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- EMDB-10835: High resolution cryo-EM structure of urease from the pathogen Yer... -

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Basic information

Entry
Database: EMDB / ID: EMD-10835
TitleHigh resolution cryo-EM structure of urease from the pathogen Yersinia enterocolitica
Map data
Sample
  • Complex: Urease oligomer from Y. enterocolitica
    • Protein or peptide: Urease subunit gamma
    • Protein or peptide: Urease subunit beta
    • Protein or peptide: Urease subunit alpha
  • Ligand: NICKEL (II) ION
  • Ligand: water
KeywordsUrease / enzyme / nickel / metalloenzyme / pathogen / METAL BINDING PROTEIN
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
Urease subunit alpha / Urease subunit beta / Urease subunit gamma
Similarity search - Component
Biological speciesYersinia enterocolitica W22703 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.98 Å
AuthorsRighetto RD / Anton L
Funding support Switzerland, 1 items
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 RD / Anton L / Adaixo R / Jakob R / Zivanov J / Mahi MA / Ringler P / Schwede T / Maier T / Stahlberg H
History
DepositionApr 6, 2020-
Header (metadata) releaseMay 6, 2020-
Map releaseMay 6, 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: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6yl3
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10835.png

Downloads & links

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Map

FileDownload / File: emd_10835.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.64 Å/pix.
x 512 pix.
= 327.168 Å		0.64 Å/pix.
x 512 pix.
= 327.168 Å		0.64 Å/pix.
x 512 pix.
= 327.168 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.639 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.035
Minimum - Maximum-0.1456621 - 0.24816307
Average (Standard dev.)0.00011374676 (±0.007022416)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 327.168 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.6390.6390.639
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z327.168327.168327.168
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.1460.2480.000

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Supplemental data

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Mask #1

Fileemd_10835_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_10835_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_10835_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Urease oligomer from Y. enterocolitica

EntireName: Urease oligomer from Y. enterocolitica
Components
  • Complex: Urease oligomer from Y. enterocolitica
    • Protein or peptide: Urease subunit gamma
    • Protein or peptide: Urease subunit beta
    • Protein or peptide: Urease subunit alpha
  • Ligand: NICKEL (II) ION
  • Ligand: water

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Supramolecule #1: Urease oligomer from Y. enterocolitica

SupramoleculeName: Urease oligomer from Y. enterocolitica / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Yersinia enterocolitica W22703 (bacteria) / Strain: E40
Molecular weightTheoretical: 1.025 MDa

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Macromolecule #1: Urease subunit gamma

MacromoleculeName: Urease subunit gamma / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO / EC number: urease
Source (natural)Organism: Yersinia enterocolitica W22703 (bacteria)
Molecular weightTheoretical: 11.063837 KDa
SequenceString:
MQLTPREVEK LMIYTLSDVA FKRKARGLKL NYPEAVSIIT VTAMEGARDG KSVEDVMKEA SKVLTKDDVM DGVADLIPNV QVEAIFTDG SRLVTVHDPI K

UniProtKB: Urease subunit gamma

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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: Yersinia enterocolitica W22703 (bacteria)
Molecular weightTheoretical: 14.611317 KDa
SequenceString:
SEQNTPLGGC ILADTPITFN ENKPVTKVKV RNTGDRPIQV GSHFHFFEVN RALEFDRAAA YGKRLNISST TAIRFEPGDE TEVPLIPFG GKQTLYGFNN LVDGWTGEGV VPNSERPDKL EAIRRAAERG FKS

UniProtKB: Urease subunit beta

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Macromolecule #3: Urease subunit alpha

MacromoleculeName: Urease subunit alpha / type: protein_or_peptide / ID: 3 / Number of copies: 12 / Enantiomer: LEVO / EC number: urease
Source (natural)Organism: Yersinia enterocolitica W22703 (bacteria)
Molecular weightTheoretical: 61.054859 KDa
SequenceString: PQISRQEYAG LFGPTTGDKI RLGDTNLFIE IEKDLRGYGE ESVYGGGKSL RDGMGANNHL TRDNGVLDLV ITNVTIVDAR LGVIKADVG IRDGKIAGIG KSGNPGVMDG VTPGLVVGVS TDAISGEHLI LTAAGIDTHI HLISPQQAYH ALSNGVATFF G GGIGPTDG ...String:
PQISRQEYAG LFGPTTGDKI RLGDTNLFIE IEKDLRGYGE ESVYGGGKSL RDGMGANNHL TRDNGVLDLV ITNVTIVDAR LGVIKADVG IRDGKIAGIG KSGNPGVMDG VTPGLVVGVS TDAISGEHLI LTAAGIDTHI HLISPQQAYH ALSNGVATFF G GGIGPTDG TNGTTVTPGP WNIRQMLRSV EGLPVNVGIL GKGNSYGRGP LLEQAIAGVV GY(KCX)VHEDWGA TANALRHS L RMADEMDIQV SVHTDSLNEC GYVEDTIDAF EGRTIHTFHT EGAGGGHAPD IIRVASQPNV LPSSTNPTLP YGVNSQAEL FDMIMVCHNL NPNVPADVSF AESRVRPETI AAENVLHDMG VISMFSSDSQ AMGRVGENWL RVMQTANAMK ASRGKLPEDA PGNDNFRVL RYVAKITINP AIAQGVSHVI GSVEVGKMAD LVLWDPRFFG AKPKMVIKGG MINWAAMGDP NASLPTPQPV F YRPMFGAM GKTMQDTCVT FVSQAALDDG VKEKAGLDRQ VIAVKNCRTI SKHDLVRNDQ TPNIEVDPET FAVKVDGVHA TC EPIDTAA MNQRYFFG

UniProtKB: Urease subunit alpha

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Macromolecule #4: NICKEL (II) ION

MacromoleculeName: NICKEL (II) ION / type: ligand / ID: 4 / Number of copies: 24 / Formula: NI
Molecular weightTheoretical: 58.693 Da
Chemical component information

ChemComp-NI:
NICKEL (II) ION

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 3672 / 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

Concentration0.39 mg/mL
BufferpH: 7
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293.15 K / Instrument: FEI VITROBOT MARK IV / Details: 3 seconds blotting.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: T (tetrahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 1.98 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 97627
Initial angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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