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- EMDB-36798: mycobacterial efflux pump, ADP+vanadate bound state -

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Basic information

Entry
Database: EMDB / ID: EMD-36798
Titlemycobacterial efflux pump, ADP+vanadate bound state
Map dataEM map of mycobacterial efflux pump, ADP vanadate bound state
Sample
  • Complex: ternary complex of an ABC transporter Rv1217c-1218c
    • Protein or peptide: Multidrug efflux system permease protein Rv1217c
    • Protein or peptide: Multidrug efflux system ATP-binding protein Rv1218c
  • Ligand: CARDIOLIPIN
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: VANADATE ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsABC transporter / efflux pump / TRANSPORT PROTEIN
Function / homology
Function and homology information


Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / response to antibiotic / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
: / Domain of unknown function DUF4162 / Domain of unknown function (DUF4162) / 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
Multidrug efflux system permease protein Rv1217c / Multidrug efflux system ATP-binding protein Rv1218c
Similarity search - Component
Biological speciesMycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsWang Y / Wu F / Zhang L / Rao Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32170703 China
CitationJournal: To Be Published
Title: mycobacterial efflux pump, ADP+vanadate bound state
Authors: Wang Y / Wu F / Zhang L / Rao Z
History
DepositionJul 11, 2023-
Header (metadata) releaseJul 17, 2024-
Map releaseJul 17, 2024-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36798.png

Downloads & links

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Map

FileDownload / File: emd_36798.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map of mycobacterial efflux pump, ADP vanadate bound state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 384 pix.
= 314.88 Å		0.82 Å/pix.
x 384 pix.
= 314.88 Å		0.82 Å/pix.
x 384 pix.
= 314.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-2.5318086 - 4.0262003
Average (Standard dev.)-0.00043787726 (±0.06427869)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 314.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map B of mycobacterial efflux pump, ADP vanadate bound state

Fileemd_36798_half_map_1.map
Annotationhalf map B of mycobacterial efflux pump, ADP vanadate bound state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A of mycobacterial efflux pump, ADP vanadate bound state

Fileemd_36798_half_map_2.map
Annotationhalf map A of mycobacterial efflux pump, ADP vanadate bound state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ternary complex of an ABC transporter Rv1217c-1218c

EntireName: ternary complex of an ABC transporter Rv1217c-1218c
Components
  • Complex: ternary complex of an ABC transporter Rv1217c-1218c
    • Protein or peptide: Multidrug efflux system permease protein Rv1217c
    • Protein or peptide: Multidrug efflux system ATP-binding protein Rv1218c
  • Ligand: CARDIOLIPIN
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: VANADATE ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: ternary complex of an ABC transporter Rv1217c-1218c

SupramoleculeName: ternary complex of an ABC transporter Rv1217c-1218c / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Molecular weightTheoretical: 120 KDa

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Macromolecule #1: Multidrug efflux system permease protein Rv1217c

MacromoleculeName: Multidrug efflux system permease protein Rv1217c / type: protein_or_peptide / ID: 1 / Details: transmembrane domain / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Molecular weightTheoretical: 56.698039 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: MSSTVIDRAR PAGHRAPHRG SGFTGTLGLL RLYLRRDRVS LPLWVLLLSV PLATVYIASV ETVYPDRSAR AAAAAAIMAS PAQRALYGP VYNDSLGAVG IWKAGMFHTL IAVAVILTVI RHTRADEESG RAELIDSTVV GRYANLTGAL LLSFGASIAT G AIGALGLL ...String:
MSSTVIDRAR PAGHRAPHRG SGFTGTLGLL RLYLRRDRVS LPLWVLLLSV PLATVYIASV ETVYPDRSAR AAAAAAIMAS PAQRALYGP VYNDSLGAVG IWKAGMFHTL IAVAVILTVI RHTRADEESG RAELIDSTVV GRYANLTGAL LLSFGASIAT G AIGALGLL ATDVAPAGSV AFGVALAASG MVFTAVAAVA AQLSPSARFT RAVAFAVLGT AFALRAIGDA GSGTLSWCSP LG WSLQVRP YAGERWWVLL LSLATAAVLT VLAYRLRAGR DVGAGLIAER PGAGTAGPML SEPFGLAWRL NRGSLLLWTV GLC LYGLVM GSVVHGIGDQ LGDNTAVRDI VTRMGGTGAL EQAFLALAFT MIGMVAAAFA VSLTLRLHQE ETGLRAETLL AGAV SRTHW LASHLAMALA GSAVATLISG VAAGLAYGMT VGDVGGKLPT VVGTAAVQLP AVWLLSAVTV GLFGLAPRFT PVAWG VLVG FIALYLLGSL AGFPQMLLNL EPFAHIPRVG GGDFTAVPLL WLLAIDAALI TLGAMAFRRR DVRC

UniProtKB: Multidrug efflux system permease protein Rv1217c

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Macromolecule #2: Multidrug efflux system ATP-binding protein Rv1218c

MacromoleculeName: Multidrug efflux system ATP-binding protein Rv1218c / type: protein_or_peptide / ID: 2 / Details: nucleotide binding domain / 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: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Molecular weightTheoretical: 33.491082 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: MSADNHQVPI EIRGLTKHFG SVRALDGLDL TVREGEVHGF LGPNGAGKST TLRILLGLVK ADGGSVRLLG GDPWTDAVDL HRHIAYVPG DVTLWPSLTG GETIDLLARM RGGIDNARRA ELIERFGLDP TKKARTYSKG NRQKVSLISA LSSHATLLLL D EPSSGLDP ...String:
MSADNHQVPI EIRGLTKHFG SVRALDGLDL TVREGEVHGF LGPNGAGKST TLRILLGLVK ADGGSVRLLG GDPWTDAVDL HRHIAYVPG DVTLWPSLTG GETIDLLARM RGGIDNARRA ELIERFGLDP TKKARTYSKG NRQKVSLISA LSSHATLLLL D EPSSGLDP LMENVFQQCI GEARQRGVTV LLSSHILAET EALCEKVTII RAGKTVESGS LDALRHLSRT SIKAEMIGDP GD LSQIKGV EDISIEGTTV RAQVDSESLR ELIQVLGHAG VRSLVSQPPT LEELFLRHYS LGPEVAAEQQ VATP

UniProtKB: Multidrug efflux system ATP-binding protein Rv1218c

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Macromolecule #3: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 3 / Number of copies: 2 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*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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Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #6: VANADATE ION

MacromoleculeName: VANADATE ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: VO4
Molecular weightTheoretical: 114.939 Da
Chemical component information

ChemComp-VN3:
VANADATE ION

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Macromolecule #7: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

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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

Concentration8 mg/mL
BufferpH: 7.4 / Details: 150mM NaCl, 20mM Tris, detergent
GridMaterial: COPPER / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK II
Detailssample mono disperse

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 4314 / Average exposure time: 2.4 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 29000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1474569
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 190347
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 5 / Software - Name: cryoSPARC

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