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- EMDB-54038: LolCDE complex with del 9-15 LolB lipoprotein -

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Basic information

Entry
Database: EMDB / ID: EMD-54038
TitleLolCDE complex with del 9-15 LolB lipoprotein
Map datamain map that Phenix refined against
Sample
  • Complex: LolCDE lipoprotein ABC transporter complex with bound del 9-15 lipoprotein LolB
    • 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: Outer-membrane lipoprotein LolB
  • 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 / protein localization to outer membrane / lipoprotein localization to outer membrane / lipoprotein metabolic process / plasma membrane protein complex / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / lipoprotein transport / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / cell outer membrane ...lipoprotein releasing activity / protein localization to outer membrane / lipoprotein localization to outer membrane / lipoprotein metabolic process / plasma membrane protein complex / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / lipoprotein transport / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / cell outer membrane / transmembrane transport / protein transport / outer membrane-bounded periplasmic space / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Outer membrane lipoprotein LolB / Outer membrane lipoprotein LolB / Lipoprotein localisation LolA/LolB/LppX / 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 / : / MacB-like periplasmic core domain / MacB-like periplasmic core domain ...Outer membrane lipoprotein LolB / Outer membrane lipoprotein LolB / Lipoprotein localisation LolA/LolB/LppX / 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 / : / MacB-like periplasmic core domain / MacB-like periplasmic core domain / ABC transporter, lipoprotein release, LolD / MacB, ATP-binding domain / ABC3 transporter permease protein domain / FtsX-like permease C-terminal / 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
Lipoprotein-releasing system transmembrane protein LolC / Outer-membrane lipoprotein LolB / 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: 3.19 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: To Be Published
Title: LolCDE complex with del 9-15 LolB lipoprotein
Authors: Symmons MF / Szewczyk P / Greene NP / Hardwick SW / Koronakis V
History
DepositionJun 16, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54038.png

Downloads & links

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Map

FileDownload / File: emd_54038.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map that Phenix refined against
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.65 Å/pix.
x 448 pix.
= 292.096 Å		0.65 Å/pix.
x 448 pix.
= 292.096 Å		0.65 Å/pix.
x 448 pix.
= 292.096 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.652 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.075
Minimum - Maximum-0.21447948 - 0.4049075
Average (Standard dev.)0.00013069151 (±0.008463096)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 292.096 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A

Fileemd_54038_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_54038_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 lipoprotein ABC transporter complex with bound del 9-15 li...

EntireName: LolCDE lipoprotein ABC transporter complex with bound del 9-15 lipoprotein LolB
Components
  • Complex: LolCDE lipoprotein ABC transporter complex with bound del 9-15 lipoprotein LolB
    • 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: Outer-membrane lipoprotein LolB
  • Ligand: PALMITIC ACID
  • Ligand: (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate

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Supramolecule #1: LolCDE lipoprotein ABC transporter complex with bound del 9-15 li...

SupramoleculeName: LolCDE lipoprotein ABC transporter complex with bound del 9-15 lipoprotein LolB
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 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 45.385977 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 TDVFNANKLV RD AGEVTNS YVYIKSWIGT YGYMYRDIQM IRAIMYLAMV LVIGVACFNI VSTLVMAVKD KSGDIAVLRT LGAKDGLIRA IFV WYGLLA GLFGSLCGVI IGVVVSLQLT PIIEWIEKLI GHQFLSSDIY FIDFLPSELH WLDVFYVLVT ALLLSLLASW YPAR RASNI DPARVLSGQ

UniProtKB: 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: Outer-membrane lipoprotein LolB

MacromoleculeName: Outer-membrane lipoprotein LolB / type: protein_or_peptide / ID: 4
Details: chain is delta 9-15 in mature form of protein with 1-21 in Uniprot sequence removed in mature form.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 22.502213 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: CSVTTPKGPQ WRQHQQDVRN LNQYQTRGAF AYISDQQKVY ARFFWQQTGQ DRYRLLLTNP LGSTELELNA QPGNVQLVDN KGQRYTADD AEEMIGKLTG MPIPLNSLRQ WILGLPGDAT DYKLDDQYRL SEITYSQNGK NWKVVYGGYD TKTQPAMPAN M ELTDGGQR ...String:
CSVTTPKGPQ WRQHQQDVRN LNQYQTRGAF AYISDQQKVY ARFFWQQTGQ DRYRLLLTNP LGSTELELNA QPGNVQLVDN KGQRYTADD AEEMIGKLTG MPIPLNSLRQ WILGLPGDAT DYKLDDQYRL SEITYSQNGK NWKVVYGGYD TKTQPAMPAN M ELTDGGQR IKLKMDNWIV KGSPSRLEEE LRRRLTE

UniProtKB: Outer-membrane lipoprotein LolB

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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: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Average electron dose: 52.79 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: 0.8 µm / Nominal magnification: 130000
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: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Warp / Number images used: 168742
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-9rlh:
LolCDE complex with del 9-15 LolB lipoprotein

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