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- EMDB-13885: CryoEM structure of the ABC transporter NosDFY complexed with nit... -
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Basic information
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Title | CryoEM structure of the ABC transporter NosDFY complexed with nitrous oxide reductase NosZ | ||||||||||||
![]() | density modified map using Phenix | ||||||||||||
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![]() | ABC transporter / metal binding protein / nitrous oxide reductase / MEMBRANE PROTEIN | ||||||||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.78 Å | ||||||||||||
![]() | Zipfel S / Mueller C | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 49.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.7 KB 17.7 KB | Display Display | ![]() |
Images | ![]() | 129.6 KB | ||
Filedesc metadata | ![]() | 6.6 KB | ||
Others | ![]() | 48.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 536.1 KB | Display | ![]() |
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Full document | ![]() | 535.7 KB | Display | |
Data in XML | ![]() | 6 KB | Display | |
Data in CIF | ![]() | 6.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7qbaMC ![]() 7o0yC ![]() 7o0zC ![]() 7o10C ![]() 7o11C ![]() 7o12C ![]() 7o13C ![]() 7o14C ![]() 7o15C ![]() 7o16C ![]() 7o17C ![]() 7osfC ![]() 7osgC ![]() 7oshC ![]() 7osiC ![]() 7osjC ![]() 7znqC 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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Annotation | density modified map using Phenix | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.87 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: unsharpened map after 3D refinement using Relion
File | emd_13885_additional_1.map | ||||||||||||
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Annotation | unsharpened map after 3D refinement using Relion | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Heteroheptamer complex of NosZDFY
Entire | Name: Heteroheptamer complex of NosZDFY |
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Components |
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-Supramolecule #1: Heteroheptamer complex of NosZDFY
Supramolecule | Name: Heteroheptamer complex of NosZDFY / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 / Details: homodimers of NosZ, NosY and NosF; monomer of NosD |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Probable ABC transporter binding protein NosD
Macromolecule | Name: Probable ABC transporter binding protein NosD / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 48.2585 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MFKAQATFSR YSAAVSLLLL FSGAAQAAPQ SITTLPLQPD GENRWRLPAG EYQGQFTIEQ PMQLRCEPGA VIQSQGQGSS LLISAPDVL VEGCTLYEWG SDLTAMDSAV FILPAAERAQ ISNNRMRGPG FGVFVDGTRD VQVIGNEIDG DAGVRSQDRG N GIHLFAVS ...String: MFKAQATFSR YSAAVSLLLL FSGAAQAAPQ SITTLPLQPD GENRWRLPAG EYQGQFTIEQ PMQLRCEPGA VIQSQGQGSS LLISAPDVL VEGCTLYEWG SDLTAMDSAV FILPAAERAQ ISNNRMRGPG FGVFVDGTRD VQVIGNEIDG DAGVRSQDRG N GIHLFAVS GARVLHNHVR NARDGIYIDT SNGNHLEGNV IEDVRYGVHY MFANENSLID NVTRRTRTGY ALMQSRKLTV TG NRSEQDQ NYGILMNYIT YSTITGNFVS DVQRGDTGGD SMISGGEGKA LFIYNSLFNT IENNHFEKSS LGIHLTAGSE DNR ISGNAF VGNQQQVKYV ASRTQEWSVD GRGNYWSDYL GWDRNNDGLG DIAYEPNDNV DRLLWLYPQV RLLMNSPSIE VLRW VQRAF PVIKSPGVQD SHPLMKLPTE KLLTEKQEPT S UniProtKB: Probable ABC transporter binding protein NosD |
-Macromolecule #2: Probable ABC transporter ATP-binding protein NosF
Macromolecule | Name: Probable ABC transporter ATP-binding protein NosF / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 34.518402 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: HHHHHHNAVE IQGVSQRYGS MTVLHDLNLN LGEGEVLGLF GHNGAGKTTS MKLILGLLSP SEGQVKVLGR APNDPQVRRQ LGYLPENVT FYPQLSGRET LRHFARLKGA ALTQVDELLE QVGLAHAADR RVKTYSKGMR QRLGLAQALL GEPRLLLLDQ P TVGLDPIA ...String: HHHHHHNAVE IQGVSQRYGS MTVLHDLNLN LGEGEVLGLF GHNGAGKTTS MKLILGLLSP SEGQVKVLGR APNDPQVRRQ LGYLPENVT FYPQLSGRET LRHFARLKGA ALTQVDELLE QVGLAHAADR RVKTYSKGMR QRLGLAQALL GEPRLLLLDQ P TVGLDPIA TQDLYLLIDR LRQRGTSIIL CSHVLPGVEA HINRAAILAK GCLQAVGSLS QLRAEAGLPV RIRASGISER DS WLQRWTD AGHSARGLSE SSIEVVAVNG HKLVLLRQLL GEGEPEDIEI HQPSLEDLYR YYMERAGDVR AQEGRL UniProtKB: Probable ABC transporter ATP-binding protein NosF |
-Macromolecule #3: Probable ABC transporter permease protein NosY
Macromolecule | Name: Probable ABC transporter permease protein NosY / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 29.449203 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MNQVWNIARK ELSDGLRNRW LLAISLLFAV LAVGIAWLGA AASGQLGFTS IPATIASLAS LATFLMPLIA LLLAYDAIVG EDEGGTLML LLTYPLGRGQ ILLGKFVGHG LILALAVLIG FGCAALAIAL LVEGVELGML FWAFGRFMIS STLLGWVFLA F AYVLSGKV ...String: MNQVWNIARK ELSDGLRNRW LLAISLLFAV LAVGIAWLGA AASGQLGFTS IPATIASLAS LATFLMPLIA LLLAYDAIVG EDEGGTLML LLTYPLGRGQ ILLGKFVGHG LILALAVLIG FGCAALAIAL LVEGVELGML FWAFGRFMIS STLLGWVFLA F AYVLSGKV NEKSSAAGLA LGVWFLFVLV FDLVLLALLV LSEGKFNPEL LPWLLLLNPT DIYRLINLSG FEGSGSAMGV LS LGADLPV PAAVLWLCLL AWIGVSLLLA YAIFRRRLT UniProtKB: Probable ABC transporter permease protein NosY |
-Macromolecule #4: Nitrous-oxide reductase
Macromolecule | Name: Nitrous-oxide reductase / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO / EC number: nitrous-oxide reductase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 71.958555 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSDKDSKNTP QVPEKLGLSR RGFLGASAVT GAAVAATALG GAVMTRESWA QAVKESKQKI HVGPGELDDY YGFWSGGHQG EVRVLGVPS MRELMRIPVF NVDSATGWGL TNESRHIMGD SAKFLNGDCH HPHISMTDGK YDGKYLFIND KANSRVARIR L DIMKCDKM ...String: MSDKDSKNTP QVPEKLGLSR RGFLGASAVT GAAVAATALG GAVMTRESWA QAVKESKQKI HVGPGELDDY YGFWSGGHQG EVRVLGVPS MRELMRIPVF NVDSATGWGL TNESRHIMGD SAKFLNGDCH HPHISMTDGK YDGKYLFIND KANSRVARIR L DIMKCDKM ITVPNVQAIH GLRLQKVPHT KYVFANAEFI IPHPNDGKVF DLQDENSYTM YNAIDAETME MAFQVIVDGN LD NTDADYT GRFAAATCYN SEKAFDLGGM MRNERDWVVV FDIHAVEAAV KAGDFITLGD SKTPVLDGRK KDGKDSKFTR YVP VPKNPH GCNTSSDGKY FIAAGKLSPT CSMIAIDKLP DLFAGKLADP RDVIVGEPEL GLGPLHTTFD GRGNAYTTLF IDSQ VVKWN MEEAVRAYKG EKVNYIKQKL DVHYQPGHLH ASLCETNEAD GKWLVALSKF SKDRFLPVGP LHPENDQLID ISGDE MKLV HDGPTFAEPH DCIMARRDQI KTKKIWDRND PFFAPTVEMA KKDGINLDTD NKVIRDGNKV RVYMTSMAPA FGVQEF TVK QGDEVTVTIT NIDQIEDVSH GFVVVNHGVS MEISPQQTSS ITFVADKPGL HWYYCSWFCH ALHMEMVGRM MVEPAWS HP QFEK UniProtKB: Nitrous-oxide reductase |
-Macromolecule #5: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #6: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 2 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ![]() ChemComp-ATP: |
-Macromolecule #7: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-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: 8 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER |
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Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.78 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 114710 |
Initial angle assignment | Type: OTHER |
Final angle assignment | Type: OTHER |