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- EMDB-11233: Helicobacter pylori urease with inhibitor bound in the active site -

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Basic information

Entry
Database: EMDB / ID: EMD-11233
TitleHelicobacter pylori urease with inhibitor bound in the active site
Map dataRelion unmasked map
Sample
  • Complex: 1.1 MDa Helicobacter pylori Urease
    • Protein or peptide: Urease subunit alpha
    • Protein or peptide: Urease subunit beta
  • Ligand: NICKEL (II) ION
  • Ligand: 2-{[1-(3,5-dimethylphenyl)-1H-imidazol-2-yl]sulfanyl}-N-hydroxyacetamide
  • Ligand: water
Keywordsdodecamer / bi nickel center / enzyme / cytoplasm / HYDROLASE
Function / homology
Function and homology information


urease complex / urease / urease activity / urea catabolic process / nickel cation binding / cytoplasm
Similarity search - Function
Urease, gamma-beta subunit / : / Urease active site / Urease active site. / Urease nickel binding site / Urease nickel ligands signature. / Urease, beta subunit / Urease, alpha subunit / Urease alpha subunit, C-terminal / Urease, beta subunit superfamily ...Urease, gamma-beta subunit / : / Urease active site / Urease active site. / Urease nickel binding site / Urease nickel ligands signature. / Urease, beta subunit / Urease, alpha subunit / Urease alpha subunit, C-terminal / Urease, beta subunit superfamily / : / Urease beta subunit / Urease domain profile. / Urease alpha-subunit, N-terminal domain / Urease alpha-subunit, N-terminal domain / Urease, gamma/gamma-beta subunit / Urease, gamma subunit superfamily / Urease, gamma subunit / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolase
Similarity search - Domain/homology
Urease subunit beta / Urease subunit alpha / Urease subunit alpha / Urease subunit beta
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.0 Å
AuthorsLuecke H / Cunha E
Funding support Norway, United States, 2 items
OrganizationGrant numberCountry
Research Council of Norway275207 Norway
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI78000 United States
CitationJournal: 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
DepositionJun 28, 2020-
Header (metadata) releaseDec 23, 2020-
Map releaseDec 23, 2020-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0252
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0252
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6zja
  • Surface level: 0.0252
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11233.png

Downloads & links

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Map

FileDownload / File: emd_11233.map.gz / Format: CCP4 / Size: 396.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRelion unmasked map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 470 pix.
= 396.022 Å		0.84 Å/pix.
x 470 pix.
= 396.022 Å		0.84 Å/pix.
x 470 pix.
= 396.022 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8426 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0252 / Movie #1: 0.0252
Minimum - Maximum-0.07896397 - 0.17281555
Average (Standard dev.)0.000009505519 (±0.005234413)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions470470470
Spacing470470470
CellA=B=C: 396.02206 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.84260.84260.8426
M x/y/z470470470
origin x/y/z0.0000.0000.000
length x/y/z396.022396.022396.022
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS470470470
D min/max/mean-0.0790.1730.000

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Supplemental data

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Mask #1

Fileemd_11233_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Density modified map

Fileemd_11233_additional_1.map
AnnotationDensity modified map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_11233_half_map_1.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_11233_half_map_2.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 1.1 MDa Helicobacter pylori Urease

EntireName: 1.1 MDa Helicobacter pylori Urease
Components
  • Complex: 1.1 MDa Helicobacter pylori Urease
    • Protein or peptide: Urease subunit alpha
    • Protein or peptide: Urease subunit beta
  • Ligand: NICKEL (II) ION
  • Ligand: 2-{[1-(3,5-dimethylphenyl)-1H-imidazol-2-yl]sulfanyl}-N-hydroxyacetamide
  • Ligand: water

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Supramolecule #1: 1.1 MDa Helicobacter pylori Urease

SupramoleculeName: 1.1 MDa Helicobacter pylori Urease / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Helicobacter pylori (bacteria) / Strain: UMAB41 / Location in cell: Cytoplasm
Molecular weightTheoretical: 1.1 MDa

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Macromolecule #1: Urease subunit alpha

MacromoleculeName: Urease subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO / EC number: urease
Source (natural)Organism: Helicobacter pylori (bacteria)
Molecular weightTheoretical: 26.645703 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

UniProtKB: Urease subunit alpha

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Macromolecule #2: Urease subunit beta

MacromoleculeName: Urease subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO / EC number: urease
Source (natural)Organism: Helicobacter pylori (bacteria)
Molecular weightTheoretical: 61.832531 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

UniProtKB: Urease subunit beta

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Macromolecule #3: NICKEL (II) ION

MacromoleculeName: NICKEL (II) ION / type: ligand / ID: 3 / Number of copies: 24 / Formula: NI
Molecular weightTheoretical: 58.693 Da
Chemical component information

ChemComp-NI:
NICKEL (II) ION

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Macromolecule #4: 2-{[1-(3,5-dimethylphenyl)-1H-imidazol-2-yl]sulfanyl}-N-hydroxyac...

MacromoleculeName: 2-{[1-(3,5-dimethylphenyl)-1H-imidazol-2-yl]sulfanyl}-N-hydroxyacetamide
type: ligand / ID: 4 / Number of copies: 12 / Formula: DJM
Molecular weightTheoretical: 277.342 Da
Chemical component information

ChemComp-DJM:
2-{[1-(3,5-dimethylphenyl)-1H-imidazol-2-yl]sulfanyl}-N-hydroxyacetamide

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 3191 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 8 / Component:
ConcentrationName
20.0 mMHepes
1.0 mMEDTA
1.0 mMBME
VitrificationCryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 203000
Startup modelType of model: OTHER
Details: 2.45 angstroms EM structure with BME bound that in turn was modeled from the 3.0 angstroms apo form of the crystal structure PBD 1E9Z
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: T (tetrahedral) / Resolution.type: BY AUTHOR / Resolution: 2.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 3.0 beta) / Details: Relion was used for resconstruction / Number images used: 187461
Initial angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.0 beta)
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.0 beta)
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 3.0 beta)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

1e9z

chain_id: A, source_name: PDB, initial_model_type: experimental model

1e9z

chain_id: B, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-6zja:
Helicobacter pylori urease with inhibitor bound in the active site

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