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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-31088 | ||||||||||||
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Title | LptB2FG-LPS from Klebsiella pneumoniae in nanodiscs | ||||||||||||
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![]() | membrane protein / ABC transporter | ||||||||||||
Function / homology | ![]() ATPase-coupled transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / transmembrane transport / hydrolase activity / ATP binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.85 Å | ||||||||||||
![]() | Luo QS / Shi HG / Huang YH | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structures of LptBFG and LptBFGC from Klebsiella pneumoniae in complex with lipopolysaccharide. Authors: Qingshan Luo / Huigang Shi / Xueqing Xu / ![]() Abstract: Lipopolysaccharide (LPS) is an essential component of the outer membrane (OM) in most Gram-negative bacteria. LPS transport from the inner membrane (IM) to the OM is achieved by seven ...Lipopolysaccharide (LPS) is an essential component of the outer membrane (OM) in most Gram-negative bacteria. LPS transport from the inner membrane (IM) to the OM is achieved by seven lipopolysaccharide transport proteins (LptA-G). LptBFG, an type VI ATP-binding cassette (ABC) transporter, forms a stable complex with LptC, extracts LPS from the IM and powers LPS transport to the OM. Here we report the cryo-EM structures of LptBFG and LptBFGC from Klebsiella pneumoniae in complex with LPS. The KpLptBFG-LPS structure provides detailed interactions between LPS and the transporter, while the KpLptBFGC-LPS structure may represent an intermediate state that the transmembrane helix of LptC has not been fully inserted into the transmembrane domains of LptBFG. | ||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 14 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.3 KB 14.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 6.7 KB | Display | ![]() |
Images | ![]() | 106.1 KB | ||
Masks | ![]() | 27 MB | ![]() | |
Filedesc metadata | ![]() | 6.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 583.3 KB | Display | ![]() |
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Full document | ![]() | 582.8 KB | Display | |
Data in XML | ![]() | 9.4 KB | Display | |
Data in CIF | ![]() | 11.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7efoMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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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: 1.04 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : LptB2FG from Klebsiella pneumoniae with bound LPS
Entire | Name: LptB2FG from Klebsiella pneumoniae with bound LPS |
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Components |
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-Supramolecule #1: LptB2FG from Klebsiella pneumoniae with bound LPS
Supramolecule | Name: LptB2FG from Klebsiella pneumoniae with bound LPS / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Lipopolysaccharide export system ATP-binding protein LptB
Macromolecule | Name: Lipopolysaccharide export system ATP-binding protein LptB type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 26.879768 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MATLTAKNLA KAYKGRRVVE DVSLTVNSGE IVGLLGPNGA GKTTTFYMVV GIVPRDAGNI IIDDEDISLL PLHARARRGI GYLPQEASI FRRLSVYDNL MAVLQIRDDL TSEQREDRAK ELMEEFHIEH LRDSLGQALS GGERRRVEIA RALAANPKFI L LDEPFAGV ...String: MATLTAKNLA KAYKGRRVVE DVSLTVNSGE IVGLLGPNGA GKTTTFYMVV GIVPRDAGNI IIDDEDISLL PLHARARRGI GYLPQEASI FRRLSVYDNL MAVLQIRDDL TSEQREDRAK ELMEEFHIEH LRDSLGQALS GGERRRVEIA RALAANPKFI L LDEPFAGV DPISVIDIKR IIEHLRDSGL GVLITDHNVR ETLAVCERAY IVSQGHLIAH GTPQQILEDE QVKRVYLGED 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: ![]() |
Molecular weight | Theoretical: 40.431551 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MIIIRYLVRE TLKSQLAILF ILLLIFFCQK LVRILGAAVD GDIPTNLVLS LLGLGIPEMA QLILPLSLFL GLLMTLGKLY TESEITVMH ACGLSKAVLI KAAMILALFT GAVAAVNVMW AGPWSSRHQD EVLAEAKANP GMAALAQGQF QQASDGNAVM F IESVNGNR ...String: MIIIRYLVRE TLKSQLAILF ILLLIFFCQK LVRILGAAVD GDIPTNLVLS LLGLGIPEMA QLILPLSLFL GLLMTLGKLY TESEITVMH ACGLSKAVLI KAAMILALFT GAVAAVNVMW AGPWSSRHQD EVLAEAKANP GMAALAQGQF QQASDGNAVM F IESVNGNR FHDVFLAQLR PKGNARPSVV VADSGELSQQ KDGSQVVTLN KGTRFEGTAM LRDFRITDFN NYQAIIGHQA VS ADPDDTE QMDMRTLWKT HTDRARAELH WRFTLVATVF IMALMVVPLS VVNPRQGRVL SMLPAMLLYL VFFLLQTSIK SNG GKGKMD PAIWMWAINL LYFALAVLLN LWDTVPMRRF RARFNKGAA UniProtKB: Lipopolysaccharide export system permease protein LptF |
-Macromolecule #3: LPS export ABC transporter permease LptG
Macromolecule | Name: LPS export ABC transporter permease LptG / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 39.662438 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MQAFGVLDRY IGKTIFNTIM MTLFMLVSLS GIIKFVDQLK KSGQGSYDAL GAGLYTILSV PKDIQIFFPM AALLGALLGL GMLAQRSEL VVMQASGFTR LQVALAVMKT AIPLVLLTMA IGEWVAPQGE QMARNYRAQQ MYGGSLLSTQ QGLWAKDGHN F VYIERVKG ...String: MQAFGVLDRY IGKTIFNTIM MTLFMLVSLS GIIKFVDQLK KSGQGSYDAL GAGLYTILSV PKDIQIFFPM AALLGALLGL GMLAQRSEL VVMQASGFTR LQVALAVMKT AIPLVLLTMA IGEWVAPQGE QMARNYRAQQ MYGGSLLSTQ QGLWAKDGHN F VYIERVKG NDELGGVSIY AFNPERRLQS VRYAASAKFD SENKVWRLSQ VDESDLTDPK QVTGSQMVSG TWKTNLTPDK LG VVALDPD ALSISGLHNY VKYLKSSGQD PGRYQLNMWS KIFQPLSVAV MMLMALSFIF GPLRSVPMGV RVVTGISFGF IFY VLDQIF GPLTLVYGIP PIIGALLPSA SFFLISLWLM MRKA UniProtKB: LPS export ABC transporter permease LptG |
-Macromolecule #4: (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: 4 / Number of copies: 1 / Formula: JSG |
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Molecular weight | Theoretical: 2.975178 KDa |
Chemical component information | ![]() ChemComp-JSG: |
-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: 283 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 / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.4000000000000001 µm |