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Yorodumi- PDB-7qba: CryoEM structure of the ABC transporter NosDFY complexed with nit... -
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-Basic information
Entry | Database: PDB / ID: 7qba | ||||||||||||
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Title | CryoEM structure of the ABC transporter NosDFY complexed with nitrous oxide reductase NosZ | ||||||||||||
Components |
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Keywords | MEMBRANE PROTEIN / ABC transporter / metal binding protein / nitrous oxide reductase | ||||||||||||
Function / homology | Function and homology information nitrous-oxide reductase / nitrous-oxide reductase activity / copper ion import / denitrification pathway / cytochrome-c oxidase activity / ABC-type transporter activity / periplasmic space / copper ion binding / calcium ion binding / ATP hydrolysis activity ...nitrous-oxide reductase / nitrous-oxide reductase activity / copper ion import / denitrification pathway / cytochrome-c oxidase activity / ABC-type transporter activity / periplasmic space / copper ion binding / calcium ion binding / ATP hydrolysis activity / ATP binding / membrane / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Pseudomonas stutzeri (bacteria) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.78 Å | ||||||||||||
Authors | Zipfel, S. / Mueller, C. / Topitsch, A. / Lutz, M. / Zhang, L. / Einsle, O. | ||||||||||||
Funding support | Germany, 3items
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Citation | Journal: Nature / Year: 2022 Title: Molecular interplay of an assembly machinery for nitrous oxide reductase. Authors: Christoph Müller / Lin Zhang / Sara Zipfel / Annika Topitsch / Marleen Lutz / Johannes Eckert / Benedikt Prasser / Mohamed Chami / Wei Lü / Juan Du / Oliver Einsle / Abstract: Emissions of the critical ozone-depleting and greenhouse gas nitrous oxide (NO) from soils and industrial processes have increased considerably over the last decades. As the final step of bacterial ...Emissions of the critical ozone-depleting and greenhouse gas nitrous oxide (NO) from soils and industrial processes have increased considerably over the last decades. As the final step of bacterial denitrification, NO is reduced to chemically inert N (refs. ) in a reaction that is catalysed by the copper-dependent nitrous oxide reductase (NOR) (ref. ). The assembly of its unique [4Cu:2S] active site cluster Cu requires both the ATP-binding-cassette (ABC) complex NosDFY and the membrane-anchored copper chaperone NosL (refs. ). Here we report cryo-electron microscopy structures of Pseudomonas stutzeri NosDFY and its complexes with NosL and NOR, respectively. We find that the periplasmic NosD protein contains a binding site for a Cu ion and interacts specifically with NosL in its nucleotide-free state, whereas its binding to NOR requires a conformational change that is triggered by ATP binding. Mutually exclusive structures of NosDFY in complex with NosL and with NOR reveal a sequential metal-trafficking and assembly pathway for a highly complex copper site. Within this pathway, NosDFY acts as a mechanical energy transducer rather than as a transporter. It links ATP hydrolysis in the cytoplasm to a conformational transition of the NosD subunit in the periplasm, which is required for NosDFY to switch its interaction partner so that copper ions are handed over from the chaperone NosL to the enzyme NOR. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qba.cif.gz | 543.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qba.ent.gz | 423.2 KB | Display | PDB format |
PDBx/mmJSON format | 7qba.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qba_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7qba_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7qba_validation.xml.gz | 78.3 KB | Display | |
Data in CIF | 7qba_validation.cif.gz | 117.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qb/7qba ftp://data.pdbj.org/pub/pdb/validation_reports/qb/7qba | HTTPS FTP |
-Related structure data
Related structure data | 13885MC 7o0yC 7o0zC 7o10C 7o11C 7o12C 7o13C 7o14C 7o15C 7o16C 7o17C 7osfC 7osgC 7oshC 7osiC 7osjC 7znqC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Probable ABC transporter ... , 3 types, 5 molecules ABCDE
#1: Protein | Mass: 48258.500 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Gene: nosD / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: P19843 | ||
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#2: Protein | Mass: 34518.402 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Gene: nosF / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: P19844 #3: Protein | Mass: 29449.203 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Gene: nosY / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: P19845 |
-Protein , 1 types, 2 molecules HI
#4: Protein | Mass: 71958.555 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Gene: nosZ / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: P19573, nitrous-oxide reductase |
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-Non-polymers , 3 types, 6 molecules
#5: Chemical | #6: Chemical | #7: Chemical | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Heteroheptamer complex of NosZDFY / Type: COMPLEX / Details: homodimers of NosZ, NosY and NosF; monomer of NosD / Entity ID: #1-#4 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Pseudomonas stutzeri ATCC 14405 = CCUG 16156 (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) / Strain: C43(DE3) / Plasmid: pET |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER |
Electron lens | Mode: OTHER |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.78 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 114710 / Symmetry type: POINT | ||||||||||||||||||||||||
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