[English] 日本語
Yorodumi
- EMDB-10835: High resolution cryo-EM structure of urease from the pathogen Yer... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-10835
TitleHigh resolution cryo-EM structure of urease from the pathogen Yersinia enterocolitica
Map data
SampleUrease oligomer from Y. enterocolitica:
(Urease subunit ...) x 3 / (ligand) x 2
Function / homology
Function and homology information


urease / urease activity / urea catabolic process / nickel cation binding / cytoplasm
Urease alpha-subunit, N-terminal domain / 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 / Metal-dependent hydrolase, composite domain superfamily ...Urease alpha-subunit, N-terminal domain / 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 / Metal-dependent hydrolase, composite domain superfamily / Urease nickel binding site / Urease, gamma subunit / Urease active site
Urease subunit alpha / Urease subunit beta / Urease subunit gamma
Biological speciesYersinia enterocolitica W22703 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.98 Å
AuthorsRighetto RD / Anton L / Adaixo R / Jakob R / Zivanov J / Mahi MA / Ringler P / Schwede T / Maier T / Stahlberg H
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
Validation ReportPDB-ID: 6yl3

SummaryFull reportAbout validation report
History
DepositionApr 6, 2020-
Header (metadata) releaseMay 6, 2020-
Map releaseMay 6, 2020-
UpdateOct 21, 2020-
Current statusOct 21, 2020Processing site: PDBe / Status: Released

-
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
  • Download
  • 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

Downloads & links

-
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
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.035
Minimum - Maximum0 - 1
Average (Standard dev.)0.04387615 (±0.19735026)
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

-
Supplemental data

-
Segmentation: #1

Fileemd_10835_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Half map: #1

Fileemd_10835_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Half map: #2

Fileemd_10835_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Sample components

+
Entire Urease oligomer from Y. enterocolitica

EntireName: Urease oligomer from Y. enterocolitica / Number of components: 6

+
Component #1: protein, Urease oligomer from Y. enterocolitica

ProteinName: Urease oligomer from Y. enterocolitica / Recombinant expression: No
MassExperimental: 1.025 MDa
SourceSpecies: Yersinia enterocolitica W22703 (bacteria) / Strain: E40

+
Component #2: protein, Urease subunit gamma

ProteinName: Urease subunit gamma / Number of Copies: 12 / Recombinant expression: No
MassTheoretical: 11.063837 kDa
SourceSpecies: Yersinia enterocolitica W22703 (bacteria)

+
Component #3: protein, Urease subunit beta

ProteinName: Urease subunit beta / Number of Copies: 12 / Recombinant expression: No
MassTheoretical: 14.611317 kDa
SourceSpecies: Yersinia enterocolitica W22703 (bacteria)

+
Component #4: protein, Urease subunit alpha

ProteinName: Urease subunit alpha / Number of Copies: 12 / Recombinant expression: No
MassTheoretical: 61.054859 kDa
SourceSpecies: Yersinia enterocolitica W22703 (bacteria)

+
Component #5: ligand, NICKEL (II) ION

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

+
Component #6: ligand, water

LigandName: water / Number of Copies: 3672 / Recombinant expression: No
MassTheoretical: 1.801505 MDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.39 mg/mL / pH: 7
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 293.15 K / Humidity: 90 % / Details: 3 seconds blotting.

-
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: 42 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD / Energy filter: GIF Quantum LS
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: T (tetrahedral) / Number of projections: 97627
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 1.98 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

-
Atomic model buiding

Output model

+
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