[English] 日本語
Yorodumi
- EMDB-4629: Helicobacter pylori urease with BME bound in the active site -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-4629
TitleHelicobacter pylori urease with BME bound in the active site
Map dataunmasked map
Sample
  • Complex: 1.1 MDa Helicobacter pylori Urease
    • Protein or peptide: Urease subunit alpha
    • Protein or peptide: Urease subunit beta
  • Ligand: NICKEL (II) ION
  • Ligand: BETA-MERCAPTOETHANOL
  • Ligand: water
Function / homology
Function and homology information


urease complex / urease / urease activity / urea catabolic process / nickel cation binding / cytoplasm
Similarity search - Function
Urease, gamma-beta 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-beta 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 beta / Urease subunit alpha / Urease subunit alpha / Urease subunit beta
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsLuecke H / Cunha E
Funding support Norway, United States, 3 items
OrganizationGrant numberCountry
Research Council of Norway Norway
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI78000 United States
Research Council of Norway275207 Norway
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.
History
DepositionFeb 22, 2019-
Header (metadata) releaseJan 20, 2021-
Map releaseJan 20, 2021-
UpdateFeb 3, 2021-
Current statusFeb 3, 2021Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6qsu
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4629.png

Downloads & links

-
Map

FileDownload / File: emd_4629.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunmasked map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 300 pix.
= 323.1 Å		1.08 Å/pix.
x 300 pix.
= 323.1 Å		1.08 Å/pix.
x 300 pix.
= 323.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.077 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.15039964 - 0.26389554
Average (Standard dev.)0.00031169914 (±0.010078388)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 323.1 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0771.0771.077
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z323.100323.100323.100
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.1500.2640.000

-
Supplemental data

-
Mask #1

Fileemd_4629_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: density modified map

Fileemd_4629_additional_1.map
Annotationdensity modified map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map

Fileemd_4629_half_map_1.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map

Fileemd_4629_half_map_2.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : 1.1 MDa Helicobacter pylori Urease

EntireName: 1.1 MDa Helicobacter pylori Urease
Components
  • Complex: 1.1 MDa Helicobacter pylori Urease
    • Protein or peptide: Urease subunit alpha
    • Protein or peptide: Urease subunit beta
  • Ligand: NICKEL (II) ION
  • Ligand: BETA-MERCAPTOETHANOL
  • Ligand: water

-
Supramolecule #1: 1.1 MDa Helicobacter pylori Urease

SupramoleculeName: 1.1 MDa Helicobacter pylori Urease / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Helicobacter pylori (bacteria) / Strain: UMAB41 / Location in cell: Cytoplasm
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pHP808, pHP902
Molecular weightTheoretical: 1.1 MDa

-
Macromolecule #1: Urease subunit alpha

MacromoleculeName: Urease subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO / EC number: urease
Source (natural)Organism: Helicobacter pylori (bacteria)
Molecular weightTheoretical: 26.645703 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKLTPKELDK LMLHYAGELA RKRKEKGIKL NYVEAVALIS AHIMEEARAG KKTAAELMQE GRTLLKPDDV MDGVASMIHE VGIEAMFPD GTKLVTVHTP IEANGKLVPG ELFLKNEDIT INEGKKAVSV KVKNVGDRPV QIGSHFHFFE VNRCLDFDRE K TFGKRLDI ...String:
MKLTPKELDK LMLHYAGELA RKRKEKGIKL NYVEAVALIS AHIMEEARAG KKTAAELMQE GRTLLKPDDV MDGVASMIHE VGIEAMFPD GTKLVTVHTP IEANGKLVPG ELFLKNEDIT INEGKKAVSV KVKNVGDRPV QIGSHFHFFE VNRCLDFDRE K TFGKRLDI ASGTAVRFEP GEEKSVELID IGGNRRIFGF NALVDRQADN ESKKIALHRA KERGFHGTKS DDNYVKTIKE

-
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: Helicobacter pylori (bacteria)
Molecular weightTheoretical: 61.832531 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKKISRKEYV SMYGPTTGDK VRLGDTDLIA EVEHDYTIYG EELKFGGGKT LREGMSQSNN PSKEELDLII TNALIVDYTG IYKADIGIK DGKIAGIGKG GNKDMQDGVK NNLSVGPATE ALAGEGLIVT AGGIDTHIHF ISPQQIPTAF ASGVTTMIGG G TGPADGTN ...String:
MKKISRKEYV SMYGPTTGDK VRLGDTDLIA EVEHDYTIYG EELKFGGGKT LREGMSQSNN PSKEELDLII TNALIVDYTG IYKADIGIK DGKIAGIGKG GNKDMQDGVK NNLSVGPATE ALAGEGLIVT AGGIDTHIHF ISPQQIPTAF ASGVTTMIGG G TGPADGTN ATTITPGRRN LKWMLRAAEE YSMNLGFLAK GNTSNDASLA DQIEAGAIGF (KCX)IHEDWGTTP SAINHALD V ADKYDVQVAI HTDTLNEAGC VEDTMAAIAG RTMHTFHTEG AGGGHAPDII KVAGEHNILP ASTNPTIPFT VNTEAEHMD MLMVCHHLDK SIKEDVQFAD SRIRPQTIAA EDTLHDMGIF SITSSDSQAM GRVGEVITRT WQTADKNKKE FGRLKEEKGD NDNFRIKRY LSKYTINPAI AHGISEYVGS VEVGKVADLV LWSPAFFGVK PNMIIKGGFI ALSQMGDANA SIPTPQPVYY R EMFAHHGK AKYDANITFV SQAAYDKGIK EELGLERQVL PVKNCRNITK KDMQFNDTTA HIEVNPETYH VFVDGKEVTS KP ANKVSLA QLFSIF

-
Macromolecule #3: NICKEL (II) ION

MacromoleculeName: NICKEL (II) ION / type: ligand / ID: 3 / Number of copies: 24 / Formula: NI
Molecular weightTheoretical: 58.693 Da
Chemical component information

ChemComp-NI:
NICKEL (II) ION

-
Macromolecule #4: BETA-MERCAPTOETHANOL

MacromoleculeName: BETA-MERCAPTOETHANOL / type: ligand / ID: 4 / Number of copies: 12 / Formula: BME
Molecular weightTheoretical: 78.133 Da
Chemical component information

ChemComp-BME:
BETA-MERCAPTOETHANOL

-
Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 1178 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2 mg/mL
BufferpH: 8 / Component:
ConcentrationName
20.0 mMHepes
1.0 mMEDTA
1.0 mMBME
GridModel: Quantifoil R2/2 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #0 - Number grids imaged: 1 / #0 - Number real images: 956 / #0 - Average electron dose: 50.0 e/Å2 / #0 - Details: Used 718 movies / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #1 - Average electron dose: 40.0 e/Å2 / #2 - Image recording ID: 3 / #2 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #2 - Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Image recording ID1
Particle selectionNumber selected: 203000
CTF correctionSoftware - Name: RELION (ver. 3.0 beta) / Details: Relion 3.0 beta per image and per particle
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1e9z


Details: 3.0 A crystal structure of apo form
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: T (tetrahedral) / Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0 beta) / Number images used: 175895
Initial angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.0 beta)
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.0 beta)
Final 3D classificationNumber classes: 6 / Avg.num./class: 28000 / Software - Name: RELION (ver. 3.0 beta)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

1e9z

chain_id: A

1e9z

chain_id: B
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-6qsu:
Helicobacter pylori urease with BME bound in the active site

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

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. 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.
  • 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 Accession Codes are Changing Soon! / 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.
  • 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

-
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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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