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Open data
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Basic information
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Title | CryoEM Structure of Klebsiella pneumoniae UreD/urease complex | |||||||||||||||
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![]() | Urease / UreA / UreB / UreC / UreF / UreD / Klebsiella pneumoniae / HYDROLASE | |||||||||||||||
Function / homology | ![]() urease complex / urease / urease activity / urea catabolic process / nickel cation binding / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||||||||
![]() | Nim YS / Fong IYH / Deme J / Tsang KL / Caesar J / Johnson S / Wong KB / Lea SM | |||||||||||||||
Funding support | ![]() ![]() ![]()
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![]() | ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 80.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.3 KB 19.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.6 KB | Display | ![]() |
Images | ![]() | 176.5 KB | ||
Filedesc metadata | ![]() | 6.4 KB | ||
Others | ![]() ![]() | 81 MB 80.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8hcnMC ![]() 8hc1C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.822 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_34659_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_34659_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Klebsiella pneumoniae UreD/urease complex
Entire | Name: Klebsiella pneumoniae UreD/urease complex |
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Components |
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-Supramolecule #1: Klebsiella pneumoniae UreD/urease complex
Supramolecule | Name: Klebsiella pneumoniae UreD/urease complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 360 KDa |
-Macromolecule #1: Urease subunit gamma
Macromolecule | Name: Urease subunit gamma / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: urease |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 11.100928 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MELTPREKDK LLLFTAALVA ERRLARGLKL NYPESVALIS AFIMEGARDG KSVASLMEEG RHVLTREQVM EGVPEMIPDI QVEATFPDG SKLVTVHNPI I UniProtKB: Urease subunit gamma |
-Macromolecule #2: Urease subunit beta
Macromolecule | Name: Urease subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: urease |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 11.712239 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MIPGEYHVKP GQIALNTGRA TCRVVVENHG DRPIQVGSHY HFAEVNPALK FDRQQAAGYR LNIPAGTAVR FEPGQKREVE LVAFAGHRA VFGFRGEVMG PLEVNDE UniProtKB: Urease subunit beta |
-Macromolecule #3: Urease subunit alpha
Macromolecule | Name: Urease subunit alpha / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO / EC number: urease |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 60.352328 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSNISRQAYA DMFGPTVGDK VRLADTELWI EVEDDLTTYG EEVKFGGGKV IRDGMGQGQM LAADCVDLVL TNALIVDHWG IVKADIGVK DGRIFAIGKA GNPDIQPNVT IPIGAATEVI AAEGKIVTAG GIDTHIHWIC PQQAEEALVS GVTTMVGGGT G PAAGTHAT ...String: MSNISRQAYA DMFGPTVGDK VRLADTELWI EVEDDLTTYG EEVKFGGGKV IRDGMGQGQM LAADCVDLVL TNALIVDHWG IVKADIGVK DGRIFAIGKA GNPDIQPNVT IPIGAATEVI AAEGKIVTAG GIDTHIHWIC PQQAEEALVS GVTTMVGGGT G PAAGTHAT TCTPGPWYIS RMLQAADSLP VNIGLLGKGN VSQPDALREQ VAAGVIGLKI HEDWGATPAA IDCALTVADE MD VQVALHS DTLNESGFVE DTLAAIGGRT IHTFHTEGAG GGHAPDIITA CAHPNILPSS TNPTLPYTLN TIDEHLDMLM VCH HLDPDI AEDVAFAESR IRRETIAAED VLHDLGAFSL TSSDSQAMGR VGEVILRTWQ VAHRMKVQRG ALAEETGDND NFRV KRYIA KYTINPALTH GIAHEVGSIE VGKLADLVVW SPAFFGVKPA TVIKGGMIAI APMGDINASI PTPQPVHYRP MFGAL GSAR HHCRLTFLSQ AAAANGVAER LNLRSAIAVV KGCRTVQKAD MVHNSLQPNI TVDAQTYEVR VDGELITSEP ADVLPM AQR YFLF UniProtKB: Urease subunit alpha |
-Macromolecule #4: Urease accessory protein UreD
Macromolecule | Name: Urease accessory protein UreD / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 31.275982 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MWSHPQFEKH GTVLPPLKKG WQATLDLRFH QAGGKTVLAS AQHVGPLTVQ RPFYPEEETC HLYLLHPPGG IVGGDELTIS AQLAPGCHT LITMPGASKF YRSSGAQALV RQQLTLAPQA TLEWLPQDAI FFPGANARLF TTFHLCASSR LLAWDLLCLG R PVIGETFS ...String: MWSHPQFEKH GTVLPPLKKG WQATLDLRFH QAGGKTVLAS AQHVGPLTVQ RPFYPEEETC HLYLLHPPGG IVGGDELTIS AQLAPGCHT LITMPGASKF YRSSGAQALV RQQLTLAPQA TLEWLPQDAI FFPGANARLF TTFHLCASSR LLAWDLLCLG R PVIGETFS HGTLSNRLEV WVDDEPLLVE RLQLQEGELS SVAERPWVGT LLCYPATDAL LDGVRDALAP LGLYAGASLT DR LLTVRFL SDDNLICQRV MRDVWQFLRP HLTGKSPVLP RIWLT UniProtKB: UNIPROTKB: A0A5D6SRX8 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 48.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination 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 |