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Yorodumi- EMDB-0499: CryoEM structure of Helicobacter pylori urea channel in open state. -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0499 | |||||||||
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Title | CryoEM structure of Helicobacter pylori urea channel in open state. | |||||||||
Map data | em-volume_P1.map | |||||||||
Sample |
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Keywords | Helicobacter pylori / urea channel / open state / TRANSPORT PROTEIN | |||||||||
Function / homology | AmiS/UreI transporter / AmiS/UreI transporter superfamily / AmiS/UreI family transporter / identical protein binding / plasma membrane / Acid-activated urea channel Function and homology information | |||||||||
Biological species | Helicobacter pylori (bacteria) / Helicobacter pylori (strain J99 / ATCC 700824) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | Cui YX / Zhou K | |||||||||
Funding support | United States, 2 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0499.map.gz | 14.6 MB | EMDB map data format | |
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Header (meta data) | emd-0499-v30.xml emd-0499.xml | 19.9 KB 19.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0499_fsc.xml | 5.7 KB | Display | FSC data file |
Images | emd_0499.png | 3 MB | ||
Masks | emd_0499_msk_1.map | 15.6 MB | Mask map | |
Filedesc metadata | emd-0499.cif.gz | 6.3 KB | ||
Others | emd_0499_half_map_1.map.gz emd_0499_half_map_2.map.gz | 11.1 MB 11.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0499 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0499 | HTTPS FTP |
-Validation report
Summary document | emd_0499_validation.pdf.gz | 813.2 KB | Display | EMDB validaton report |
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Full document | emd_0499_full_validation.pdf.gz | 812.7 KB | Display | |
Data in XML | emd_0499_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | emd_0499_validation.cif.gz | 15.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0499 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0499 | HTTPS FTP |
-Related structure data
Related structure data | 6nskMC 0498C 6nsjC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_0499.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | em-volume_P1.map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_0499_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: em-half-volume P1
File | emd_0499_half_map_1.map | ||||||||||||
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Annotation | em-half-volume_P1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: em-half-volume P2
File | emd_0499_half_map_2.map | ||||||||||||
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Annotation | em-half-volume_P2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : urea channel of Helicobacter pylori
Entire | Name: urea channel of Helicobacter pylori |
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Components |
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-Supramolecule #1: urea channel of Helicobacter pylori
Supramolecule | Name: urea channel of Helicobacter pylori / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Helicobacter pylori (bacteria) / Strain: J99 |
Molecular weight | Theoretical: 20 KDa |
-Macromolecule #1: Acid-activated urea channel
Macromolecule | Name: Acid-activated urea channel / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Helicobacter pylori (strain J99 / ATCC 700824) (bacteria) Strain: J99 / ATCC 700824 |
Molecular weight | Theoretical: 22.533258 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MLGLVLLYVG IVLISNGICG LTKVDPKSTA VMNFFVGGLS IVCNVVVITY SALHPTAPVE GHHHHHHAED IVQVSHHLTS FYGPATGLL FGFTYLYAAI NHTFGLDWRP YSWYSLFVAI NTVPAAILSH YSDMLDDHKV LGITEGDWWA IIWLAWGVLW L TAFIENIL ...String: MLGLVLLYVG IVLISNGICG LTKVDPKSTA VMNFFVGGLS IVCNVVVITY SALHPTAPVE GHHHHHHAED IVQVSHHLTS FYGPATGLL FGFTYLYAAI NHTFGLDWRP YSWYSLFVAI NTVPAAILSH YSDMLDDHKV LGITEGDWWA IIWLAWGVLW L TAFIENIL KIPLGKFTPW LAIIEGILTA WIPAWLLFIQ HWV UniProtKB: Acid-activated urea channel |
-Macromolecule #2: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHATE
Macromolecule | Name: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHATE / type: ligand / ID: 2 / Number of copies: 18 / Formula: XP4 |
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Molecular weight | Theoretical: 591.777 Da |
Chemical component information | ChemComp-XP4: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | 2D array |
-Sample preparation
Concentration | 2 mg/mL | ||||||||
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Buffer | pH: 7 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: FORMVAR / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE | ||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 98.0 K / Max: 100.0 K |
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Frames/image: 2-59 / Number grids imaged: 1 / Number real images: 2901 / Average exposure time: 9.0 sec. / Average electron dose: 43.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: 2.6 µm / Calibrated defocus min: 1.2 µm / Calibrated magnification: 46730 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |