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Yorodumi- EMDB-10835: High resolution cryo-EM structure of urease from the pathogen Yer... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10835 | |||||||||
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Title | High resolution cryo-EM structure of urease from the pathogen Yersinia enterocolitica | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information urease complex / urease / urease activity / urea catabolic process / nickel cation binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Yersinia enterocolitica W22703 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 1.98 Å | |||||||||
Authors | Righetto RD / Anton L / Adaixo R / Jakob R / Zivanov J / Mahi MA / Ringler P / Schwede T / Maier T / Stahlberg H | |||||||||
Funding support | Switzerland, 1 items
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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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10835.map.gz | 302.4 MB | EMDB map data format | |
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Header (meta data) | emd-10835-v30.xml emd-10835.xml | 20.2 KB 20.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10835_fsc.xml | 18 KB | Display | FSC data file |
Images | emd_10835.png | 169.2 KB | ||
Masks | emd_10835_msk_1.map | 512 MB | Mask map | |
Others | emd_10835_half_map_1.map.gz emd_10835_half_map_2.map.gz | 410.4 MB 410.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10835 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10835 | HTTPS FTP |
-Validation report
Summary document | emd_10835_validation.pdf.gz | 461.2 KB | Display | EMDB validaton report |
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Full document | emd_10835_full_validation.pdf.gz | 460.3 KB | Display | |
Data in XML | emd_10835_validation.xml.gz | 23.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10835 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10835 | HTTPS FTP |
-Related structure data
Related structure data | 6yl3MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10389 (Title: High resolution cryo-EM structure of urease from the pathogen Yersinia enterocolitica Data size: 839.9 Data #1: Aligned averages of Y. enterocolitica urease [micrographs - single frame] Data #2: Raw multi-frame micrographs of Y. enterocolitica urease [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10835.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.639 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_10835_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_10835_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_10835_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Urease oligomer from Y. enterocolitica
Entire | Name: Urease oligomer from Y. enterocolitica |
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Components |
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-Supramolecule #1: Urease oligomer from Y. enterocolitica
Supramolecule | Name: Urease oligomer from Y. enterocolitica / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Yersinia enterocolitica W22703 (bacteria) / Strain: E40 |
Molecular weight | Experimental: 1.025 MDa |
-Macromolecule #1: Urease subunit gamma
Macromolecule | Name: Urease subunit gamma / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO / EC number: urease |
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Source (natural) | Organism: Yersinia enterocolitica W22703 (bacteria) |
Molecular weight | Theoretical: 11.063837 KDa |
Sequence | String: MQLTPREVEK LMIYTLSDVA FKRKARGLKL NYPEAVSIIT VTAMEGARDG KSVEDVMKEA SKVLTKDDVM DGVADLIPNV QVEAIFTDG SRLVTVHDPI K |
-Macromolecule #2: Urease subunit beta
Macromolecule | Name: Urease subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO / EC number: urease |
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Source (natural) | Organism: Yersinia enterocolitica W22703 (bacteria) |
Molecular weight | Theoretical: 14.611317 KDa |
Sequence | String: SEQNTPLGGC ILADTPITFN ENKPVTKVKV RNTGDRPIQV GSHFHFFEVN RALEFDRAAA YGKRLNISST TAIRFEPGDE TEVPLIPFG GKQTLYGFNN LVDGWTGEGV VPNSERPDKL EAIRRAAERG FKS |
-Macromolecule #3: Urease subunit alpha
Macromolecule | Name: Urease subunit alpha / type: protein_or_peptide / ID: 3 / Number of copies: 12 / Enantiomer: LEVO / EC number: urease |
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Source (natural) | Organism: Yersinia enterocolitica W22703 (bacteria) |
Molecular weight | Theoretical: 61.054859 KDa |
Sequence | String: 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 |
-Macromolecule #4: NICKEL (II) ION
Macromolecule | Name: NICKEL (II) ION / type: ligand / ID: 4 / Number of copies: 24 / Formula: NI |
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Molecular weight | Theoretical: 58.693 Da |
Chemical component information | ChemComp-NI: |
-Macromolecule #5: water
Macromolecule | Name: water / type: ligand / ID: 5 / Number of copies: 3672 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.39 mg/mL |
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Buffer | pH: 7 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293.15 K / Instrument: FEI VITROBOT MARK IV / Details: 3 seconds blotting. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 42.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |