+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10122 | |||||||||
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Title | Cryo-EM structure of LptB2FG in complex with LPS | |||||||||
Map data | ||||||||||
Sample |
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Keywords | lipopolysaccharide transporter / LPS / LptB2FGC / LptB / LptBFG / outer membrane / Gram-negative bacteria / ABC transporter / Inner membrane protein complex / TRANSPORT PROTEIN | |||||||||
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: 3.7 Å | |||||||||
Authors | Tang XD / Chang SH | |||||||||
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_10122.map.gz | 15.7 MB | EMDB map data format | |
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Header (meta data) | emd-10122-v30.xml emd-10122.xml | 18.1 KB 18.1 KB | Display Display | EMDB header |
Images | emd_10122.png | 55.5 KB | ||
Filedesc metadata | emd-10122.cif.gz | 6.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10122 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10122 | HTTPS FTP |
-Related structure data
Related structure data | 6s8hMC 6s8gC 6s8nC C: citing same article (ref.) M: atomic model generated by this map |
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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_10122.map.gz / Format: CCP4 / Size: 22.2 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 : LptB2FG
Entire | Name: LptB2FG |
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Components |
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-Supramolecule #1: LptB2FG
Supramolecule | Name: LptB2FG / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / Details: LPS transporter LptB2FG in complex with LPS |
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Source (natural) | Organism: Shigella flexneri (bacteria) |
-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 UniProtKB: Lipopolysaccharide export system ATP-binding protein LptB |
-Macromolecule #2: Lipopolysaccharide export system permease protein LptF
Macromolecule | Name: Lipopolysaccharide export system permease protein 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: 40.34543 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MIIIRYLVRE TLKSQLAILF ILLLIFFCQK LVRILGAAVD GDIPANLVLS LLGLGVPEMA QLILPLSLFL GLLMTLGKLY TESEITVMH ACGLSKAVLV KAAMILAVFT AIVAAVNVMW AGPWSSRHQD EVLAEAKANP GMAALAQGQF QQATNGSSVL F IESVDGSD ...String: MIIIRYLVRE TLKSQLAILF ILLLIFFCQK LVRILGAAVD GDIPANLVLS LLGLGVPEMA QLILPLSLFL GLLMTLGKLY TESEITVMH ACGLSKAVLV KAAMILAVFT AIVAAVNVMW AGPWSSRHQD EVLAEAKANP GMAALAQGQF QQATNGSSVL F IESVDGSD FKDVFLAQIR PKGNARPSVV VADSGHLTQL RDGSQVVTLN QGTRFEGTAL LRDFRITDFQ DYQAIIGHQA VA LDPNDTD QMDMRTLWNT DTDRARAELN WRITLVVTVF MMALMVVPLS VVNPRQGRVL SMLPAMLLYL LFFLIQTSLK SNG GKGKLD PTLWMWTVNL IYLALAIVLN LWDTVPVRRL RASFSRKGAV UniProtKB: Lipopolysaccharide export system permease protein LptF |
-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 UniProtKB: Inner membrane protein yjgQ |
-Macromolecule #4: Lauryl Maltose Neopentyl Glycol
Macromolecule | Name: Lauryl Maltose Neopentyl Glycol / type: ligand / ID: 4 / Number of copies: 2 / Formula: LMN |
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Molecular weight | Theoretical: 1.005188 KDa |
Chemical component information | ChemComp-AV0: |
-Macromolecule #5: (2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-[(...
Macromolecule | Name: (2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-[(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-5-[(2~{S},3~{S},4~{R},5~{R},6~{R})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl] ...Name: (2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-[(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-5-[(2~{S},3~{S},4~{R},5~{R},6~{R})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-4-[(2~{R},3~{S},4~{R},5~{S},6~{R})-6-[(1~{S})-2-[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-1-oxidanyl-ethyl]-3,4-bis(oxidanyl)-5-phosphonooxy-oxan-2-yl]oxy-3-oxidanyl-5-phosphonooxy-oxan-2-yl]oxy-2-carboxy-2-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-5-[[(3~{R})-3-dodecanoyloxytetradecanoyl]amino]-6-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-3-oxidanyl-5-[[(3~{R})-3-oxidanyltetradecanoyl]amino]-4-[(3~{R})-3-oxidanyltetradecanoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-3-phosphonooxy-4-[(3~{R})-3-tetradecanoyloxytetradecanoyl]oxy-oxan-2-yl]methoxy]oxan-4-yl]oxy-4,5-bis(oxidanyl)oxane-2-carboxylic acid type: ligand / ID: 5 / Number of copies: 1 / Formula: JSG |
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Molecular weight | Theoretical: 2.975178 KDa |
Chemical component information | ChemComp-JSG: |
-Macromolecule #6: 2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione
Macromolecule | Name: 2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione type: ligand / ID: 6 / Number of copies: 2 / Formula: DCQ |
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Molecular weight | Theoretical: 322.439 Da |
Chemical component information | ChemComp-DCQ: |
-Macromolecule #7: DODECYL-BETA-D-MALTOSIDE
Macromolecule | Name: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 7 / Number of copies: 2 / Formula: LMT |
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Molecular weight | Theoretical: 510.615 Da |
Chemical component information | ChemComp-LMT: |
-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 | #0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #0 - Detector mode: COUNTING / #0 - Average electron dose: 40.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K2 QUANTUM (4k x 4k) / #1 - Detector mode: SUPER-RESOLUTION / #1 - Average electron dose: 40.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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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: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 95887 |
Image recording ID | 1 |