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- EMDB-71296: Constituent EM map: Focused refinement inner membrane portion Lpt... -

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Basic information

Entry
Database: EMDB / ID: EMD-71296
TitleConstituent EM map: Focused refinement inner membrane portion LptBFGC of the lipopolysaccharide transport bridge from E. coli in complex with lipopolysaccharide
Map dataUnsharpened map
Sample
  • Complex: Intermembrane lipopolysaccharide transport bridge composed of LptD, LptE, LptA, LptC, LptF, LptG, and two molecules of LptB in complex with lipopolysaccharide
    • Complex: Inner membrane portion of lipopolysaccharide transporter
      • Protein or peptide: LptB
      • Protein or peptide: LptF
      • Protein or peptide: LptG
      • Protein or peptide: LptC fusion with LptA
    • 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: 3.3 Å
AuthorsTaylor RJ / Pahil KS / Walsh Jr RM / 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
DepositionJun 17, 2025-
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_71296.png

Downloads & links

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Map

FileDownload / File: emd_71296.map.gz / Format: CCP4 / Size: 64 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.)
0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0293
Minimum - Maximum-0.049155828 - 0.111830615
Average (Standard dev.)0.0008770857 (±0.0053569037)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened map

Fileemd_71296_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_71296_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_71296_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 in complex with lipopolysaccharide
Components
  • Complex: Intermembrane lipopolysaccharide transport bridge composed of LptD, LptE, LptA, LptC, LptF, LptG, and two molecules of LptB in complex with lipopolysaccharide
    • Complex: Inner membrane portion of lipopolysaccharide transporter
      • Protein or peptide: LptB
      • Protein or peptide: LptF
      • Protein or peptide: LptG
      • Protein or peptide: LptC fusion with LptA
    • 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 in complex with lipopolysaccharide
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: LptB

MacromoleculeName: LptB / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MATLTAKNLA KAYKGRRVV E DVSLTVNS GE IVGLLGP NGA GKTTTF YMVV GIVPR DAGNI IIDD DDISLL PLH ARARRGI GY LPQEASIF R RLSVYDNLM AVLQIRDDLS AEQREDRAN E LMEEFHIE HL RDSMGQS LSG GERRRV EIAR ALAAN ...String:
MATLTAKNLA KAYKGRRVV E DVSLTVNS GE IVGLLGP NGA GKTTTF YMVV GIVPR DAGNI IIDD DDISLL PLH ARARRGI GY LPQEASIF R RLSVYDNLM AVLQIRDDLS AEQREDRAN E LMEEFHIE HL RDSMGQS LSG GERRRV EIAR ALAAN PKFIL LDEP FAGVDP ISV IDIKRII EH LRDSGLGV L ITDHNVRET LAVCERAYIV SQGHLIAHG T PTEILQDE HV KRVYLGE DFR L

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Macromolecule #2: LptF

MacromoleculeName: LptF / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MIIIRYLVRE TLKSQLAILF ILLLIFFCQK LVRILGAAVD GDIPANLVLS LLGLGVPEMA QLILPLSLFL GLLMTLGKLY TESEITVMHA CGLSKAVLVK AAMILAVFTA IVAAVNVMWA GPWSSRHQDE VLAEAKANPG MAALAQGQFQ QATNGSSVLF IESVDGSDFK ...String:
MIIIRYLVRE TLKSQLAILF ILLLIFFCQK LVRILGAAVD GDIPANLVLS LLGLGVPEMA QLILPLSLFL GLLMTLGKLY TESEITVMHA CGLSKAVLVK AAMILAVFTA IVAAVNVMWA GPWSSRHQDE VLAEAKANPG MAALAQGQFQ QATNGSSVLF IESVDGSDFK DVFLAQIRPK GNARPSVVVA DSGHLTQLRD GSQVVTLNQG TRFEGTALLR DFRITDFQDY QAIIGHQAVA LDPNDTDQMD MRTLWNTDTD RARAELNWRI TLVFTVFMMA LMVVPLSVVN PRQGRVLSML PAMLLYLLFF LIQTSLKSNG GKGKLDPTLW MWTVNLIYLA LAIVLNLWDT VPVRRLRASF SRKGAV

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Macromolecule #3: LptG

MacromoleculeName: LptG / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MQPFGVLDRY IGKTIFTTIM MTLFMLVSLS GIIKFVDQLK KAGQGSYDAL GAGMYTLLSV PKDVQIFFPM AALLGALLGL GMLAQRSELV VMQASGFTRM QVALSVMKTA IPLVLLTMAI GEWVAPQGEQ MARNYRAQAM YGGSLLSTQQ GLWAKDGNNF VYIERVKGDE ...String:
MQPFGVLDRY IGKTIFTTIM MTLFMLVSLS GIIKFVDQLK KAGQGSYDAL GAGMYTLLSV PKDVQIFFPM AALLGALLGL GMLAQRSELV VMQASGFTRM QVALSVMKTA IPLVLLTMAI GEWVAPQGEQ MARNYRAQAM YGGSLLSTQQ GLWAKDGNNF VYIERVKGDE ELGGISIYAF NENRRLQSVR YAATAKFDPE HKVWRLSQVD ESDLTNPKQI TGSQTVSGTW KTNLTPDKLG VVALDPDALS ISGLHNYVKY LKSSGQDAGR YQLNMWSKIF QPLSVAVMML MALSFIFGPL RSVPMGVRVV TGISFGFVFY VLDQIFGPLT LVYGIPPIIG ALLPSASFFL ISLWLLMRKS

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Macromolecule #4: LptC fusion with LptA

MacromoleculeName: LptC fusion with LptA / type: protein_or_peptide / ID: 4 / Details: LptC expressed as a fusion with LptA and a his tag / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSKARRWVII VLSLAVLVMI GINMAEKDDT AQVVVNNNDP TYKSEHTDTL VYNPEGALSY RLIAQHVEYY SDQAVSWFTQ PVLTTFDKDK IPTWSVKADK AKLTNDRMLY LYGHVEV NA LVPDSQLRRI TTDNAQINLV TQDVTSEDLV TLYGTTFNSS GLKMRGNLRS ...String:
MSKARRWVII VLSLAVLVMI GINMAEKDDT AQVVVNNNDP TYKSEHTDTL VYNPEGALSY RLIAQHVEYY SDQAVSWFTQ PVLTTFDKDK IPTWSVKADK AKLTNDRMLY LYGHVEV NA LVPDSQLRRI TTDNAQINLV TQDVTSEDLV TLYGTTFNSS GLKMRGNLRS KNAELIEKVR TSYEIQNKQT QPLVP GGSG GGGSGGGGSG GGGSVTGDTD QPIHIESDQQ SLDMQG NVV TFTGNVIVTQ GTIKINADKV VVTRPGGEQG KEVIDGYGKP ATFYQMQDNG KPVEGHASQM HYELAKDFVV LTGNAYLQQV DSNIKGDKIT YLVKEQKMQA FSDKGKRVTT VLVP SQLQD KNNKGQTPAQ KKGNLVPRGS HHHHHHH

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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

Details: 20mM Tris HCl, 150mM NaCl, 1% glycerol, 1% DMSO, 1% ethylene glycol, 0.02% GDN
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: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 50.0 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: 1.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 666000
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: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 157094
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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