[English] 日本語
Yorodumi
- PDB-6qsu: Helicobacter pylori urease with BME bound in the active site -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qsu
TitleHelicobacter pylori urease with BME bound in the active site
Components
  • Urease subunit alpha
  • Urease subunit beta
KeywordsHYDROLASE / dodecamer / bi nickel center / enzyme / cytoplasm
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsLuecke, H. / Cunha, E.
Funding support Norway, United States, 3items
OrganizationGrant numberCountry
Research Council of Norway Norway
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.
Validation Report
SummaryFull reportAbout validation report
History
DepositionFeb 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-4629
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Urease subunit alpha
B: Urease subunit beta
C: Urease subunit alpha
E: Urease subunit alpha
G: Urease subunit alpha
I: Urease subunit alpha
K: Urease subunit alpha
M: Urease subunit alpha
O: Urease subunit alpha
Q: Urease subunit alpha
S: Urease subunit alpha
U: Urease subunit alpha
W: Urease subunit alpha
J: Urease subunit beta
D: Urease subunit beta
F: Urease subunit beta
H: Urease subunit beta
L: Urease subunit beta
N: Urease subunit beta
P: Urease subunit beta
R: Urease subunit beta
T: Urease subunit beta
V: Urease subunit beta
X: Urease subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,064,08560
Polymers1,061,73924
Non-polymers2,34636
Water21,2221178
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Runs with an apparent MW of 550 kDa
  • Download structure data
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area210660 Å2
ΔGint-1285 kcal/mol
Surface area247510 Å2
MethodPISA

-
Components

#1: Protein
Urease subunit alpha / / Urea amidohydrolase subunit alpha


Mass: 26645.703 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: ureA, BGL58_00110, D2C78_00705, DD749_00755 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A293SGE9, urease
#2: Protein
Urease subunit beta / / Urea amidohydrolase subunit beta


Mass: 61832.531 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria)
Gene: ureC, ureB, ACM26_03100, ACM31_01665, AEY53_07315, AEY54_04500, BB390_03210, BB400_00890, BB458_02040, BB472_00115, BB483_06885, BCM300_00080, BGL59_06905, BGL62_00955, BGL74_08355, BGL78_ ...Gene: ureC, ureB, ACM26_03100, ACM31_01665, AEY53_07315, AEY54_04500, BB390_03210, BB400_00890, BB458_02040, BB472_00115, BB483_06885, BCM300_00080, BGL59_06905, BGL62_00955, BGL74_08355, BGL78_03465, BGL80_00980, BZK19_03120, BZK22_02015, BZK28_01040, C2R48_07340, C2R49_05480, C2R51_07515, C2R54_00600, C2R57_07640, C2R76_03750, C2R81_00275, C2R85_01915, C2R92_02560, CV727_07335, CV730_01155, D2C74_07740, D2C77_03985, D2C79_06860, DD741_00890, DD749_00750, DD779_00665, DD783_00075, DDP32_00750, DDP35_00500, EC528_04020, EC532_02160, EC572_01665, EC592_02340, EC594_04345, EC598_01685, ECB88_00905, ECB90_01230, ECC11_01355, ECC14_06065, ECC20_02355, ECC23_04175, ECC26_01225, ECC27_04455, ECC29_00335, ECC38_01340, ECC45_00115, ECE48_05900, EDB75_03310, EPC84_05055, HPY1198_04550, NCTC13207_01207, NCTC13338_01433, NCTC13345_00234
Production host: Escherichia coli (E. coli) / References: UniProt: A0A086RWB6, urease
#3: Chemical...
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Ni
#4: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1178 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: 1.1 MDa Helicobacter pylori Urease / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 1.1 MDa / Experimental value: NO
Source (natural)Organism: Helicobacter pylori (bacteria) / Strain: UMAB41 / Cellular location: Cytoplasm
Source (recombinant)Organism: Escherichia coli (E. coli) / Plasmid: pHP808, pHP902
Buffer solutionpH: 8
Buffer component
IDConc.NameBuffer-ID
120 mMHepes1
21 mMEDTAEthylenediaminetetraacetic acid1
31 mMBME1
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 70 % / Chamber temperature: 283 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recording
IDImaging-IDElectron dose (e/Å2)Film or detector modelNum. of grids imagedNum. of real imagesDetails
1150GATAN K2 SUMMIT (4k x 4k)1956Used 718 movies
2140GATAN K2 SUMMIT (4k x 4k)
3140GATAN K2 SUMMIT (4k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.18.1_3865: / Classification: refinement
EM software
IDNameVersionCategory
4RELION3.0 betaCTF correction
7Coot0.8.9model fitting
9RELION3.0 betainitial Euler assignment
10RELION3.0 betafinal Euler assignment
11RELION3.0 betaclassification
12RELION3.0 beta3D reconstruction
13PHENIX1.13model refinement
CTF correctionDetails: Relion 3.0 beta per image and per particle / Type: NONE
Particle selectionNum. of particles selected: 203000
SymmetryPoint symmetry: T (tetrahedral)
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 175895 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building
IDPDB-IDPdb chain-ID3D fitting-ID
11E9ZA1
21E9ZB1
Refine LS restraints
Refinement-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00675888
ELECTRON MICROSCOPYf_angle_d0.627102348
ELECTRON MICROSCOPYf_dihedral_angle_d17.83528272
ELECTRON MICROSCOPYf_chiral_restr0.0511400
ELECTRON MICROSCOPYf_plane_restr0.00513404

+
About Yorodumi

-
News

-
Aug 12, 2020. New: Covid-19 info

New: Covid-19 info

  • New page: Covid-19 featured information page in EM Navigator

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. New: Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB at PDBe / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more