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- EMDB-62611: Cryo-EM structure of MsRv1273c/72c(E553Q) mutant from Mycobacteri... -

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Basic information

Entry
Database: EMDB / ID: EMD-62611
TitleCryo-EM structure of MsRv1273c/72c(E553Q) mutant from Mycobacterium smegmatis in the ATP-bound Occ state
Map data
Sample
  • Complex: MsRv1273c/72c,MSMEG_5008-MSMEG_5009
    • Protein or peptide: ABC transporter, ATP-binding protein
    • Protein or peptide: ABC transporter
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsABC Transporter / exporter / TRANSPORT PROTEIN
Function / homology
Function and homology information


ABC-type oligopeptide transporter activity / ABC-type transporter activity / 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
ABC transporter, ATP-binding protein / Fatty acid ABC transporter ATP-binding/permease protein
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsLan Y / Yu J / Li J
Funding support China, 2 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFA1300900 China
Other government22ZR1441600
CitationJournal: Nat Commun / Year: 2025
Title: Structure and mechanism of a mycobacterial isoniazid efflux pump MsRv1273c/72c with a degenerate nucleotide-binding site.
Authors: Jing Yu / Yuhui Lan / Chen Zhu / Zhendong Chen / Junyi Pan / Yanfeng Shi / Lan Yang / Tianyu Hu / Yan Gao / Yao Zhao / Xiaobo Chen / Xiuna Yang / Shuihua Lu / Luke W Guddat / Haitao Yang / Zihe Rao / Jun Li /
Abstract: Heterodimeric ATP-binding cassette (ABC) transporters containing one catalytically impaired degenerate nucleotide-binding site (NBS) have a mechanism different from those with two active NBSs. ...Heterodimeric ATP-binding cassette (ABC) transporters containing one catalytically impaired degenerate nucleotide-binding site (NBS) have a mechanism different from those with two active NBSs. However, the structural basis of their transport mechanism remains to be explained. Here, we determine mycobacterial MsRv1273c/72c to be an isoniazid efflux pump and determine several structures by cryo-electron microscopy showing specific asymmetrical features including an N-terminal extending loop and a periplasmic helical hairpin only found in MsRv1272c. In addition, we capture three distinct asymmetric states where the nucleotide-binding domains are partially dimerized at the degenerate site. Using these intermediate states, the D-WalkerB loop and X-signature loop of MsRv1272c modulate and couple the function of both NBSs through conformational changes. Thus, these data provide insights into the mechanism of this heterodimeric ABC transporter containing a degenerate NBS. The structures also provide a framework for the rational design of anti-tuberculosis drugs targeting this drug-efflux pump.
History
DepositionDec 5, 2024-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62611.png

Downloads & links

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Map

FileDownload / File: emd_62611.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 249.6 Å		0.83 Å/pix.
x 300 pix.
= 249.6 Å		0.83 Å/pix.
x 300 pix.
= 249.6 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-1.5608801 - 3.0926483
Average (Standard dev.)-0.0021263764 (±0.06757309)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 249.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62611_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62611_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : MsRv1273c/72c,MSMEG_5008-MSMEG_5009

EntireName: MsRv1273c/72c,MSMEG_5008-MSMEG_5009
Components
  • Complex: MsRv1273c/72c,MSMEG_5008-MSMEG_5009
    • Protein or peptide: ABC transporter, ATP-binding protein
    • Protein or peptide: ABC transporter
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: MsRv1273c/72c,MSMEG_5008-MSMEG_5009

SupramoleculeName: MsRv1273c/72c,MSMEG_5008-MSMEG_5009 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)

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Macromolecule #1: ABC transporter, ATP-binding protein

MacromoleculeName: ABC transporter, ATP-binding protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 61.872266 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: SNMLWALLRQ YVRPYRWLLA VVAVLQVISN MASLYLPTVN AAIIDDGVAK GDTARIVELG AVMLGVTALQ VVCAVGAVFF GARAATGFG HDLRAAVFTH VTTFSAEEAG RFGAASLLTR TTNDVGHIQQ LVQLTVTMLI TAPIMSIGGI FMALHQDAGL S WLLLVSVP ...String:
SNMLWALLRQ YVRPYRWLLA VVAVLQVISN MASLYLPTVN AAIIDDGVAK GDTARIVELG AVMLGVTALQ VVCAVGAVFF GARAATGFG HDLRAAVFTH VTTFSAEEAG RFGAASLLTR TTNDVGHIQQ LVQLTVTMLI TAPIMSIGGI FMALHQDAGL S WLLLVSVP VLGLANYWII RHLMPVFTRM QSLIDGINRV LRDQLSGIRV IRAFAREPLE RVRFAEANQT LSDSALEAGR WQ ALMLPVT TLVINVSSVA LIWFGGLRID AGQMQVGSLI AFLAYFMQIL MAVLMATFML VIFPRAAVCA DRIGEVLSTQ TAI TNPADP VRPAAIAGDI GVHDATFCYP GADRPVLQDV SFTVPRGTTT AVVGSTGSGK STLISLICRL YDVTSGSLRI DGVD VRDLD IEQLWSAIGL VPQRGYLFSG TVAENLRYGR ADATDDEMWE ALRVAAAADF VRAHPQGLDM PVAQGGINFS GGQRQ RLAI ARAVIRRPAI YLFDDAFSAL DVHTDARVRD ALREVAADAT VVIVSQRIST VIEADQVVVI DDGRVVGIGT HDTLLA DCP IYAEFAESQA L

UniProtKB: ABC transporter, ATP-binding protein

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Macromolecule #2: ABC transporter

MacromoleculeName: ABC transporter / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 66.987422 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: TRDFKGSAIR LARRLLPQRA LTLAVILLGV GGIAIGVIGP RILGHATDLL FNGVIGRELP AGLTKEQAVE AARARGDGTF ADLLSGMDI VPGQGVDFGA VGRTLALALG LYLVAALLVW VQARLLNVTV QRTMVALRAE VQEKIHRLPL SYFDSRQRGE V LSRVTNDV ...String:
TRDFKGSAIR LARRLLPQRA LTLAVILLGV GGIAIGVIGP RILGHATDLL FNGVIGRELP AGLTKEQAVE AARARGDGTF ADLLSGMDI VPGQGVDFGA VGRTLALALG LYLVAALLVW VQARLLNVTV QRTMVALRAE VQEKIHRLPL SYFDSRQRGE V LSRVTNDV DNIQNSVSMT ISQLLTSVLT VFAVLVMMLT ISPLLTLFTV VTVPASLWVT RWITRRSQPL FVAQWRNTGR LA AHLEETY SGFTIVKTFG HREAAAGKFA ELNSETQQSS FGAQFFSGLV SPATMFIGNL SYVAVAVVGG LQVATGQITL GSI QAFIQY VRQFNQPLTQ VAGMYNTLQS GIASAERVFD LLDTEEESAD SPRRADVRTG RVEFEHVSFS YVPGTPVIED LSLV AEPGS TVAIVGPTGA GKTTLVNLLM RFYDVDSGRI TIDGVDIASV SRESLRASIG MVLQDTWLFA GTIYDNIAYG RPDAD EDEV IEAATAAYVD RFVHTLPNGY DTRVDDDGGA ISAGEKQLIT IARAVLARPK LLVLDQATSS VDTRTELLIA HAMAEL RRD RTSFIIAHRL STIRDADLIL VMDSGRIIER GTHEELLARH GRYWEMTRVH LGG

UniProtKB: Fatty acid ABC transporter ATP-binding/permease protein

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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 79033
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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