[English] 日本語
Yorodumi
- EMDB-45939: BmrCD in the inward-facing conformation bound to Hoechsts and lipids -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-45939
TitleBmrCD in the inward-facing conformation bound to Hoechsts and lipids
Map dataBmrCD in inward-facing conformation with Hoechsts and lipids
Sample
  • Complex: Heterodimeric BmrCD with ligands ATP and lipids
    • Protein or peptide: Probable multidrug resistance ABC transporter ATP-binding/permease protein YheH
    • Protein or peptide: Probable multidrug resistance ABC transporter ATP-binding/permease protein YheI
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: 2'-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE
  • Ligand: MAGNESIUM ION
KeywordsABC transporter / Exporter / membrane protein / transport
Function / homology
Function and homology information


ATPase-coupled lipid transmembrane transporter activity / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / transmembrane transport / response to antibiotic / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane 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. ...Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane 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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Probable multidrug resistance ABC transporter ATP-binding/permease protein YheH / Probable multidrug resistance ABC transporter ATP-binding/permease protein YheI
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsTang Q / Mchaourab HS
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIGMS R01-128087 United States
CitationJournal: bioRxiv / Year: 2025
Title: Lipid-mediated mechanism of drug extrusion by a heterodimeric ABC exporter.
Authors: Qingyu Tang / Matt Sinclair / Paola Bisignano / Yunsen Zhang / Emad Tajkhorshid / Hassane S Mchaourab /
Abstract: Multidrug transport by ATP binding cassette (ABC) exporters entails a mechanism to modulate drug affinity across the transport cycle. Here, we combine cryo-EM and molecular dynamics (MD) simulations ...Multidrug transport by ATP binding cassette (ABC) exporters entails a mechanism to modulate drug affinity across the transport cycle. Here, we combine cryo-EM and molecular dynamics (MD) simulations to illuminate how lipid competition modulates substrate affinity to drive its translocation by ABC exporters. We determined cryo-EM structures of the ABC transporter BmrCD in drug-loaded inward-facing (IF) and outward-facing (OF) conformations in lipid nanodiscs to reveal the structural basis of alternating access, details of drug-transporter interactions, and the scale of drug movement between the two conformations. Remarkably, the structures uncovered lipid molecules bound in or near the transporter vestibule along with the drugs. MD trajectories from the IF structure show that these lipids stimulate drug disorder and translocation towards the vestibule apex. Similarly, bound lipids enter the OF vestibule and weaken drug-transporter interactions facilitating drug release. Our results complete a near-atomic model of BmrCD's conformational cycle and advance a general mechanism of lipid-driven drug transport by ABC exporters.
History
DepositionJul 26, 2024-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_45939.png

Downloads & links

-
Map

FileDownload / File: emd_45939.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBmrCD in inward-facing conformation with Hoechsts and lipids
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 480 pix.
= 310.56 Å		0.65 Å/pix.
x 480 pix.
= 310.56 Å		0.65 Å/pix.
x 480 pix.
= 310.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.647 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.036
Minimum - Maximum-0.4081308 - 0.51682454
Average (Standard dev.)-0.0001570632 (±0.012266526)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 310.56 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Additional Map

Fileemd_45939_additional_1.map
AnnotationAdditional Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half Map A

Fileemd_45939_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_45939_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Heterodimeric BmrCD with ligands ATP and lipids

EntireName: Heterodimeric BmrCD with ligands ATP and lipids
Components
  • Complex: Heterodimeric BmrCD with ligands ATP and lipids
    • Protein or peptide: Probable multidrug resistance ABC transporter ATP-binding/permease protein YheH
    • Protein or peptide: Probable multidrug resistance ABC transporter ATP-binding/permease protein YheI
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: 2'-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: Heterodimeric BmrCD with ligands ATP and lipids

SupramoleculeName: Heterodimeric BmrCD with ligands ATP and lipids / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)

-
Macromolecule #1: Probable multidrug resistance ABC transporter ATP-binding/permeas...

MacromoleculeName: Probable multidrug resistance ABC transporter ATP-binding/permease protein YheH
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 77.467078 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MKIGKTLWRY ALLYRKLLIT AVLLLTVAVG AELTGPFIGK KMIDDHILGI EKTWYEAAEK DKNAVQFHGV SYVREDRLQE PVSKAKEAH IYQVGMAFYF VDQAVSFDGN RTVSDGKLTI TNGDKSRAYA AEKLTKQELF QFYQPEIKGM VLLICLYGGL L VFSVFFQY ...String:
MKIGKTLWRY ALLYRKLLIT AVLLLTVAVG AELTGPFIGK KMIDDHILGI EKTWYEAAEK DKNAVQFHGV SYVREDRLQE PVSKAKEAH IYQVGMAFYF VDQAVSFDGN RTVSDGKLTI TNGDKSRAYA AEKLTKQELF QFYQPEIKGM VLLICLYGGL L VFSVFFQY GQHYLLQMSA NRIIQKMRQD VFSHIQKMPI RYFDNLPAGK VVARITNDTE AIRDLYVTVL STFVTSGIYM FG IFTALFL LDVKLAFVCL AIVPIIWLWS VIYRRYASYY NQKIRSINSD INAKMNESIQ GMTIIQAFRH QKETMREFEE LNE SHFYFQ NRMLNLNSLM SHNLVNVIRN LAFVCLIWHF GGASLNAAGI VSIGVLYAFV DYLNRLFQPI TGIVNQFSKL ELAR VSAGR VFELLEEKNT EEAGEPAKER ALGRVEFRDV SFAYQEGEEV LKHISFTAQK GETVALVGHT GSGKSSILNL LFRFY DAQK GDVLIDGKSI YNMSRQELRS HMGIVLQDPY LFSGTIGSNV SLDDERMTEE EIKNALRQVG AEPLLKKLPK GINEPV IEK GSTLSSGERQ LISFARALAF DPAILILDEA TAHIDTETEA VIQKALDVVK QGRTTFVIAH RLSTIRNADQ ILVLDKG EI VERGNHEELM ALEGQYYQMY ELQKGQKHSI ALEHHHHHH

UniProtKB: Probable multidrug resistance ABC transporter ATP-binding/permease protein YheH

-
Macromolecule #2: Probable multidrug resistance ABC transporter ATP-binding/permeas...

MacromoleculeName: Probable multidrug resistance ABC transporter ATP-binding/permease protein YheI
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 67.589922 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSH MLEFSVLKKL GWFFKAYWLR YTIAIVLLLA VNVIEMFPPK LLGNAIDDMK AGAFTAEGLL FYIGIFFVL TAAVYIMSYF WMHQLFGGAN LMEKILRTKL MGHLLTMSPP FYEKNRTGDL MARGTNDLQA VSLTTGFGIL T LVDSTMFM ...String:
MGSSHHHHHH SSGLVPRGSH MLEFSVLKKL GWFFKAYWLR YTIAIVLLLA VNVIEMFPPK LLGNAIDDMK AGAFTAEGLL FYIGIFFVL TAAVYIMSYF WMHQLFGGAN LMEKILRTKL MGHLLTMSPP FYEKNRTGDL MARGTNDLQA VSLTTGFGIL T LVDSTMFM MTIFLTMGFL ISWKLTFAAI IPLPVMAIAI SLYGSKIHER FTEAQNAFGA LNDRVLESVS GVRVIRAYVQ ET NDVRRFN EMTADVYQKN MKVAFIDSLF EPTVKLLVGA SYLIGLGYGA FLVFRNELTL GELVSFNVYL GMMIWPMFAI GEL INVMQR GNASLDRVNE TLSYETDVTD PKQPADLKEP GDIVFSHVSF TYPSSTSDNL QDISFTVRKG QTVGIAGKTG SGKT TIIKQ LLRQYPPGEG SITFSGVPIQ QIPLDRLRGW IGYVPQDHLL FSRTVKENIL YGKQDATDKE VQQAIAEAHF EKDLH MLPS GLETMVGEKG VALSGGQKQR ISIARALMAN PEILILDDSL SAVDAKTEAA IIKNIRENRK GKTTFILTHR LSAVEH ADL ILVMDGGVIA ERGTHQELLA NNGWYREQYE RQQLFTAEEG GAGA

UniProtKB: Probable multidrug resistance ABC transporter ATP-binding/permease protein YheI

-
Macromolecule #3: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 3 / Number of copies: 27 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

-
Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

-
Macromolecule #5: 2'-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE

MacromoleculeName: 2'-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE
type: ligand / ID: 5 / Number of copies: 2 / Formula: HT1
Molecular weightTheoretical: 452.551 Da
Chemical component information

ChemComp-HT1:
2'-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE

-
Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 15.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.4 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8fhk

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 74260
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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