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- EMDB-76432: Constituent EM map: Focused refinement of inner membrane portions... -

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Basic information

Entry
Database: EMDB / ID: EMD-76432
TitleConstituent EM map: Focused refinement of inner membrane portions of the E. coli lipopolysaccharide transport bridge LptBFGC in complex with ATP
Map dataUnsharpened map
Sample
  • Complex: Intermembrane lipopolysaccharide transport bridge composed of LptD, LptE, LptA, LptC, LptF, LptG, and two molecules of LptB
    • Complex: Inner membrane portion of lipopolysaccharide transporter
      • Protein or peptide: Lipopolysaccharide export system ATP-binding protein LptB
      • Protein or peptide: Lipopolysaccharide export system protein LptC,Lipopolysaccharide export system protein LptA
      • Protein or peptide: Lipopolysaccharide export system permease protein LptF
      • Protein or peptide: Lipopolysaccharide export system permease protein LptG
    • Complex: Outer membrane portion of lipopolysaccharide transporter
KeywordsComplex / Lipopolysaccharide / ABC / ATP binding cassette / transporter / bridge / intermembrane / LIPID TRANSPORT
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.4 Å
AuthorsTaylor RJ / Pahil KS / Walsh Jr RM / Caruso A / Kahne DE
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI149778 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI081059 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI153358 United States
CitationJournal: To Be Published
Title: Structural basis for regulating lipopolysaccharide transmembrane transport
Authors: Taylor RJ / Pahil KS / Walsh Jr RM / Kahne DE
History
DepositionApr 5, 2026-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76432.png

Downloads & links

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Map

FileDownload / File: emd_76432.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.48 Å/pix.
x 200 pix.
= 296. Å		1.48 Å/pix.
x 200 pix.
= 296. Å		1.48 Å/pix.
x 200 pix.
= 296. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.48 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0982
Minimum - Maximum-0.071730934 - 0.24773584
Average (Standard dev.)0.0010391837 (±0.011905989)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 296.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened map

Fileemd_76432_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map

Fileemd_76432_half_map_1.map
AnnotationHalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map

Fileemd_76432_half_map_2.map
AnnotationHalf 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 : Intermembrane lipopolysaccharide transport bridge composed of Lpt...

EntireName: Intermembrane lipopolysaccharide transport bridge composed of LptD, LptE, LptA, LptC, LptF, LptG, and two molecules of LptB
Components
  • Complex: Intermembrane lipopolysaccharide transport bridge composed of LptD, LptE, LptA, LptC, LptF, LptG, and two molecules of LptB
    • Complex: Inner membrane portion of lipopolysaccharide transporter
      • Protein or peptide: Lipopolysaccharide export system ATP-binding protein LptB
      • Protein or peptide: Lipopolysaccharide export system protein LptC,Lipopolysaccharide export system protein LptA
      • Protein or peptide: Lipopolysaccharide export system permease protein LptF
      • Protein or peptide: Lipopolysaccharide export system permease protein LptG
    • Complex: Outer membrane portion of lipopolysaccharide transporter

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Supramolecule #1: Intermembrane lipopolysaccharide transport bridge composed of Lpt...

SupramoleculeName: Intermembrane lipopolysaccharide transport bridge composed of LptD, LptE, LptA, LptC, LptF, LptG, and two molecules of LptB
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Supramolecule #2: Inner membrane portion of lipopolysaccharide transporter

SupramoleculeName: Inner membrane portion of lipopolysaccharide transporter
type: complex / ID: 2 / Parent: 1 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Supramolecule #3: Outer membrane portion of lipopolysaccharide transporter

SupramoleculeName: Outer membrane portion of lipopolysaccharide transporter
type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Escherichia coli (E. coli)

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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 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MATLTAKNLA KAYKGRRVVE DVSLTVNSGE IVGLLGPNGA GKTTTFYMVV GIVPRDAGNI IIDDDDISLL PLHARARRGI GYLPQEASIF RRLSVYDNLM AVLQIRDDLS AEQREDRANE LMEEFHIEHL RDSMGQSLSG GERRRVEIAR ALAANPKFIL LDQPFAGVDP ...String:
MATLTAKNLA KAYKGRRVVE DVSLTVNSGE IVGLLGPNGA GKTTTFYMVV GIVPRDAGNI IIDDDDISLL PLHARARRGI GYLPQEASIF RRLSVYDNLM AVLQIRDDLS AEQREDRANE LMEEFHIEHL RDSMGQSLSG GERRRVEIAR ALAANPKFIL LDQPFAGVDP ISVIDIKRII EHLRDSGLGV LITDHNVRET LAVCERAYIV SQGHLIAHGT PTEILQDEHV KRVYLGEDFR L

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Macromolecule #2: Lipopolysaccharide export system protein LptC,Lipopolysaccharide ...

MacromoleculeName: Lipopolysaccharide export system protein LptC,Lipopolysaccharide export system protein LptA
type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSKARRWVII VLSLAVLVMI GINMAEKDDT AQVVVNNNDP TYKSEHTDTL VYNPEGALSY RLIAQHVEYY SDQAVSWFTQ PVLTTFDKD KIPTWSVKAD KAKLTNDRML YLYGHVEVNA LVPDSQLRRI TTDNAQINLV TQDVTSEDLV TLYGTTFNSS G LKMRGNLR ...String:
MSKARRWVII VLSLAVLVMI GINMAEKDDT AQVVVNNNDP TYKSEHTDTL VYNPEGALSY RLIAQHVEYY SDQAVSWFTQ PVLTTFDKD KIPTWSVKAD KAKLTNDRML YLYGHVEVNA LVPDSQLRRI TTDNAQINLV TQDVTSEDLV TLYGTTFNSS G LKMRGNLR SKNAELIEKV RTSYEIQNKQ TQPLVPGGSG GGGSGGGGSG GGGSVTGDTD QPIHIESDQQ SLDMQGNVVT FT GNVIVTQ GTIKINADKV VVTRPGGEQG KEVIDGYGKP ATFYQMQDNG KPVEGHASQM HYELAKDFVV LTGNAYLQQV DSN IKGDKI TYLVKEQKMQ AFSDKGKRVT TVLVPSQLQD KNNKGQTPAQ KKGNLVPRGS HHHHHHH

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Macromolecule #3: Lipopolysaccharide export system permease protein LptF

MacromoleculeName: Lipopolysaccharide export system permease protein LptF
type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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 WRITLVFTVF MMALMVVPLS VVNPRQGRVL SMLPAMLLYL LFFLIQTSLK SNG GKGKLD PTLWMWTVNL IYLALAIVLN LWDTVPVRRL RASFSRKGAV

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Macromolecule #4: Lipopolysaccharide export system permease protein LptG

MacromoleculeName: Lipopolysaccharide export system permease protein LptG
type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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 DEELGGISIY AFNENRRLQS VRYAATAKFD PEHKVWRLSQ VDESDLTNPK QITGSQTVSG TWKTNLTPDK LG VVALDPD ALSISGLHNY VKYLKSSGQD AGRYQLNMWS KIFQPLSVAV MMLMALSFIF GPLRSVPMGV RVVTGISFGF VFY VLDQIF GPLTLVYGIP PIIGALLPSA SFFLISLWLL MRKS

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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
Component:
ConcentrationFormulaName
20.0 mMNH2C(CH2OH)3Tris pH 8
150.0 mMNaClSodium Chloride
0.02 %C56H92O25glyco-diosgenin
1.0 %C3H8O3glycerol
1.0 %C2H6OSDMSO
1.0 %C2H6O2ethylene glycol
5.0 mMC10H14N5Na2O13P3ATP
1.0 mMMgCl2MgCl2

Details: 20mM Tris HCl, 150mM NaCl, 1% glycerol, 1% DMSO, 1% ethylene glycol, 0.02% GDN, 5 mM ATP, 1 mM MgCl2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample was monodisperse as determined by SEC.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 51.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: Ab initio model generated based on the data using cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 43207
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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