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- EMDB-62452: Cryo-EM structure of LptDEM complex from Escherichia coli -

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Basic information

Entry
Database: EMDB / ID: EMD-62452
TitleCryo-EM structure of LptDEM complex from Escherichia coli
Map data
Sample
  • Complex: LptDEM complex in Nanodisc
    • Protein or peptide: LPS-assembly protein LptD
    • Protein or peptide: LPS-assembly lipoprotein LptE
    • Protein or peptide: Uncharacterized lipoprotein YifL
KeywordsLPS / Transporter / Complex / MEMBRANE PROTEIN
Function / homology
Function and homology information


transporter complex / lipopolysaccharide transport / Gram-negative-bacterium-type cell outer membrane assembly / cell outer membrane / lipopolysaccharide binding / plasma membrane
Similarity search - Function
Prokaryotic lipoprotein-attachment site / LPS-assembly lipoprotein LptM, conserved region / LptD, C-terminal / LPS-assembly protein LptD / : / LPS transport system D / LPS-assembly lipoprotein LptE / Lipopolysaccharide-assembly / Organic solvent tolerance-like, N-terminal / LptA/(LptD N-terminal domain) LPS transport protein / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
LPS-assembly lipoprotein LptE / Uncharacterized lipoprotein YifL / LPS-assembly protein LptD
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsTsukazaki T / Kohga H / Miyazaki R
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Cell Rep / Year: 2025
Title: Structural basis of lipopolysaccharide translocon assembly mediated by the small lipoprotein LptM
Authors: Miyazaki R / Kimoto M / Kohga H / Tsukazaki T
History
DepositionNov 18, 2024-
Header (metadata) releaseJul 23, 2025-
Map releaseJul 23, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62452.png

Downloads & links

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Map

FileDownload / File: emd_62452.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 256 pix.
= 236.544 Å		0.92 Å/pix.
x 256 pix.
= 236.544 Å		0.92 Å/pix.
x 256 pix.
= 236.544 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.924 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.011
Minimum - Maximum-0.06304303 - 0.12440188
Average (Standard dev.)0.002758753 (±0.0047369283)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 236.544 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62452_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62452_half_map_2.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 : LptDEM complex in Nanodisc

EntireName: LptDEM complex in Nanodisc
Components
  • Complex: LptDEM complex in Nanodisc
    • Protein or peptide: LPS-assembly protein LptD
    • Protein or peptide: LPS-assembly lipoprotein LptE
    • Protein or peptide: Uncharacterized lipoprotein YifL

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Supramolecule #1: LptDEM complex in Nanodisc

SupramoleculeName: LptDEM complex in Nanodisc / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli K-12 (bacteria)

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Macromolecule #1: LPS-assembly protein LptD

MacromoleculeName: LPS-assembly protein LptD / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 87.149516 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: ADLASQCMLG VPSYDRPLVQ GDTNDLPVTI NADHAKGDYP DDAVFTGSVD IMQGNSRLQA DEVQLHQKEA PGQPEPVRTV DALGNVHYD DNQVILKGPK GWANLNTKDT NVWEGDYQMV GRQGRGKADL MKQRGENRYT ILDNGSFTSC LPGSDTWSVV G SEIIHDRE ...String:
ADLASQCMLG VPSYDRPLVQ GDTNDLPVTI NADHAKGDYP DDAVFTGSVD IMQGNSRLQA DEVQLHQKEA PGQPEPVRTV DALGNVHYD DNQVILKGPK GWANLNTKDT NVWEGDYQMV GRQGRGKADL MKQRGENRYT ILDNGSFTSC LPGSDTWSVV G SEIIHDRE EQVAEIWNAR FKVGPVPIFY SPYLQLPVGD KRRSGFLIPN AKYTTTNYFE FYLPYYWNIA PNMDATITPH YM HRRGNIM WENEFRYLSQ AGAGLMELDY LPSDKVYEDE HPNDDSSRRW LFYWNHSGVM DQVWRFNVDY TKVSDPSYFN DFD NKYGSS TDGYATQKFS VGYAVQNFNA TVSTKQFQVF SEQNTSSYSA EPQLDVNYYQ NDVGPFDTRI YGQAVHFVNT RDDM PEATR VHLEPTINLP LSNNWGSINT EAKLLATHYQ QTNLDWYNSR NTTKLDESVN RVMPQFKVDG KMVFERDMEM LAPGY TQTL EPRAQYLYVP YRDQSDIYNY DSSLLQSDYS GLFRDRTYGG LDRIASANQV TTGVTSRIYD DAAVERFNIS VGQIYY FTE SRTGDDNITW ENDDKTGSLV WAGDTYWRIS ERWGLRGGIQ YDTRLDNVAT SNSSIEYRRD EDRLVQLNYR YASPEYI QA TLPKYYSTAE QYKNGISQVG AVASWPIADR WSIVGAYYYD TNANKQADSM LGVQYSSCCY AIRVGYERKL NGWDNDKQ H AVYDNAIGFN IELRGLSSNY GLGTQEMLRS NILPYQNTL

UniProtKB: LPS-assembly protein LptD

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Macromolecule #2: LPS-assembly lipoprotein LptE

MacromoleculeName: LPS-assembly lipoprotein LptE / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 19.479148 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
CGWHLRDTTQ VPSTMKVMIL DSGDPNGPLS RAVRNQLRLN GVELLDKETT RKDVPSLRLG KVSIAKDTAS VFRNGQTAEY QMIMTVNAT VLIPGRDIYP ISAKVFRSFF DNPQMALAKD NEQDMIVKEM YDRAAEQLIR KLPSIRAADI RSDEEQTSTT T DTPATPAR VSTTLGN

UniProtKB: LPS-assembly lipoprotein LptE

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Macromolecule #3: Uncharacterized lipoprotein YifL

MacromoleculeName: Uncharacterized lipoprotein YifL / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 6.727348 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
CGLKGPLYFP PADKNAPPPT KPVETQTQST VPDKNDRATG DGPSQVNYLE HHHHHHHHHH

UniProtKB: Uncharacterized lipoprotein YifL

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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

Concentration4.648 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -1.6 µm / Nominal defocus min: -0.6 µm

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 428907
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL / Overall B value: 108.5
Output model

PDB-9kn3:
Cryo-EM structure of LptDEM complex from Escherichia coli

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