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- EMDB-76430: Constituent EM map: Focused refinement LptADE of outer membrane a... -

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Basic information

Entry
Database: EMDB / ID: EMD-76430
TitleConstituent EM map: Focused refinement LptADE of outer membrane and periplasmic portions of the E. coli lipopolysaccharide transport bridge 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
    • Complex: Outer membrane portion of lipopolysaccharide transporter
      • Protein or peptide: Lipopolysaccharide export system protein LptC,Lipopolysaccharide export system protein LptA
      • Protein or peptide: LPS-assembly protein LptD
      • Protein or peptide: LPS-assembly lipoprotein LptE
KeywordsComplex / Lipopolysaccharide / ABC / ATP binding cassette / transporter / bridge / intermembrane / LIPID TRANSPORT
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.0 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_76430.png

Downloads & links

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Map

FileDownload / File: emd_76430.map.gz / Format: CCP4 / Size: 132.2 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 326 pix.
= 482.48 Å		1.48 Å/pix.
x 326 pix.
= 482.48 Å		1.48 Å/pix.
x 326 pix.
= 482.48 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: 0.172
Minimum - Maximum-0.17106733 - 0.35621154
Average (Standard dev.)0.00040151353 (±0.01280021)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions326326326
Spacing326326326
CellA=B=C: 482.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened map

Fileemd_76430_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_76430_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_76430_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
    • Complex: Outer membrane portion of lipopolysaccharide transporter
      • Protein or peptide: Lipopolysaccharide export system protein LptC,Lipopolysaccharide export system protein LptA
      • Protein or peptide: LPS-assembly protein LptD
      • Protein or peptide: LPS-assembly lipoprotein LptE

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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
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 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Lipopolysaccharide export system protein LptC,Lipopolysaccharide ...

MacromoleculeName: Lipopolysaccharide export system protein LptC,Lipopolysaccharide export system protein LptA
type: protein_or_peptide / ID: 1 / 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 #2: LPS-assembly protein LptD

MacromoleculeName: LPS-assembly protein LptD / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKKRIPTLLA TMIATALYSQ QGLAADLASQ CMLGVPSYDR PLVQGDTNDL PVTINADHAK GDYPDDAVFT GSVDIMQGNS RLQADEVQL HQKEAPGQPE PVRTVDALGN VHYDDNQVIL KGPKGWANLN TKDTNVWEGD YQMVGRQGRG KADLMKQRGE N RYTILDNG ...String:
MKKRIPTLLA TMIATALYSQ QGLAADLASQ CMLGVPSYDR PLVQGDTNDL PVTINADHAK GDYPDDAVFT GSVDIMQGNS RLQADEVQL HQKEAPGQPE PVRTVDALGN VHYDDNQVIL KGPKGWANLN TKDTNVWEGD YQMVGRQGRG KADLMKQRGE N RYTILDNG SFTSCLPGSD TWSVVGSEII HDREEQVAEI WNARFKVGPV PIFYSPYLQL PVGDKRRSGF LIPNAKYTTT NY FEFYLPY YWNIAPNMDA TITPHYMHRR GNIMWENEFR YLSQAGAGLM ELDYLPSDKV YEDEHPNDDS SRRWLFYWNH SGV MDQVWR FNVDYTKVSD PSYFNDFDNK YGSSTDGYAT QKFSVGYAVQ NFNATVSTKQ FQVFSEQNTS SYSAEPQLDV NYYQ NDVGP FDTRIYGQAV HFVNTRDDMP EATRVHLEPT INLPLSNNWG SINTEAKLLA THYQQTNLDW YNSRNTTKLD ESVNR VMPQ FKVDGKMVFE RDMEMLAPGY TQTLEPRAQY LYVPYRDQSD IYNYDSSLLQ SDYSGLFRDR TYGGLDRIAS ANQVTT GVT SRIYDDAAVE RFNISVGQIY YFTESRTGDD NITWENDDKT GSLVWAGDTY WRISERWGLR GGIQYDTRLD NVATSNS SI EYRRDEDRLV QLNYRYASPE YIQATLPKYY STAEQYKNGI SQVGAVASWP IADRWSIVGA YYYDTNANKQ ADSMLGVQ Y SSCCYAIRVG YERKLNGWDN DKQHAVYDNA IGFNIELRGL SSNYGLGTQE MLRSNILPYQ NTL

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Macromolecule #3: LPS-assembly lipoprotein LptE

MacromoleculeName: LPS-assembly lipoprotein LptE / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRYLATLLLS LAVLITAGCG WHLRDTTQVP STMKVMILDS GDPNGPLSRA VRNQLRLNGV ELLDKETTRK DVPSLRLGKV SIAKDTASV FRNGQTAEYQ MIMTVNATVL IPGRDIYPIS AKVFRSFFDN PQMALAKDNE QDMIVKEMYD RAAEQLIRKL P SIRAADIR ...String:
MRYLATLLLS LAVLITAGCG WHLRDTTQVP STMKVMILDS GDPNGPLSRA VRNQLRLNGV ELLDKETTRK DVPSLRLGKV SIAKDTASV FRNGQTAEYQ MIMTVNATVL IPGRDIYPIS AKVFRSFFDN PQMALAKDNE QDMIVKEMYD RAAEQLIRKL P SIRAADIR SDEEQTSTTT DTPATPARVS TTLGN

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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: 7.0 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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