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- EMDB-34648: CryoEM structure of Helicobacter pylori UreFD/urease complex -

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Basic information

Entry
Database: EMDB / ID: EMD-34648
TitleCryoEM structure of Helicobacter pylori UreFD/urease complex
Map data
Sample
  • Complex: Helicobacter pylori UreFD/urease complex
    • Protein or peptide: Urease subunit alpha
    • Protein or peptide: Urease subunit beta
    • Protein or peptide: Urease accessory protein UreH
    • Protein or peptide: Urease accessory protein UreF
KeywordsUrease / activation complex / UreA / UreB / UreC / UreF / UreD / UreH / Helicobacter pylori / HYDROLASE
Function / homology
Function and homology information


metabolic process / urease complex / urease / urease activity / urea catabolic process / nickel cation binding / cytoplasm
Similarity search - Function
Urease accessory protein UreD / UreD urease accessory protein / Urease accessory protein UreF / UreF domain superfamily / UreF / Urease, gamma-beta subunit / : / Urease active site / Urease active site. / Urease nickel binding site ...Urease accessory protein UreD / UreD urease accessory protein / Urease accessory protein UreF / UreF domain superfamily / UreF / 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 alpha / Urease subunit beta / Urease accessory protein UreF / Urease accessory protein UreH
Similarity search - Component
Biological speciesHelicobacter pylori 26695 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsNim YS / Fong IYH / Deme J / Tsang KL / Caesar J / Johnson S / Wong KB / Lea SM
Funding support Hong Kong, United States, United Kingdom, 4 items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)C4041-18E, C4033-19EF, C4012-16E, 14117321, AoE/M-403/16, AoE/M-05/12 Hong Kong
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
Wellcome Trust219477 United Kingdom
Medical Research Council (MRC, United Kingdom)S021264 United Kingdom
CitationJournal: Sci Adv / Year: 2023
Title: Delivering a toxic metal to the active site of urease.
Authors: Yap Shing Nim / Ivan Yu Hang Fong / Justin Deme / Ka Lung Tsang / Joseph Caesar / Steven Johnson / Longson Tsz Hin Pang / Nicholas Man Hon Yuen / Tin Long Chris Ng / Tung Choi / Yakie Yat ...Authors: Yap Shing Nim / Ivan Yu Hang Fong / Justin Deme / Ka Lung Tsang / Joseph Caesar / Steven Johnson / Longson Tsz Hin Pang / Nicholas Man Hon Yuen / Tin Long Chris Ng / Tung Choi / Yakie Yat Hei Wong / Susan M Lea / Kam-Bo Wong /
Abstract: Urease is a nickel (Ni) enzyme that is essential for the colonization of in the human stomach. To solve the problem of delivering the toxic Ni ion to the active site without diffusing into the ...Urease is a nickel (Ni) enzyme that is essential for the colonization of in the human stomach. To solve the problem of delivering the toxic Ni ion to the active site without diffusing into the cytoplasm, cells have evolved metal carrier proteins, or metallochaperones, to deliver the toxic ions to specific protein complexes. Ni delivery requires urease to form an activation complex with the urease accessory proteins UreFD and UreG. Here, we determined the cryo-electron microscopy structures of UreFD/urease and UreD/urease complexes at 2.3- and 2.7-angstrom resolutions, respectively. Combining structural, mutagenesis, and biochemical studies, we show that the formation of the activation complex opens a 100-angstrom-long tunnel, where the Ni ion is delivered through UreFD to the active site of urease.
History
DepositionNov 1, 2022-
Header (metadata) releaseMay 3, 2023-
Map releaseMay 3, 2023-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_34648.png

Downloads & links

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Map

FileDownload / File: emd_34648.map.gz / Format: CCP4 / Size: 240.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 398 pix.
= 327.156 Å		0.82 Å/pix.
x 398 pix.
= 327.156 Å		0.82 Å/pix.
x 398 pix.
= 327.156 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0026525
Minimum - Maximum-0.01793784 - 0.053576563
Average (Standard dev.)-0.00008608922 (±0.0026525364)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions398398398
Spacing398398398
CellA=B=C: 327.156 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_34648_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_34648_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 : Helicobacter pylori UreFD/urease complex

EntireName: Helicobacter pylori UreFD/urease complex
Components
  • Complex: Helicobacter pylori UreFD/urease complex
    • Protein or peptide: Urease subunit alpha
    • Protein or peptide: Urease subunit beta
    • Protein or peptide: Urease accessory protein UreH
    • Protein or peptide: Urease accessory protein UreF

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Supramolecule #1: Helicobacter pylori UreFD/urease complex

SupramoleculeName: Helicobacter pylori UreFD/urease complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Helicobacter pylori 26695 (bacteria)
Molecular weightTheoretical: 1.76 MDa

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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 26695 (bacteria) / Strain: ATCC 700392 / 26695
Molecular weightTheoretical: 26.587662 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKLTPKELDK LMLHYAGELA KKRKEKGIKL NYVEAVALIS AHIMEEARAG KKTAAELMQE GRTLLKPDDV MDGVASMIHE VGIEAMFPD GTKLVTVHTP IEANGKLVPG ELFLKNEDIT INEGKKAVSV KVKNVGDRPV QIGSHFHFFE VNRCLDFDRE K TFGKRLDI ...String:
MKLTPKELDK LMLHYAGELA KKRKEKGIKL NYVEAVALIS AHIMEEARAG KKTAAELMQE GRTLLKPDDV MDGVASMIHE VGIEAMFPD GTKLVTVHTP IEANGKLVPG ELFLKNEDIT INEGKKAVSV KVKNVGDRPV QIGSHFHFFE VNRCLDFDRE K TFGKRLDI ASGTAVRFEP GEEKSVELID IGGNRRIFGF NALVDRQADN ESKKIALHRA KERGFHGAKS DDNYVKTIKE

UniProtKB: Urease subunit alpha

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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: Helicobacter pylori 26695 (bacteria) / Strain: ATCC 700392 / 26695
Molecular weightTheoretical: 61.759508 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 GNASNDASLA DQIEAGAIGF KIHEDWGTTP SAINHALDVA DK YDVQVAI HTDTLNEAGC VEDTMAAIAG RTMHTFHTEG AGGGHAPDII KVAGEHNILP ASTNPTIPFT VNTEAEHMDM LMV CHHLDK SIKEDVQFAD SRIRPQTIAA EDTLHDMGIF SITSSDSQAM GRVGEVITRT WQTADKNKKE FGRLKEEKGD NDNF RIKRY LSKYTINPAI AHGISEYVGS VEVGKVADLV LWSPAFFGVK PNMIIKGGFI ALSQMGDANA SIPTPQPVYY REMFA HHGK AKYDANITFV SQAAYDKGIK EELGLERQVL PVKNCRNITK KDMQFNDTTA HIEVNPETYH VFVDGKEVTS KPANKV SLA QLFSIF

UniProtKB: Urease subunit beta

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Macromolecule #3: Urease accessory protein UreH

MacromoleculeName: Urease accessory protein UreH / type: protein_or_peptide / ID: 3 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Helicobacter pylori 26695 (bacteria) / Strain: ATCC 700392 / 26695
Molecular weightTheoretical: 30.741244 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNTYAQESKL RLKTKIGADG RCVIEDNFFT PPFKLMAPFY PKDDLAEIML LAVSPGMMRG DAQDVQLNIG PNCKLRITSQ SFEKIHNTE DGFASRDMHI VVGENAFLDF APFPLIPFEN AHFKGNTTIS LRSSSQLLYS AIIVAGRVAR NELFKFNRLH T KISILQDE ...String:
MNTYAQESKL RLKTKIGADG RCVIEDNFFT PPFKLMAPFY PKDDLAEIML LAVSPGMMRG DAQDVQLNIG PNCKLRITSQ SFEKIHNTE DGFASRDMHI VVGENAFLDF APFPLIPFEN AHFKGNTTIS LRSSSQLLYS AIIVAGRVAR NELFKFNRLH T KISILQDE KPIYYDNTIL DPKTTDLNNM CMFDGYTHYL NLVLVNCPIE LSGVRECIEE SEGVDGAVSE TASSHLCVKA LA KGSEPLL HLREKIARLV TQTTTQKVWS HPQFEK

UniProtKB: Urease accessory protein UreH

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Macromolecule #4: Urease accessory protein UreF

MacromoleculeName: Urease accessory protein UreF / type: protein_or_peptide / ID: 4 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Helicobacter pylori 26695 (bacteria) / Strain: ATCC 700392 / 26695
Molecular weightTheoretical: 28.517635 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDKGKSVKST EKSVGMPPKT PKTDNNAHVD NEFLILQVND AVFPIGSYTH SFGLETYIQQ KKVTNKESAL EYLKANLSSQ FLYTEMLSL KLTYESALQQ DLKKILGVEE VIMLSTSPME LRLANQKLGN RFIKTLQAMN ELDMGEFFNA YAQKTKDPTH A TSYGVFAA ...String:
MDKGKSVKST EKSVGMPPKT PKTDNNAHVD NEFLILQVND AVFPIGSYTH SFGLETYIQQ KKVTNKESAL EYLKANLSSQ FLYTEMLSL KLTYESALQQ DLKKILGVEE VIMLSTSPME LRLANQKLGN RFIKTLQAMN ELDMGEFFNA YAQKTKDPTH A TSYGVFAA SLGIELKKAL AHYLDAQTSN MVINCVKSVP LSQNDGQKIL LSLQSPFNQL IEKTLELDES HLCTASVQND IK AMQHESL YSRLYMS

UniProtKB: Urease accessory protein UreF

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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

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: -1.5 µm / Nominal defocus min: -0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1e9z


Details: Together with 4HI0
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 68516
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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