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Yorodumi- EMDB-11233: Helicobacter pylori urease with inhibitor bound in the active site -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11233 | |||||||||
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Title | Helicobacter pylori urease with inhibitor bound in the active site | |||||||||
Map data | Relion unmasked map | |||||||||
Sample |
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Function / homology | Function and homology information urease complex / urease / urease activity / urea catabolic process / nickel cation binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Helicobacter pylori (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.0 Å | |||||||||
Authors | Luecke H / Cunha E | |||||||||
Funding support | Norway, United States, 2 items
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Citation | Journal: Nat Commun / Year: 2021 Title: Cryo-EM structure of Helicobacter pylori urease with an inhibitor in the active site at 2.0 Å resolution. Authors: Eva S Cunha / Xiaorui Chen / Marta Sanz-Gaitero / Deryck J Mills / Hartmut Luecke / Abstract: Infection of the human stomach by Helicobacter pylori remains a worldwide problem and greatly contributes to peptic ulcer disease and gastric cancer. Without active intervention approximately 50% of ...Infection of the human stomach by Helicobacter pylori remains a worldwide problem and greatly contributes to peptic ulcer disease and gastric cancer. Without active intervention approximately 50% of the world population will continue to be infected with this gastric pathogen. Current eradication, called triple therapy, entails a proton-pump inhibitor and two broadband antibiotics, however resistance to either clarithromycin or metronidazole is greater than 25% and rising. Therefore, there is an urgent need for a targeted, high-specificity eradication drug. Gastric infection by H. pylori depends on the expression of a nickel-dependent urease in the cytoplasm of the bacteria. Here, we report the 2.0 Å resolution structure of the 1.1 MDa urease in complex with an inhibitor by cryo-electron microscopy and compare it to a β-mercaptoethanol-inhibited structure at 2.5 Å resolution. The structural information is of sufficient detail to aid in the development of inhibitors with high specificity and affinity. | |||||||||
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_11233.map.gz | 370.2 MB | EMDB map data format | |
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Header (meta data) | emd-11233-v30.xml emd-11233.xml | 22.6 KB 22.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11233_fsc.xml | 16.5 KB | Display | FSC data file |
Images | emd_11233.png | 274 KB | ||
Masks | emd_11233_msk_1.map | 396.1 MB | Mask map | |
Others | emd_11233_additional_1.map.gz emd_11233_half_map_1.map.gz emd_11233_half_map_2.map.gz | 70.9 MB 314.8 MB 314.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11233 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11233 | HTTPS FTP |
-Validation report
Summary document | emd_11233_validation.pdf.gz | 388.6 KB | Display | EMDB validaton report |
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Full document | emd_11233_full_validation.pdf.gz | 387.8 KB | Display | |
Data in XML | emd_11233_validation.xml.gz | 22.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11233 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11233 | HTTPS FTP |
-Related structure data
Related structure data | 6zjaMC 4629C 6qsuC M: atomic model generated by this map C: citing same article (ref.) |
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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_11233.map.gz / Format: CCP4 / Size: 396.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Relion unmasked map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.8426 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_11233_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Density modified map
File | emd_11233_additional_1.map | ||||||||||||
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Annotation | Density modified map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_11233_half_map_1.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_11233_half_map_2.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : 1.1 MDa Helicobacter pylori Urease
Entire | Name: 1.1 MDa Helicobacter pylori Urease |
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Components |
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-Supramolecule #1: 1.1 MDa Helicobacter pylori Urease
Supramolecule | Name: 1.1 MDa Helicobacter pylori Urease / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Helicobacter pylori (bacteria) / Strain: UMAB41 / Location in cell: Cytoplasm |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant plasmid: pHP808, pHP902 |
Molecular weight | Theoretical: 1.1 MDa |
-Macromolecule #1: Urease subunit alpha
Macromolecule | Name: Urease subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO / EC number: urease |
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Source (natural) | Organism: Helicobacter pylori (bacteria) |
Molecular weight | Theoretical: 26.645703 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKLTPKELDK LMLHYAGELA RKRKEKGIKL NYVEAVALIS AHIMEEARAG KKTAAELMQE GRTLLKPDDV MDGVASMIHE VGIEAMFPD GTKLVTVHTP IEANGKLVPG ELFLKNEDIT INEGKKAVSV KVKNVGDRPV QIGSHFHFFE VNRCLDFDRE K TFGKRLDI ...String: MKLTPKELDK LMLHYAGELA RKRKEKGIKL NYVEAVALIS AHIMEEARAG KKTAAELMQE GRTLLKPDDV MDGVASMIHE VGIEAMFPD GTKLVTVHTP IEANGKLVPG ELFLKNEDIT INEGKKAVSV KVKNVGDRPV QIGSHFHFFE VNRCLDFDRE K TFGKRLDI ASGTAVRFEP GEEKSVELID IGGNRRIFGF NALVDRQADN ESKKIALHRA KERGFHGTKS DDNYVKTIKE |
-Macromolecule #2: Urease subunit beta
Macromolecule | Name: Urease subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO / EC number: urease |
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Source (natural) | Organism: Helicobacter pylori (bacteria) |
Molecular weight | Theoretical: 61.832531 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKKISRKEYV SMYGPTTGDK VRLGDTDLIA EVEHDYTIYG EELKFGGGKT LREGMSQSNN PSKEELDLII TNALIVDYTG IYKADIGIK DGKIAGIGKG GNKDMQDGVK NNLSVGPATE ALAGEGLIVT AGGIDTHIHF ISPQQIPTAF ASGVTTMIGG G TGPADGTN ...String: MKKISRKEYV SMYGPTTGDK VRLGDTDLIA EVEHDYTIYG EELKFGGGKT LREGMSQSNN PSKEELDLII TNALIVDYTG IYKADIGIK DGKIAGIGKG GNKDMQDGVK NNLSVGPATE ALAGEGLIVT AGGIDTHIHF ISPQQIPTAF ASGVTTMIGG G TGPADGTN ATTITPGRRN LKWMLRAAEE YSMNLGFLAK GNTSNDASLA DQIEAGAIGF (KCX)IHEDWGTTP SAINHALD V ADKYDVQVAI HTDTLNEAGC VEDTMAAIAG RTMHTFHTEG AGGGHAPDII KVAGEHNILP ASTNPTIPFT VNTEAEHMD MLMVCHHLDK SIKEDVQFAD SRIRPQTIAA EDTLHDMGIF SITSSDSQAM GRVGEVITRT WQTADKNKKE FGRLKEEKGD NDNFRIKRY LSKYTINPAI AHGISEYVGS VEVGKVADLV LWSPAFFGVK PNMIIKGGFI ALSQMGDANA SIPTPQPVYY R EMFAHHGK AKYDANITFV SQAAYDKGIK EELGLERQVL PVKNCRNITK KDMQFNDTTA HIEVNPETYH VFVDGKEVTS KP ANKVSLA QLFSIF |
-Macromolecule #3: NICKEL (II) ION
Macromolecule | Name: NICKEL (II) ION / type: ligand / ID: 3 / Number of copies: 24 / Formula: NI |
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Molecular weight | Theoretical: 58.693 Da |
Chemical component information | ChemComp-NI: |
-Macromolecule #4: 2-{[1-(3,5-dimethylphenyl)-1H-imidazol-2-yl]sulfanyl}-N-hydroxyac...
Macromolecule | Name: 2-{[1-(3,5-dimethylphenyl)-1H-imidazol-2-yl]sulfanyl}-N-hydroxyacetamide type: ligand / ID: 4 / Number of copies: 12 / Formula: DJM |
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Molecular weight | Theoretical: 277.342 Da |
Chemical component information | ChemComp-DJM: |
-Macromolecule #5: water
Macromolecule | Name: water / type: ligand / ID: 5 / Number of copies: 3191 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL | ||||||||
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Buffer | pH: 8 / Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number grids imaged: 1 / Number real images: 956 / Average electron dose: 50.0 e/Å2 / Details: Used 718 movies |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |