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Yorodumi- PDB-6nsk: CryoEM structure of Helicobacter pylori urea channel in open state. -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nsk | |||||||||
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Title | CryoEM structure of Helicobacter pylori urea channel in open state. | |||||||||
Components | Acid-activated urea channel | |||||||||
Keywords | TRANSPORT PROTEIN / Helicobacter pylori / urea channel / open state | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Helicobacter pylori (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | Cui, Y.X. / Zhou, K. / Strugatsky, D. / Wen, Y. / Sachs, G. / Munson, K. / Zhou, Z.H. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Sci Adv / Year: 2019 Title: pH-dependent gating mechanism of the urea channel revealed by cryo-EM. Authors: Yanxiang Cui / Kang Zhou / David Strugatsky / Yi Wen / George Sachs / Z Hong Zhou / Keith Munson / Abstract: The urea channel of (UreI) is an ideal drug target for preventing gastric cancer but incomplete understanding of its gating mechanism has hampered development of inhibitors for the eradication of . ...The urea channel of (UreI) is an ideal drug target for preventing gastric cancer but incomplete understanding of its gating mechanism has hampered development of inhibitors for the eradication of . Here, we present the cryo-EM structures of UreI in closed and open conformations, both at a resolution of 2.7 Å. Our hexameric structures of this small membrane protein (~21 kDa/protomer) resolve its periplasmic loops and carboxyl terminus that close and open the channel, and define a gating mechanism that is pH dependent and requires cooperativity between protomers in the hexamer. Gating is further associated with well-resolved changes in the channel-lining residues that modify the shape and length of the urea pore. Site-specific mutations in the periplasmic domain and urea pore identified key residues important for channel function. Drugs blocking the urea pore based on our structures should lead to a new strategy for eradication. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6nsk.cif.gz | 206 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nsk.ent.gz | 165.8 KB | Display | PDB format |
PDBx/mmJSON format | 6nsk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6nsk_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 6nsk_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 6nsk_validation.xml.gz | 45.5 KB | Display | |
Data in CIF | 6nsk_validation.cif.gz | 63 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ns/6nsk ftp://data.pdbj.org/pub/pdb/validation_reports/ns/6nsk | HTTPS FTP |
-Related structure data
Related structure data | 0499MC 0498C 6nsjC 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: 22533.258 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (strain J99 / ATCC 700824) (bacteria) Strain: J99 / ATCC 700824 / Gene: ureI, jhp_0066 / Production host: Escherichia coli (E. coli) / References: UniProt: P56874 #2: Chemical | ChemComp-XP4 / |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: 2D ARRAY / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: urea channel of Helicobacter pylori / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT | ||||||||||||||||
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Molecular weight | Value: 0.02 MDa / Experimental value: YES | ||||||||||||||||
Source (natural) | Organism: Helicobacter pylori (bacteria) / Strain: J99 | ||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||||||
Buffer solution | pH: 7 | ||||||||||||||||
Buffer component |
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Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 | ||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-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: BRIGHT FIELD / Nominal magnification: 130000 X / Calibrated magnification: 46730 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1400 nm / Calibrated defocus min: 1200 nm / Calibrated defocus max: 2600 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 100 K / Temperature (min): 98 K |
Image recording | Average exposure time: 9 sec. / Electron dose: 43 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2901 |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV |
Image scans | Sampling size: 5 µm / Width: 3710 / Height: 3838 / Movie frames/image: 60 / Used frames/image: 2-59 |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1017209 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C6 (6 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 279840 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 89.5 / Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 3UX4 Accession code: 3UX4 / Source name: PDB / Type: experimental model |