[English] 日本語
Yorodumi
- EMDB-54038: LolCDE complex with del 9-15 LolB lipoprotein -

+
Open data


ID or keywords:

Loading...

-
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 transport / lipoprotein metabolic process / plasma membrane protein complex / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / 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 transport / lipoprotein metabolic process / plasma membrane protein complex / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / 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: 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

-
Structure visualization

Supplemental images

emd_54038.png

Downloads & links

-
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 °

-
Supplemental data

-
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)

-
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)

-
Sample components

-
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

-
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)

-
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

-
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

-
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

-
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

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

-
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

+
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)

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more