS FTP |
-Validation report
Summary document | emd_11883_validation.pdf.gz | 381.6 KB | Display | EMDB validaton report |
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Full document | emd_11883_full_validation.pdf.gz | 381.2 KB | Display | |
Data in XML | emd_11883_validation.xml.gz | 5.7 KB | Display | |
Data in CIF | emd_11883_validation.cif.gz | 6.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11883 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11883 | HTTPS FTP |
-Related structure data
Related structure data | 7ariMC 7arhC 7arjC 7arkC 7arlC 7armC 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_11883.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.014 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : LolCDE apo structure
Entire | Name: LolCDE apo structure |
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Components |
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-Supramolecule #1: LolCDE apo structure
Supramolecule | Name: LolCDE apo structure / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Escherichia coli (E. coli) / Strain: K12 |
-Macromolecule #1: Lipoprotein-releasing ABC transporter permease subunit LolC
Macromolecule | Name: Lipoprotein-releasing ABC transporter permease subunit LolC type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12 |
Molecular weight | Theoretical: 43.295516 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
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 ABC transporter permease subunit LolC |
-Macromolecule #2: Lipoprotein-releasing system transmembrane protein LolE
Macromolecule | Name: Lipoprotein-releasing system transmembrane protein LolE type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12 |
Molecular weight | Theoretical: 45.385977 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
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 |
-Macromolecule #3: Lipoprotein-releasing system ATP-binding protein LolD
Macromolecule | Name: Lipoprotein-releasing system ATP-binding protein LolD / type: protein_or_peptide / ID: 3 / 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: Escherichia coli (strain K12) (bacteria) / Strain: K12 |
Molecular weight | Theoretical: 26.576465 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
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 LMGAEHHHHH HH H UniProtKB: Lipoprotein-releasing system ATP-binding protein LolD |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 4 mg/mL |
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Buffer | pH: 7.8 / Details: 20 mM Tris-HCl, pH 7.8, 150 mM NaCl and 0.05% LMNG |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % |
Details | Three protein complex |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Phase plate: VOLTA PHASE PLATE |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model |
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Output model | PDB-7ari: |