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- EMDB-29362: Heterodimeric ABC transporter BmrCD in the inward-facing conforma... -

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Basic information

Entry
Database: EMDB / ID: EMD-29362
TitleHeterodimeric ABC transporter BmrCD in the inward-facing conformation bound to ATP: BmrCD_IF-ATP
Map dataStructure0524
Sample
  • Complex: Heterodimeric BmrCD with ATP in lipid bilayers
    • 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
Keywordstransporter / complex / lipids / MEMBRANE PROTEIN / TRANSLOCASE / TRANSPORT PROTEIN
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: 3.27 Å
AuthorsQingyu T / Hassane M
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: Nat Commun / Year: 2023
Title: Asymmetric conformations and lipid interactions shape the ATP-coupled cycle of a heterodimeric ABC transporter.
Authors: Qingyu Tang / Matt Sinclair / Hale S Hasdemir / Richard A Stein / Erkan Karakas / Emad Tajkhorshid / Hassane S Mchaourab /
Abstract: Here we used cryo-electron microscopy (cryo-EM), double electron-electron resonance spectroscopy (DEER), and molecular dynamics (MD) simulations, to capture and characterize ATP- and substrate-bound ...Here we used cryo-electron microscopy (cryo-EM), double electron-electron resonance spectroscopy (DEER), and molecular dynamics (MD) simulations, to capture and characterize ATP- and substrate-bound inward-facing (IF) and occluded (OC) conformational states of the heterodimeric ATP binding cassette (ABC) multidrug exporter BmrCD in lipid nanodiscs. Supported by DEER analysis, the structures reveal that ATP-powered isomerization entails changes in the relative symmetry of the BmrC and BmrD subunits that propagates from the transmembrane domain to the nucleotide binding domain. The structures uncover asymmetric substrate and Mg binding which we hypothesize are required for triggering ATP hydrolysis preferentially in one of the nucleotide-binding sites. MD simulations demonstrate that multiple lipid molecules differentially bind the IF versus the OC conformation thus establishing that lipid interactions modulate BmrCD energy landscape. Our findings are framed in a model that highlights the role of asymmetric conformations in the ATP-coupled transport with general implications to the mechanism of ABC transporters.
History
DepositionJan 4, 2023-
Header (metadata) releaseNov 22, 2023-
Map releaseNov 22, 2023-
UpdateNov 22, 2023-
Current statusNov 22, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29362.png

Downloads & links

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Map

FileDownload / File: emd_29362.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure0524
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.43
Minimum - Maximum-0.36842576 - 5.439068
Average (Standard dev.)0.027218858 (±0.06704318)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 330.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Additional Map 1

Fileemd_29362_additional_1.map
AnnotationAdditional Map 1
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Additional map: Additional Map 2

Fileemd_29362_additional_2.map
AnnotationAdditional Map 2
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Additional map: Additional Map 3

Fileemd_29362_additional_3.map
AnnotationAdditional Map 3
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Additional map: Additional Map 4

Fileemd_29362_additional_4.map
AnnotationAdditional Map 4
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Additional map: Additional Map 5

Fileemd_29362_additional_5.map
AnnotationAdditional Map 5
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Additional map: Additional Map 6

Fileemd_29362_additional_6.map
AnnotationAdditional Map 6
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Half map: Half Map 1

Fileemd_29362_half_map_1.map
AnnotationHalf Map 1
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Half map: Half Map 2

Fileemd_29362_half_map_2.map
AnnotationHalf Map 2
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Sample components

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Entire : Heterodimeric BmrCD with ATP in lipid bilayers

EntireName: Heterodimeric BmrCD with ATP in lipid bilayers
Components
  • Complex: Heterodimeric BmrCD with ATP in lipid bilayers
    • 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

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Supramolecule #1: Heterodimeric BmrCD with ATP in lipid bilayers

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

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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: 77.369898 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKIGKTLWRY ALLYRKLLIT AVLLLTVAVG AELTGPFIGK KMIDDHILGI EKTWYEAAEK DKNAVQFHGV SYVREDRLQE PVSKAKEAH IYQVGMAFYF VDQAVSFDGN RTVSDGKLTI TNGDKSRAYA AEKLTKQELF QFYQPEIKGM VLLIALYGGL L VFSVFFQY ...String:
MKIGKTLWRY ALLYRKLLIT AVLLLTVAVG AELTGPFIGK KMIDDHILGI EKTWYEAAEK DKNAVQFHGV SYVREDRLQE PVSKAKEAH IYQVGMAFYF VDQAVSFDGN RTVSDGKLTI TNGDKSRAYA AEKLTKQELF QFYQPEIKGM VLLIALYGGL L VFSVFFQY GQHYLLQMSA NRIIQKMRQD VFSHIQKMPI RYFDNLPAGK VVARITNDTE AIRDLYVTVL STFVTSGIYM FG IFTALFL LDVKLAFVAL AIVPIIWLWS VIYRRYASYY NQKIRSINSD INAKMNESIQ GMTIIQAFRH QKETMREFEE LNE SHFYFQ NRMLNLNSLM SHNLVNVIRN LAFVALIWHF 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 DPAILILDQA TAHIDTETEA VIQKALDVVK QGRTTFVIAH RLSTIRNADQ ILVLDKG EI VERGNHEELM ALEGQYYQMY ELQKGQKHSI ALEHHHHHH

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

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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: 67.602961 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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 PEILILDQSL SAVDAKTEAA IIKNIRENRK GKTTFILTHR LSAVEH ADL ILVMDGGVIA ERGTHQELLA NNGWYREQYE RQQLFTAEEG GAGA

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

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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: 25 / 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 / POPC

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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 / Adenosine triphosphate

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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

Concentration3 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 54.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7m33

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 255381

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