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- EMDB-31088: LptB2FG-LPS from Klebsiella pneumoniae in nanodiscs -

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Basic information

Entry
Database: EMDB / ID: EMD-31088
TitleLptB2FG-LPS from Klebsiella pneumoniae in nanodiscs
Map data
Sample
  • Complex: LptB2FG from Klebsiella pneumoniae with bound LPS
    • Protein or peptide: Lipopolysaccharide export system ATP-binding protein LptB
    • Protein or peptide: Lipopolysaccharide export system permease protein LptF
    • Protein or peptide: LPS export ABC transporter permease LptG
  • Ligand: (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
Keywordsmembrane protein / ABC transporter
Function / homology
Function and homology information


lipopolysaccharide transport / ATP-binding cassette (ABC) transporter complex / transmembrane transport / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Permease LptG/LptF-related / LPS export ABC transporter permease LptF / LPS export ABC transporter permease LptG / Lipopolysaccharide export system permease LptF/LptG / Branched-chain amino acid ATP-binding cassette transporter, C-terminal / Branched-chain amino acid ATP-binding cassette transporter / LPS export ABC transporter, ATP-binding protein LptB / : / ABC transporter-like, conserved site / ABC transporters family signature. ...Permease LptG/LptF-related / LPS export ABC transporter permease LptF / LPS export ABC transporter permease LptG / Lipopolysaccharide export system permease LptF/LptG / Branched-chain amino acid ATP-binding cassette transporter, C-terminal / Branched-chain amino acid ATP-binding cassette transporter / LPS export ABC transporter, ATP-binding protein LptB / : / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Permease / Lipopolysaccharide export system permease protein LptF / Lipopolysaccharide export system ATP-binding protein LptB
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae 1158 (bacteria) / Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.85 Å
AuthorsLuo QS / Shi HG / Huang YH
Funding support China, 3 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2016YFA0500404 China
Chinese Academy of SciencesXDB37020201 China
National Natural Science Foundation of China (NSFC)31625009 China
CitationJournal: Biochem Biophys Res Commun / Year: 2021
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
DepositionMar 22, 2021-
Header (metadata) releaseMar 2, 2022-
Map releaseMar 2, 2022-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.612
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.612
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7efo
  • Surface level: 0.612
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31088.png

Downloads & links

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Map

FileDownload / File: emd_31088.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 192 pix.
= 199.68 Å		1.04 Å/pix.
x 192 pix.
= 199.68 Å		1.04 Å/pix.
x 192 pix.
= 199.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.612 / Movie #1: 0.612
Minimum - Maximum-1.9604559 - 2.762698
Average (Standard dev.)0.003728885 (±0.12806249)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 199.68 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z199.680199.680199.680
α/β/γ90.00090.00090.000
start NX/NY/NZ535455
NX/NY/NZ134138134
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-1.9602.7630.004

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Supplemental data

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Mask #1

Fileemd_31088_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : LptB2FG from Klebsiella pneumoniae with bound LPS

EntireName: LptB2FG from Klebsiella pneumoniae with bound LPS
Components
  • Complex: LptB2FG from Klebsiella pneumoniae with bound LPS
    • Protein or peptide: Lipopolysaccharide export system ATP-binding protein LptB
    • Protein or peptide: Lipopolysaccharide export system permease protein LptF
    • Protein or peptide: LPS export ABC transporter permease LptG
  • Ligand: (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

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Supramolecule #1: LptB2FG from Klebsiella pneumoniae with bound LPS

SupramoleculeName: LptB2FG from Klebsiella pneumoniae with bound LPS / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Klebsiella pneumoniae subsp. pneumoniae 1158 (bacteria)

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Macromolecule #1: Lipopolysaccharide export system ATP-binding protein LptB

MacromoleculeName: Lipopolysaccharide export system ATP-binding protein LptB
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Molecular weightTheoretical: 26.879768 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #2: Lipopolysaccharide export system permease protein LptF

MacromoleculeName: Lipopolysaccharide export system permease protein LptF
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Molecular weightTheoretical: 40.431551 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #3: LPS export ABC transporter permease LptG

MacromoleculeName: LPS export ABC transporter permease LptG / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Molecular weightTheoretical: 39.662438 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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: Permease

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Macromolecule #4: (2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-[(...

MacromoleculeName: (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
Molecular weightTheoretical: 2.975178 KDa
Chemical component information

ChemComp-JSG:
(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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
GridModel: Quantifoil R2/2 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: NITROGEN / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.4000000000000001 µm

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5l75

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.85 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 71000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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