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- EMDB-54039: LolCDEdelta(235-252) complex with Pal lipoprotein -

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Basic information

Entry
Database: EMDB / ID: EMD-54039
TitleLolCDEdelta(235-252) complex with Pal lipoprotein
Map datamain map Phenix refined against
Sample
  • Complex: LolCDE(delta 235-252) lipoprotein ABC transporter complex with bound lipoprotein Pal
    • Protein or peptide: Lipoprotein-releasing system transmembrane protein LolC
    • Protein or peptide: Lipoprotein-releasing system transmembrane protein LolE
    • Protein or peptide: Lipoprotein-releasing system ATP-binding protein LolD
    • Protein or peptide: Peptidoglycan-associated lipoprotein
  • Ligand: PALMITIC ACID
  • Ligand: (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate
KeywordsGram-negative / envelope biogenesis / outer membrane protein / PROTEIN TRANSPORT
Function / homology
Function and homology information


lipoprotein releasing activity / regulation of membrane invagination / cell septum assembly / protein localization to outer membrane / lipoprotein localization to outer membrane / lipoprotein transport / plasma membrane protein complex / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / cell division site / transmembrane transporter activity ...lipoprotein releasing activity / regulation of membrane invagination / cell septum assembly / protein localization to outer membrane / lipoprotein localization to outer membrane / lipoprotein transport / plasma membrane protein complex / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / cell division site / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / cell outer membrane / transmembrane transport / outer membrane-bounded periplasmic space / cell division / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
Peptidoglycan-associated lipoprotein, C-terminal / Peptidoglycan-associated lipoprotein / Lipoprotein releasing system, ATP-binding protein / Lipoprotein-releasing system transmembrane protein LolE, gammaproteobacteria type / Lipoprotein release ATP-binding protein lolD family profile. / Lipoprotein-releasing system transmembrane protein LolC/E / : / Outer membrane protein, OmpA-like, conserved site / OmpA-like domain. / MacB-like periplasmic core domain ...Peptidoglycan-associated lipoprotein, C-terminal / Peptidoglycan-associated lipoprotein / Lipoprotein releasing system, ATP-binding protein / Lipoprotein-releasing system transmembrane protein LolE, gammaproteobacteria type / Lipoprotein release ATP-binding protein lolD family profile. / Lipoprotein-releasing system transmembrane protein LolC/E / : / Outer membrane protein, OmpA-like, conserved site / OmpA-like domain. / MacB-like periplasmic core domain / MacB-like periplasmic core domain / Outer membrane protein, bacterial / ABC transporter, lipoprotein release, LolD / MacB, ATP-binding domain / ABC3 transporter permease protein domain / FtsX-like permease C-terminal / : / OmpA-like domain profile. / OmpA family / OmpA-like domain / OmpA-like domain superfamily / 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. / Prokaryotic membrane lipoprotein lipid attachment site profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Peptidoglycan-associated lipoprotein / Lipoprotein-releasing system transmembrane protein LolC / Lipoprotein-releasing system ATP-binding protein LolD / Lipoprotein-releasing system transmembrane protein LolE
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.63 Å
AuthorsSymmons MF / Szewczyk P / Greene NP / Hardwick SW / Koronakis V
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/V000616/1 United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Liganded LolCDE structures reveal a common substrate-LolE interaction guiding bacterial lipoprotein transport.
Authors: Paul Szewczyk / Nicholas P Greene / Martyn F Symmons / Steven W Hardwick / Vassilis Koronakis /
Abstract: Bacterial lipoproteins are key structural components of the outer membrane in Gram-negative bacteria and vital components of machineries required for its biosynthesis and maintenance. The Lol system, ...Bacterial lipoproteins are key structural components of the outer membrane in Gram-negative bacteria and vital components of machineries required for its biosynthesis and maintenance. The Lol system, essential for viability, directs transport of lipoproteins from the site of biosynthesis on the inner membrane to the outer membrane and has been the target of extensive efforts to develop novel antimicrobial drugs. In the first stage of this transport process, newly synthesized lipoproteins are released from the inner membrane by the ABC transporter LolCDE and passed to the periplasmic chaperone, LolA. Here, we show cryo-EM structures of LolCDE in complex with three different lipoprotein substrates, Lpp, Pal, and LolB, with the latter two bearing a disordered peptide linker between the acyl chains and the globular domain. Our work reveals that when the mature lipoprotein lacks an unstructured linker, the N-terminal portion of the protein is in an unfolded state for transport. The lipoproteins make a sequence-independent but structurally conserved interaction with a cleft on the surface of the periplasmic domain of LolE that promotes efficient transport. We propose a model of lipoprotein export where this interaction acts as pivot point for the peptide portion of the lipoprotein allowing the acyl chains to rotate 180° from their initial position in LolCDE to their binding site in LolA. Our results demonstrate how LolCDE can extrude lipoproteins of diverse sequence and structure and reveal an important detail of a transport process fundamental to bacterial physiology.
History
DepositionJun 16, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54039.png

Downloads & links

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Map

FileDownload / File: emd_54039.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map Phenix refined against
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.73 Å/pix.
x 384 pix.
= 279.936 Å		0.73 Å/pix.
x 384 pix.
= 279.936 Å		0.73 Å/pix.
x 384 pix.
= 279.936 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.729 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.075
Minimum - Maximum-0.15045814 - 0.25818548
Average (Standard dev.)0.00014750974 (±0.008518033)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 279.93597 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A

Fileemd_54039_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_54039_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : LolCDE(delta 235-252) lipoprotein ABC transporter complex with bo...

EntireName: LolCDE(delta 235-252) lipoprotein ABC transporter complex with bound lipoprotein Pal
Components
  • Complex: LolCDE(delta 235-252) lipoprotein ABC transporter complex with bound lipoprotein Pal
    • Protein or peptide: Lipoprotein-releasing system transmembrane protein LolC
    • Protein or peptide: Lipoprotein-releasing system transmembrane protein LolE
    • Protein or peptide: Lipoprotein-releasing system ATP-binding protein LolD
    • Protein or peptide: Peptidoglycan-associated lipoprotein
  • Ligand: PALMITIC ACID
  • Ligand: (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate

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Supramolecule #1: LolCDE(delta 235-252) lipoprotein ABC transporter complex with bo...

SupramoleculeName: LolCDE(delta 235-252) lipoprotein ABC transporter complex with bound lipoprotein Pal
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Escherichia coli K-12 (bacteria)

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Macromolecule #1: Lipoprotein-releasing system transmembrane protein LolC

MacromoleculeName: Lipoprotein-releasing system transmembrane protein LolC
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 43.295516 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MYQPVALFIG LRYMRGRAAD RFGRFVSWLS TIGITLGVMA LVTVLSVMNG FERELQNNIL GLMPQAILSS EHGSLNPQQL PETAVKLDG VNRVAPITTG DVVLQSARSV AVGVMLGIDP AQKDPLTPYL VNVKQTDLEP GKYNVILGEQ LASQLGVNRG D QIRVMVPS ...String:
MYQPVALFIG LRYMRGRAAD RFGRFVSWLS TIGITLGVMA LVTVLSVMNG FERELQNNIL GLMPQAILSS EHGSLNPQQL PETAVKLDG VNRVAPITTG DVVLQSARSV AVGVMLGIDP AQKDPLTPYL VNVKQTDLEP GKYNVILGEQ LASQLGVNRG D QIRVMVPS ASQFTPMGRI PSQRLFNVIG TFAANSEVDG YEMLVNIEDA SRLMRYPAGN ITGWRLWLDE PLKVDSLSQQ KL PEGSKWQ DWRDRKGELF QAVRMEKNMM GLLLSLIVAV AAFNIITSLG LMVMEKQGEV AILQTQGLTP RQIMMVFMVQ GAS AGIIGA ILGAALGALL ASQLNNLMPI IGVLLDGAAL PVAIEPLQVI VIALVAMAIA LLSTLYPSWR AAATQPAEAL RYE

UniProtKB: Lipoprotein-releasing system transmembrane protein LolC

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Macromolecule #2: Lipoprotein-releasing system transmembrane protein LolE

MacromoleculeName: Lipoprotein-releasing system transmembrane protein LolE
type: protein_or_peptide / ID: 2
Details: Uniprot residues 235-252 inclusive engineered out and replaced with GS linker,Uniprot residues 235-252 inclusive engineered out and replaced with GS linker,Uniprot residues 235-252 inclusive ...Details: Uniprot residues 235-252 inclusive engineered out and replaced with GS linker,Uniprot residues 235-252 inclusive engineered out and replaced with GS linker,Uniprot residues 235-252 inclusive engineered out and replaced with GS linker,Uniprot residues 235-252 inclusive engineered out and replaced with GS linker
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 43.475781 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAMPLSLLIG LRFSRGRRRG GMVSLISVIS TIGIALGVAV LIVGLSAMNG FERELNNRIL AVVPHGEIEA VDQPWTNWQE ALDHVQKVP GIAAAAPYIN FTGLVESGAN LRAIQVKGVN PQQEQRLSAL PSFVQGDAWR NFKAGEQQII IGKGVADALK V KQGDWVSI ...String:
MAMPLSLLIG LRFSRGRRRG GMVSLISVIS TIGIALGVAV LIVGLSAMNG FERELNNRIL AVVPHGEIEA VDQPWTNWQE ALDHVQKVP GIAAAAPYIN FTGLVESGAN LRAIQVKGVN PQQEQRLSAL PSFVQGDAWR NFKAGEQQII IGKGVADALK V KQGDWVSI MIPNSNPEHK LMQPKRVRLH VAGILQLSGQ LDHSFAMIPL ADAQQYLDMG SSVSGIALKM TDVFNAGSSW IG TYGYMYR DIQMIRAIMY LAMVLVIGVA CFNIVSTLVM AVKDKSGDIA VLRTLGAKDG LIRAIFVWYG LLAGLFGSLC GVI IGVVVS LQLTPIIEWI EKLIGHQFLS SDIYFIDFLP SELHWLDVFY VLVTALLLSL LASWYPARRA SNIDPARVLS GQ

UniProtKB: Lipoprotein-releasing system transmembrane protein LolE, Lipoprotein-releasing system transmembrane protein LolE

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Macromolecule #3: Lipoprotein-releasing system ATP-binding protein LolD

MacromoleculeName: Lipoprotein-releasing system ATP-binding protein LolD / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 26.444301 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MNKILLQCDN LCKRYQEGSV QTDVLHNVSF SVGEGEMMAI VGSSGSGKST LLHLLGGLDT PTSGDVIFNG QPMSKLSSAA KAELRNQKL GFIYQFHHLL PDFTALENVA MPLLIGKKKP AEINSRALEM LKAVGLDHRA NHRPSELSGG ERQRVAIARA L VNNPRLVL ...String:
MNKILLQCDN LCKRYQEGSV QTDVLHNVSF SVGEGEMMAI VGSSGSGKST LLHLLGGLDT PTSGDVIFNG QPMSKLSSAA KAELRNQKL GFIYQFHHLL PDFTALENVA MPLLIGKKKP AEINSRALEM LKAVGLDHRA NHRPSELSGG ERQRVAIARA L VNNPRLVL ADEPTGNLDA RNADSIFQLL GELNRLQGTA FLVVTHDLQL AKRMSRQLEM RDGRLTAELS LMGAEGSHHH HH H

UniProtKB: Lipoprotein-releasing system ATP-binding protein LolD

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Macromolecule #4: Peptidoglycan-associated lipoprotein

MacromoleculeName: Peptidoglycan-associated lipoprotein / type: protein_or_peptide / ID: 4 / Details: Residues 1-21 removed in vivo signal sequence / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 17.821592 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
CSSNKNASND GSEGMLGAGT GMDANGGNGN MSSEEQARLQ MQQLQQNNIV YFDLDKYDIR SDFAQMLDAH ANFLRSNPSY KVTVEGHAD ERGTPEYNIS LGERRANAVK MYLQGKGVSA DQISIVSYGK EKPAVLGHDE AAYSKNRRAV LVYGSWSHPQ F EK

UniProtKB: Peptidoglycan-associated lipoprotein

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Macromolecule #5: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 5 / Number of copies: 1 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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Macromolecule #6: (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate

MacromoleculeName: (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate / type: ligand / ID: 6 / Number of copies: 1 / Formula: Z41
Molecular weightTheoretical: 568.911 Da
Chemical component information

ChemComp-Z41:
(2S)-3-hydroxypropane-1,2-diyl dihexadecanoate

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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
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 53.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 165000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
In silico model: Previously determined LPP(L10P) LolCDE complex
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Warp / Number images used: 23445
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: previously refined Lpp (L10P) complex
SoftwareName: Coot
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9rli:
LolCDEdelta(235-252) complex with Pal lipoprotein

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