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- PDB-6yl3: High resolution cryo-EM structure of urease from the pathogen Yer... -

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Basic information

Entry
Database: PDB / ID: 6yl3
TitleHigh resolution cryo-EM structure of urease from the pathogen Yersinia enterocolitica
Components
  • Urease subunit alpha
  • Urease subunit beta
  • Urease subunit gamma
KeywordsMETAL BINDING PROTEIN / Urease / enzyme / nickel / metalloenzyme / pathogen
Function / homology
Function and homology information


urease complex / urease / urease activity / urea catabolic process / nickel cation binding / cytoplasm
Similarity search - Function
Urease, gamma 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 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
NICKEL (II) ION / Urease subunit alpha / Urease subunit beta / Urease subunit gamma
Similarity search - Component
Biological speciesYersinia enterocolitica W22703 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.98 Å
AuthorsRighetto, R.D. / Anton, L. / Adaixo, R. / Jakob, R. / Zivanov, J. / Mahi, M.A. / Ringler, P. / Schwede, T. / Maier, T. / Stahlberg, H.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
Citation
Journal: Nat Commun / Year: 2020
Title: High-resolution cryo-EM structure of urease from the pathogen Yersinia enterocolitica.
Authors: Ricardo D Righetto / Leonie Anton / Ricardo Adaixo / Roman P Jakob / Jasenko Zivanov / Mohamed-Ali Mahi / Philippe Ringler / Torsten Schwede / Timm Maier / Henning Stahlberg /
Abstract: Urease converts urea into ammonia and carbon dioxide and makes urea available as a nitrogen source for all forms of life except animals. In human bacterial pathogens, ureases also aid in the invasion ...Urease converts urea into ammonia and carbon dioxide and makes urea available as a nitrogen source for all forms of life except animals. In human bacterial pathogens, ureases also aid in the invasion of acidic environments such as the stomach by raising the surrounding pH. Here, we report the structure of urease from the pathogen Yersinia enterocolitica at 2 Å resolution from cryo-electron microscopy. Y. enterocolitica urease is a dodecameric assembly of a trimer of three protein chains, ureA, ureB and ureC. The high data quality enables detailed visualization of the urease bimetal active site and of the impact of radiation damage. The obtained structure is of sufficient quality to support drug development efforts.
#1: Journal: Biorxiv / Year: 2020
Title: High-resolution cryo-EM structure of urease from the pathogen Yersinia enterocolitica
Authors: Righetto, R.D. / Anton, L. / Adaixo, R. / Jakob, R. / Zivanov, J. / Mahi, M.A. / Ringler, P. / Schwede, T. / Maier, T. / Stahlberg, H.
History
DepositionApr 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
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Revision 1.1Oct 21, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / struct_conn / struct_conn_type
Item: _struct_conn.conn_type_id / _struct_conn.id ..._struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.2Apr 9, 2025Group: Data collection / Database references / Structure summary
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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Urease subunit gamma
B: Urease subunit beta
C: Urease subunit alpha
D: Urease subunit gamma
E: Urease subunit beta
F: Urease subunit alpha
G: Urease subunit gamma
H: Urease subunit beta
I: Urease subunit alpha
J: Urease subunit gamma
K: Urease subunit beta
L: Urease subunit alpha
M: Urease subunit gamma
N: Urease subunit beta
O: Urease subunit alpha
P: Urease subunit gamma
Q: Urease subunit beta
R: Urease subunit alpha
S: Urease subunit gamma
T: Urease subunit beta
V: Urease subunit alpha
W: Urease subunit gamma
X: Urease subunit beta
Y: Urease subunit alpha
Z: Urease subunit gamma
0: Urease subunit beta
1: Urease subunit alpha
2: Urease subunit gamma
3: Urease subunit beta
4: Urease subunit alpha
5: Urease subunit gamma
6: Urease subunit beta
7: Urease subunit alpha
8: Urease subunit gamma
9: Urease subunit beta
U: Urease subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,042,16960
Polymers1,040,76036
Non-polymers1,40924
Water66,1513672
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy, Single-particle analysis
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area207530 Å2
ΔGint-1168 kcal/mol
Surface area228160 Å2
MethodPISA

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Components

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


Mass: 11063.837 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Yersinia enterocolitica W22703 (bacteria) / References: UniProt: F4MWM9, urease
#2: Protein
Urease subunit beta / Urea amidohydrolase subunit beta


Mass: 14611.317 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Yersinia enterocolitica W22703 (bacteria) / References: UniProt: F4MWM8, urease
#3: Protein
Urease subunit alpha / Urea amidohydrolase subunit alpha


Mass: 61054.859 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Yersinia enterocolitica W22703 (bacteria) / References: UniProt: F4MWM7, urease
#4: Chemical...
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3672 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Urease oligomer from Y. enterocolitica / Type: COMPLEX / Entity ID: #1-#3 / Source: NATURAL
Molecular weightValue: 1.025 MDa / Experimental value: YES
Source (natural)Organism: Yersinia enterocolitica W22703 (bacteria) / Strain: E40
Buffer solutionpH: 7
SpecimenConc.: 0.39 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 293.15 K / Details: 3 seconds blotting

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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 FIELD / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 42 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
4CTFFIND4.1CTF correction
9RELION3initial Euler assignment
10RELION3.1final Euler assignment
12RELION3.13D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: T (tetrahedral)
3D reconstructionResolution: 1.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 97627 / Algorithm: FOURIER SPACE / Symmetry type: POINT

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