+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10121 | |||||||||
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Title | Cryo-EM structure of LptB2FGC in complex with AMP-PNP | |||||||||
Map data | None | |||||||||
Sample |
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Function / homology | Function and homology information Translocases; Catalysing the translocation of carbohydrates and their derivatives; Linked to the hydrolysis of a nucleoside triphosphate / ATP-binding cassette (ABC) transporter complex / transmembrane transport / ATP hydrolysis activity / ATP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Shigella flexneri (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Tang XD / Chang SH / Luo QH / Zhang ZY / Qiao W / Xu CH / Zhang CB / Niu Y / Yang WX / Wang T ...Tang XD / Chang SH / Luo QH / Zhang ZY / Qiao W / Xu CH / Zhang CB / Niu Y / Yang WX / Wang T / Zhang ZB / Zhu XF / Dong CJ / Zhang X / Dong HH | |||||||||
Citation | Journal: Nat Commun / Year: 2019 Title: Cryo-EM structures of lipopolysaccharide transporter LptBFGC in lipopolysaccharide or AMP-PNP-bound states reveal its transport mechanism. Authors: Xiaodi Tang / Shenghai Chang / Qinghua Luo / Zhengyu Zhang / Wen Qiao / Caihuang Xu / Changbin Zhang / Yang Niu / Wenxian Yang / Ting Wang / Zhibo Zhang / Xiaofeng Zhu / Xiawei Wei / ...Authors: Xiaodi Tang / Shenghai Chang / Qinghua Luo / Zhengyu Zhang / Wen Qiao / Caihuang Xu / Changbin Zhang / Yang Niu / Wenxian Yang / Ting Wang / Zhibo Zhang / Xiaofeng Zhu / Xiawei Wei / Changjiang Dong / Xing Zhang / Haohao Dong / Abstract: Lipopolysaccharides (LPS) of Gram-negative bacteria are critical for the defence against cytotoxic substances and must be transported from the inner membrane (IM) to the outer membrane (OM) through ...Lipopolysaccharides (LPS) of Gram-negative bacteria are critical for the defence against cytotoxic substances and must be transported from the inner membrane (IM) to the outer membrane (OM) through a bridge formed by seven membrane proteins (LptBFGCADE). The IM component LptBFG powers the process through a yet unclarified mechanism. Here we report three high-resolution cryo-EM structures of LptBFG alone and complexed with LptC (LptBFGC), trapped in either the LPS- or AMP-PNP-bound state. The structures reveal conformational changes between these states and substrate binding with or without LptC. We identify two functional transmembrane arginine-containing loops interacting with the bound AMP-PNP and elucidate allosteric communications between the domains. AMP-PNP binding induces an inward rotation and shift of the transmembrane helices of LptFG and LptC to tighten the cavity, with the closure of two lateral gates, to eventually expel LPS into the bridge. Functional assays reveal the functionality of the LptF and LptG periplasmic domains. Our findings shed light on the LPS 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_10121.map.gz | 20.5 MB | EMDB map data format | |
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Header (meta data) | emd-10121-v30.xml emd-10121.xml | 16.7 KB 16.7 KB | Display Display | EMDB header |
Images | emd_10121.png | 54.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10121 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10121 | HTTPS FTP |
-Related structure data
Related structure data | 6s8gMC 6s8hC 6s8nC 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_10121.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : LptB2FGC
Entire | Name: LptB2FGC |
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Components |
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-Supramolecule #1: LptB2FGC
Supramolecule | Name: LptB2FGC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / Details: LPS transporter LptB2FGC |
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Source (natural) | Organism: Shigella flexneri (bacteria) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: Lipopolysaccharide ABC transporter, ATP-binding protein LptB
Macromolecule | Name: Lipopolysaccharide ABC transporter, ATP-binding protein LptB type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Shigella flexneri (bacteria) |
Molecular weight | Theoretical: 26.837668 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MATLTAKNLA KAYKGRRVVE DVSLTVNSGE IVGLLGPNGA GKTTTFYMVV GIVPRDAGNI IIDDDDISLL PLHARARRGI GYLPQEASI FRRLSVYDNL MAVLQIRDDL SAEQREDRAN ELMEEFHIEH LRDSMGQSLS GGERRRVEIA RALAANPKFI L LDEPFAGV ...String: MATLTAKNLA KAYKGRRVVE DVSLTVNSGE IVGLLGPNGA GKTTTFYMVV GIVPRDAGNI IIDDDDISLL PLHARARRGI GYLPQEASI FRRLSVYDNL MAVLQIRDDL SAEQREDRAN ELMEEFHIEH LRDSMGQSLS GGERRRVEIA RALAANPKFI L LDEPFAGV DPISVIDIKR IIEHLRDSGL GVLITDHNVR ETLAVCERAY IVSQGHLIAH GTPTEILQDE HVKRVYLGED FR L |
-Macromolecule #2: LPS export ABC transporter permease LptF
Macromolecule | Name: LPS export ABC transporter permease LptF / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Shigella flexneri (bacteria) |
Molecular weight | Theoretical: 40.45352 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MIIIRYLVRE TLKSQLAILF ILLLIFFCQK LVRILGAAVD GDIPANLVLS LLGLGVPEMA QLILPLSLFL GLLMTLGKLY TESEITVMH ACGLSKAVLV KAAMILAVFT AIVAAVNVMW AGPWSSRHQD EVLEEAKANP GMAALAQGQF QQATNGSSVL F IESVDGSD ...String: MIIIRYLVRE TLKSQLAILF ILLLIFFCQK LVRILGAAVD GDIPANLVLS LLGLGVPEMA QLILPLSLFL GLLMTLGKLY TESEITVMH ACGLSKAVLV KAAMILAVFT AIVAAVNVMW AGPWSSRHQD EVLEEAKANP GMAALAQGQF QQATNGSSVL F IESVDGSD FKDVFLAQIR PKGNARPSVV VADSGHLTQL RDGSQVVTLN QGTRFEGTAL LRDFRITDFQ DYQAIIGHQA VA LDPNDTD QMDMRTLWNT DTDRARAELN WRITLVVTVF MMALMVVPLS VVNPRQGRVL SMLPAMLLYL LFFLIQTSLK SNG GKGKLD PTLWMWTVNL IYLALAIVLN LWDTVFVRRL RASFSRKGAV |
-Macromolecule #3: Inner membrane protein yjgQ
Macromolecule | Name: Inner membrane protein yjgQ / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Shigella flexneri (bacteria) |
Molecular weight | Theoretical: 39.622414 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MQPFGVLDRY IGKTIFTTIM MTLFMLVSLS GIIKFVDQLK KAGQGSYDAL GAGMYTLLSV PKDVQIFFPM AALLGALLGL GMLAQRSEL VVMQASGFTR MQVALSVMKT AIPLVLLTMA IGEWVAPQGE QMARNYRAQA MYGGSLLSTQ QGLWAKDGNN F VYIERVKG ...String: MQPFGVLDRY IGKTIFTTIM MTLFMLVSLS GIIKFVDQLK KAGQGSYDAL GAGMYTLLSV PKDVQIFFPM AALLGALLGL GMLAQRSEL VVMQASGFTR MQVALSVMKT AIPLVLLTMA IGEWVAPQGE QMARNYRAQA MYGGSLLSTQ QGLWAKDGNN F VYIERVKG DEVLGGISIY AFNENRRLQS VRYAATAKFD PEHKVWRLSQ VDESDLTNPK QITGSQTVSG TWKTDLTPDK LG VVALDPD ALSISGLHNY VKYLKSSGQD AGRYQLNMWS KIFQPLSVAV MMLMALSFIF GPLRSVPMGV RVVTGISFGF VFY VLDQIF GPLTLVYGIP PIIGALLPSA SFFLISLWLL MRKS |
-Macromolecule #4: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Macromolecule | Name: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 4 / Number of copies: 2 / Formula: ANP |
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Molecular weight | Theoretical: 506.196 Da |
Chemical component information | ChemComp-ANP: |
-Macromolecule #5: tetradecyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside
Macromolecule | Name: tetradecyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside type: ligand / ID: 5 / Number of copies: 1 / Formula: LMD |
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Molecular weight | Theoretical: 538.669 Da |
Chemical component information | ChemComp-LMD: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL | ||||||||
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Buffer | pH: 7.8 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: EMAN2 (ver. 4) |
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Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 149178 |