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- EMDB-4629: Helicobacter pylori urease with BME bound in the active site -

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Basic information

Entry
Database: EMDB / ID: EMD-4629
TitleHelicobacter pylori urease with BME bound in the active site
Map data
Sample1.1 MDa Helicobacter pylori Urease:
(Urease subunit ...) x 2 / (ligand) x 3
Function / homology
Function and homology information


urease complex / urease / urease activity / urea catabolic process / nickel cation binding / cytoplasm
Urease, gamma-beta subunit / Urease alpha subunit, C-terminal / Urease, gamma subunit superfamily / Urease, beta subunit superfamily / Metal-dependent hydrolase / Urease, beta subunit / Urease, gamma/gamma-beta subunit / Urease, alpha subunit / Amidohydrolase-related / Urease nickel binding site ...Urease, gamma-beta subunit / Urease alpha subunit, C-terminal / Urease, gamma subunit superfamily / Urease, beta subunit superfamily / Metal-dependent hydrolase / Urease, beta subunit / Urease, gamma/gamma-beta subunit / Urease, alpha subunit / Amidohydrolase-related / Urease nickel binding site / Metal-dependent hydrolase, composite domain superfamily / Urease alpha-subunit, N-terminal domain / Urease active site
Urease subunit beta / Urease subunit alpha
Biological speciesHelicobacter pylori (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsLuecke H / Cunha E
Funding support Norway, United States, 3 items
OrganizationGrant numberCountry
Research Council of Norway Norway
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI78000 United States
Research Council of Norway275207 Norway
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.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionFeb 22, 2019-
Header (metadata) releaseJan 20, 2021-
Map releaseJan 20, 2021-
UpdateFeb 3, 2021-
Current statusFeb 3, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6qsu
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_4629.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 300 pix.
= 323.1 Å
1.08 Å/pix.
x 300 pix.
= 323.1 Å
1.08 Å/pix.
x 300 pix.
= 323.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.077 Å
Density
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.15039964 - 0.26389554
Average (Standard dev.)0.00031169914 (±0.010078388)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 323.1 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0771.0771.077
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z323.100323.100323.100
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.1500.2640.000

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Supplemental data

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Segmentation: #1

Fileemd_4629_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: density modified map

Fileemd_4629_additional_1.map
Annotationdensity modified map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: half map

Fileemd_4629_half_map_1.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: half map

Fileemd_4629_half_map_2.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire 1.1 MDa Helicobacter pylori Urease

EntireName: 1.1 MDa Helicobacter pylori Urease / Number of components: 6

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Component #1: protein, 1.1 MDa Helicobacter pylori Urease

ProteinName: 1.1 MDa Helicobacter pylori Urease / Recombinant expression: No
MassTheoretical: 1.1 MDa
SourceSpecies: Helicobacter pylori (bacteria) / Strain: UMAB41
Source (engineered)Expression System: Escherichia coli (E. coli) / Vector: pHP808, pHP902
Source (natural)Location in cell: Cytoplasm

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Component #2: protein, Urease subunit alpha

ProteinName: Urease subunit alpha / Number of Copies: 12 / Recombinant expression: No
MassTheoretical: 26.645703 kDa
SourceSpecies: Helicobacter pylori (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, Urease subunit beta

ProteinName: Urease subunit beta / Number of Copies: 12 / Recombinant expression: No
MassTheoretical: 61.832531 kDa
SourceSpecies: Helicobacter pylori (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: ligand, NICKEL (II) ION

LigandName: NICKEL (II) ION / Number of Copies: 24 / Recombinant expression: No
MassTheoretical: 5.869305 MDa

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Component #5: ligand, BETA-MERCAPTOETHANOL

LigandName: BETA-MERCAPTOETHANOL2-Mercaptoethanol / Number of Copies: 12 / Recombinant expression: No
MassTheoretical: 7.813305 MDa

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Component #6: ligand, water

LigandName: water / Number of Copies: 1178 / Recombinant expression: No
MassTheoretical: 1.801505 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 2 mg/mL / pH: 8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 283 K / Humidity: 70 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisition #1Number of digital images: 956 / Details: Used 718 movies

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: T (tetrahedral) / Number of projections: 175895
3D reconstructionSoftware: RELION / CTF correction: Relion 3.0 beta per image and per particle / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL
Input PDB model: 1E9Z, 1E9Z
Chain ID: A, B
Output model

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