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Open data
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Basic information
Entry | Database: PDB / ID: 8k1p | |||||||||||||||||||||
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Title | mycobacterial efflux pump, ADP+vanadate bound state | |||||||||||||||||||||
![]() | (Multidrug efflux system ...) x 2 | |||||||||||||||||||||
![]() | TRANSPORT PROTEIN / ABC transporter / efflux pump | |||||||||||||||||||||
Function / homology | ![]() 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 | |||||||||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||||||||||||||
![]() | Wang, Y. / Wu, F. / Zhang, L. / Rao, Z. | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: mycobacterial efflux pump, ADP+vanadate bound state Authors: Wang, Y. / Wu, F. / Zhang, L. / Rao, Z. | |||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 174.2 KB | Display | ![]() |
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PDB format | ![]() | 133 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 618.9 KB | Display | ![]() |
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Full document | ![]() | 629.3 KB | Display | |
Data in XML | ![]() | 20.8 KB | Display | |
Data in CIF | ![]() | 31.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 36798MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Multidrug efflux system ... , 2 types, 3 molecules ABC
#1: Protein | Mass: 56698.039 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: transmembrane domain Source: (gene. exp.) ![]() Gene: Rv1217c / Plasmid: PMV261 Production host: ![]() References: UniProt: O05318 |
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#2: Protein | Mass: 33491.082 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: nucleotide binding domain Source: (gene. exp.) ![]() Gene: Rv1218c / Plasmid: PMV261 Production host: ![]() References: UniProt: O86311, Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate |
-Non-polymers , 5 types, 7 molecules 








#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-ADP / | #6: Chemical | ChemComp-VO4 / | #7: Chemical | ChemComp-ATP / | |
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-Details
Has ligand of interest | Y |
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Has protein modification | N |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: ternary complex of an ABC transporter Rv1217c-1218c / Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES |
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Molecular weight | Value: 0.12 MDa / Experimental value: YES |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 7.4 / Details: 150mM NaCl, 20mM Tris, detergent |
Specimen | Conc.: 8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: sample mono disperse |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. |
Vitrification | Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 29000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: BASIC |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 2.4 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4314 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1474569 | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 190347 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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