[English] 日本語
Yorodumi
- EMDB-53150: Structure of the YbjP lipoprotein bound to the MacAB-TolC tripart... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-53150
TitleStructure of the YbjP lipoprotein bound to the MacAB-TolC tripartite efflux pump
Map dataMain map
Sample
  • Complex: complex of TolC outer membrane protein, lipoprotein YbjP, MacA and the resolved portion of the ABC transporter MacB
    • Protein or peptide: Outer membrane protein TolC
    • Protein or peptide: Uncharacterized lipoprotein YbjP
    • Protein or peptide: Macrolide export protein MacA
    • Protein or peptide: Macrolide export ATP-binding/permease protein MacB
  • Ligand: CHLORIDE ION
  • Ligand: (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate
  • Ligand: water
Keywordsmulti-drug efflux pump / MacAB-TolC / AcrABZ-TolC / type I secretion / lipoprotein / membrane protein assembly / MEMBRANE PROTEIN
Function / homology
Function and homology information


polymyxin transport / polymyxin transmembrane transporter activity / MacAB-TolC complex / enterobactin transport / enterobactin transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the cell outer membrane / periplasmic side of plasma membrane / efflux pump complex / Iron assimilation using enterobactin / bile acid transmembrane transporter activity ...polymyxin transport / polymyxin transmembrane transporter activity / MacAB-TolC complex / enterobactin transport / enterobactin transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the cell outer membrane / periplasmic side of plasma membrane / efflux pump complex / Iron assimilation using enterobactin / bile acid transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the plasma membrane / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / extrinsic component of membrane / Antimicrobial resistance / ABC-type xenobiotic transporter activity / bile acid and bile salt transport / porin activity / Secretion of toxins / efflux transmembrane transporter activity / monoatomic ion channel activity / transmembrane transporter activity / cell outer membrane / response to toxic substance / monoatomic ion transmembrane transport / response to xenobiotic stimulus / response to antibiotic / protein homodimerization activity / ATP hydrolysis activity / ATP binding / membrane / identical protein binding / plasma membrane
Similarity search - Function
Macrolide export protein MacA / Domain of unknown function DUF3828 / RND efflux pump, membrane fusion protein, barrel-sandwich domain / Protein of unknown function (DUF3828) / Macrolide export ATP-binding/permease protein macB family profile. / : / : / : / Type I secretion outer membrane protein, TolC / : ...Macrolide export protein MacA / Domain of unknown function DUF3828 / RND efflux pump, membrane fusion protein, barrel-sandwich domain / Protein of unknown function (DUF3828) / Macrolide export ATP-binding/permease protein macB family profile. / : / : / : / Type I secretion outer membrane protein, TolC / : / RND efflux pump, membrane fusion protein / Outer membrane efflux protein / Outer membrane efflux protein / MacB-like periplasmic core domain / MacB-like periplasmic core domain / 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
Outer membrane protein TolC / Uncharacterized lipoprotein YbjP / Macrolide export protein MacA / Macrolide export ATP-binding/permease protein MacB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.48 Å
AuthorsHorne J / Kaplan E / Luisi BF
Funding support United Kingdom, European Union, 2 items
OrganizationGrant numberCountry
Wellcome Trust222451/Z/21/Z United Kingdom
European Research Council (ERC)742210European Union
CitationJournal: To Be Published
Title: Structure of the YbjP lipoprotein bound to the MacAB-TolC tripartite efflux pump
Authors: Kaplan E / Horne J / Luisi BF
History
DepositionMar 14, 2025-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_53150.png

Downloads & links

-
Map

FileDownload / File: emd_53150.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 600 pix.
= 498. Å		0.83 Å/pix.
x 600 pix.
= 498. Å		0.83 Å/pix.
x 600 pix.
= 498. 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: 0.04
Minimum - Maximum-0.06834852 - 0.22115698
Average (Standard dev.)0.00011264081 (±0.0035941459)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 498.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_53150_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half-map B

Fileemd_53150_half_map_1.map
AnnotationHalf-map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half-map A

Fileemd_53150_half_map_2.map
AnnotationHalf-map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : complex of TolC outer membrane protein, lipoprotein YbjP, MacA an...

EntireName: complex of TolC outer membrane protein, lipoprotein YbjP, MacA and the resolved portion of the ABC transporter MacB
Components
  • Complex: complex of TolC outer membrane protein, lipoprotein YbjP, MacA and the resolved portion of the ABC transporter MacB
    • Protein or peptide: Outer membrane protein TolC
    • Protein or peptide: Uncharacterized lipoprotein YbjP
    • Protein or peptide: Macrolide export protein MacA
    • Protein or peptide: Macrolide export ATP-binding/permease protein MacB
  • Ligand: CHLORIDE ION
  • Ligand: (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate
  • Ligand: water

-
Supramolecule #1: complex of TolC outer membrane protein, lipoprotein YbjP, MacA an...

SupramoleculeName: complex of TolC outer membrane protein, lipoprotein YbjP, MacA and the resolved portion of the ABC transporter MacB
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Escherichia coli (E. coli)

-
Macromolecule #1: Outer membrane protein TolC

MacromoleculeName: Outer membrane protein TolC / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 51.495555 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: ENLMQVYQQA RLSNPELRKS AADRDAAFEK INEARSPLLP QLGLGADYTY SNGYRDANGI NSNATSASLQ LTQSIFDMSK WRALTLQEK AAGIQDVTYQ TDQQTLILNT ATAYFNVLNA IDVLSYTQAQ KEAIYRQLDQ TTQRFNVGLV AITDVQNARA Q YDTVLANE ...String:
ENLMQVYQQA RLSNPELRKS AADRDAAFEK INEARSPLLP QLGLGADYTY SNGYRDANGI NSNATSASLQ LTQSIFDMSK WRALTLQEK AAGIQDVTYQ TDQQTLILNT ATAYFNVLNA IDVLSYTQAQ KEAIYRQLDQ TTQRFNVGLV AITDVQNARA Q YDTVLANE VTARNNLDNA VEQLRQITGN YYPELAALNV ENFKTDKPQP VNALLKEAEK RNLSLLQARL SQDLAREQIR QA QDGHLPT LDLTASTGIS DTSYSGSKTR GAAGTQYDDS NMGQNKVGLS FSLPIYQGGM VNSQVKQAQY NFVGASEQLE SAH RSVVQT VRSSFNNINA SISSINAYKQ AVVSAQSSLD AMEAGYSVGT RTIVDVLDAT TTLYNAKQEL ANARYNYLIN QLNI KSALG TLNEQDLLAL NNALSKPVST NPENVAPQTP EQNAIADGYA PDSPAPVVQQ TSARTTTSNG HNPFRN

UniProtKB: Outer membrane protein TolC

-
Macromolecule #2: Uncharacterized lipoprotein YbjP

MacromoleculeName: Uncharacterized lipoprotein YbjP / type: protein_or_peptide / ID: 2 / Details: Lipid modified at N-termina cysteine / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 17.004725 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
CTTVTPAYKD NGTRSGPCVE GGPDNVAQQF YDYRILHRSN DITALRPYLS DKLATLLSDA SRDNNHRELL TNDPFSSRTT LPDSAHVAS ASTIPNRDAR NIPLRVDLKQ GDQGWQDEVL MIQEGQCWVI DDVRYLGGSV HATAGTLRQS IENR

UniProtKB: Uncharacterized lipoprotein YbjP

-
Macromolecule #3: Macrolide export protein MacA

MacromoleculeName: Macrolide export protein MacA / type: protein_or_peptide / ID: 3 / Details: MacA hexamer / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 40.672785 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKKRKTVKKR YVIALVIVIA GLITLWRILN APVPTYQTLI VRPGDLQQSV LATGKLDALR KVDVGAQVSG QLKTLSVAIG DKVKKDQLL GVIDPEQAEN QIKEVEATLM ELRAQRQQAE AELKLARVTY SRQQRLAQTK AVSQQDLDTA ATEMAVKQAQ I GTIDAQIK ...String:
MKKRKTVKKR YVIALVIVIA GLITLWRILN APVPTYQTLI VRPGDLQQSV LATGKLDALR KVDVGAQVSG QLKTLSVAIG DKVKKDQLL GVIDPEQAEN QIKEVEATLM ELRAQRQQAE AELKLARVTY SRQQRLAQTK AVSQQDLDTA ATEMAVKQAQ I GTIDAQIK RNQASLDTAK TNLDYTRIVA PMAGEVTQIT TLQGQTVIAA QQAPNILTLA DMSAMLVKAQ VSEADVIHLK PG QKAWFTV LGDPLTRYEG QIKDVLPTPE KVNDAIFYYA RFEVPNPNGL LRLDMTAQVH IQLTDVKNVL TIPLSALGDP VGD NRYKVK LLRNGETRER EVTIGARNDT DVEIVKGLEA GDEVVIGEAK PGAAQ

UniProtKB: Macrolide export protein MacA

-
Macromolecule #4: Macrolide export ATP-binding/permease protein MacB

MacromoleculeName: Macrolide export ATP-binding/permease protein MacB / type: protein_or_peptide / ID: 4 / Details: segment of MacB / 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 (E. coli)
Molecular weightTheoretical: 23.354293 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MVLADIRSIG TNTIDVYPGK DFGDDDPQYQ QALKYDDLIA IQKQPWVASA TPAVSQNLRL RYNNVDVAAS ANGVSGDYFN VYGMTFSEG NTFNQEQLNG RAQVVVLDSN TRRQLFPHKA DVVGEVILVG NMPARVIGVA EEKQSMFGSS KVLRVWLPYS T MSGRVMGQ ...String:
MVLADIRSIG TNTIDVYPGK DFGDDDPQYQ QALKYDDLIA IQKQPWVASA TPAVSQNLRL RYNNVDVAAS ANGVSGDYFN VYGMTFSEG NTFNQEQLNG RAQVVVLDSN TRRQLFPHKA DVVGEVILVG NMPARVIGVA EEKQSMFGSS KVLRVWLPYS T MSGRVMGQ SWLNSITVRV KEGFDSAEAE QQLTRLLSLR HGKKDFFTWN M

UniProtKB: Macrolide export ATP-binding/permease protein MacB

-
Macromolecule #5: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 5 / Number of copies: 3 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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

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

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

-
Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 22 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 49.75 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5nik

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.48 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 233775
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

+
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