+Open data
-Basic information
Entry | Database: PDB / ID: 6tqf | ||||||
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Title | The structure of ABC transporter Rv1819c in AMP-PNP bound state | ||||||
Components | ABC transporter ATP-binding protein/permease | ||||||
Keywords | TRANSPORT PROTEIN / cobalamin / vitamin B12 / ABC transporter / exporter fold / import / tuberculosis | ||||||
Function / homology | Function and homology information long-chain fatty acid import into peroxisome / very long-chain fatty acid catabolic process / peroxisome organization / response to host immune response / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / peroxisomal membrane / long-chain fatty acid transmembrane transporter activity / fatty acid beta-oxidation / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity ...long-chain fatty acid import into peroxisome / very long-chain fatty acid catabolic process / peroxisome organization / response to host immune response / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / peroxisomal membrane / long-chain fatty acid transmembrane transporter activity / fatty acid beta-oxidation / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / ATP hydrolysis activity / extracellular region / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
Authors | Rempel, S. / Gati, C. / Slotboom, D.J. / Guskov, A. | ||||||
Citation | Journal: Nature / Year: 2020 Title: A mycobacterial ABC transporter mediates the uptake of hydrophilic compounds. Authors: S Rempel / C Gati / M Nijland / C Thangaratnarajah / A Karyolaimos / J W de Gier / A Guskov / D J Slotboom / Abstract: Mycobacterium tuberculosis (Mtb) is an obligate human pathogen and the causative agent of tuberculosis. Although Mtb can synthesize vitamin B (cobalamin) de novo, uptake of cobalamin has been linked ...Mycobacterium tuberculosis (Mtb) is an obligate human pathogen and the causative agent of tuberculosis. Although Mtb can synthesize vitamin B (cobalamin) de novo, uptake of cobalamin has been linked to pathogenesis of tuberculosis. Mtb does not encode any characterized cobalamin transporter; however, the gene rv1819c was found to be essential for uptake of cobalamin. This result is difficult to reconcile with the original annotation of Rv1819c as a protein implicated in the transport of antimicrobial peptides such as bleomycin. In addition, uptake of cobalamin seems inconsistent with the amino acid sequence, which suggests that Rv1819c has a bacterial ATP-binding cassette (ABC)-exporter fold. Here, we present structures of Rv1819c, which reveal that the protein indeed contains the ABC-exporter fold, as well as a large water-filled cavity of about 7,700 Å, which enables the protein to transport the unrelated hydrophilic compounds bleomycin and cobalamin. On the basis of these structures, we propose that Rv1819c is a multi-solute transporter for hydrophilic molecules, analogous to the multidrug exporters of the ABC transporter family, which pump out structurally diverse hydrophobic compounds from cells. | ||||||
History |
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-Structure visualization
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Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6tqf.cif.gz | 236.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tqf.ent.gz | 191.7 KB | Display | PDB format |
PDBx/mmJSON format | 6tqf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tqf_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6tqf_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 6tqf_validation.xml.gz | 39.9 KB | Display | |
Data in CIF | 6tqf_validation.cif.gz | 59.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tq/6tqf ftp://data.pdbj.org/pub/pdb/validation_reports/tq/6tqf | HTTPS FTP |
-Related structure data
Related structure data | 10550MC 6tqeC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 72422.000 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) Gene: yddA, yddA_3, DSI35_15825, ERS007665_02362, ERS007670_02474, ERS023446_03427, ERS027651_03600, ERS027652_02163, ERS027654_01933, ERS027656_03005, ERS027659_02286, ERS027661_01835, ERS027666_ ...Gene: yddA, yddA_3, DSI35_15825, ERS007665_02362, ERS007670_02474, ERS023446_03427, ERS027651_03600, ERS027652_02163, ERS027654_01933, ERS027656_03005, ERS027659_02286, ERS027661_01835, ERS027666_01377, ERS124361_03074, EZX46_07135, FDK60_09470, SAMEA2682835_03741, SAMEA2682864_01404, SAMEA2683035_00870 Production host: Escherichia coli (E. coli) / References: UniProt: A0A045ITS3, UniProt: P9WQI9*PLUS #2: Sugar | ChemComp-LMT / #3: Chemical | #4: Chemical | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: dimer of Rv1819c / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Mycobacterium tuberculosis (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 6.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: OTHER |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.16_3549: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 314691 / Symmetry type: POINT | ||||||||||||||||||||||||
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