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Open data
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Basic information
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Title | ABC transporter complex NosDFYL in GDN | ||||||||||||
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Function / homology | ![]() ABC-type transporter activity / periplasmic space / ATP hydrolysis activity / ATP binding / metal ion binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.04 Å | ||||||||||||
![]() | Zhang L / Mueller C / Zipfel S / Chami M / Einsle O | ||||||||||||
Funding support | European Union, ![]()
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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 | ![]() | 74.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 21.7 KB 21.7 KB | Display Display | ![]() |
Images | ![]() | 119.6 KB | ||
Masks | ![]() | 83.7 MB | ![]() | |
Others | ![]() ![]() ![]() | 78.1 MB 77.7 MB 77.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 770.9 KB | Display | ![]() |
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Full document | ![]() | 770.5 KB | Display | |
Data in XML | ![]() | 12.9 KB | Display | |
Data in CIF | ![]() | 15.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7znqMC ![]() 7o0yC ![]() 7o0zC ![]() 7o10C ![]() 7o11C ![]() 7o12C ![]() 7o13C ![]() 7o14C ![]() 7o15C ![]() 7o16C ![]() 7o17C ![]() 7osfC ![]() 7osgC ![]() 7oshC ![]() 7osiC ![]() 7osjC ![]() 7qbaC 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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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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-Additional map: #1
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-Half map: #1
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-Half map: #2
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Sample components
-Entire : Hetero-hexameric complex of NosDF2Y2L
Entire | Name: Hetero-hexameric complex of NosDF2Y2L |
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Components |
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-Supramolecule #1: Hetero-hexameric complex of NosDF2Y2L
Supramolecule | Name: Hetero-hexameric complex of NosDF2Y2L / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
Molecular weight | Theoretical: 192 KDa |
-Macromolecule #1: Probable ABC transporter ATP-binding protein NosF
Macromolecule | Name: Probable ABC transporter ATP-binding protein NosF / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 33.821703 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MNAVEIQGVS QRYGSMTVLH DLNLNLGEGE VLGLFGHNGA GKTTSMKLIL GLLSPSEGQV KVLGRAPNDP QVRRQLGYLP ENVTFYPQL SGRETLRHFA RLKGAALTQV DELLEQVGLA HAADRRVKTY SKGMRQRLGL AQALLGEPRL LLLDEPTVGL D PIATQDLY ...String: MNAVEIQGVS QRYGSMTVLH DLNLNLGEGE VLGLFGHNGA GKTTSMKLIL GLLSPSEGQV KVLGRAPNDP QVRRQLGYLP ENVTFYPQL SGRETLRHFA RLKGAALTQV DELLEQVGLA HAADRRVKTY SKGMRQRLGL AQALLGEPRL LLLDEPTVGL D PIATQDLY LLIDRLRQRG TSIILCSHVL PGVEAHINRA AILAKGCLQA VGSLSQLRAE AGLPVRIRAS GISERDSWLQ RW TDAGHSA RGLSESSIEV VAVNGHKLVL LRQLLGEGEP EDIEIHQPSL EDLYRYYMER AGDVRAQEGR L |
-Macromolecule #2: Probable ABC transporter permease protein NosY
Macromolecule | Name: Probable ABC transporter permease protein NosY / type: protein_or_peptide / ID: 2 / 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 |
-Macromolecule #3: Probable ABC transporter binding protein NosD
Macromolecule | Name: Probable ABC transporter binding protein NosD / type: protein_or_peptide / ID: 3 / 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 |
-Macromolecule #4: Copper-binding lipoprotein NosL
Macromolecule | Name: Copper-binding lipoprotein NosL / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 21.512299 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MNALHRIGAG TLLAVLLAFG LTGCGEKEEV QQSLEPVAFH DSDECHVCGM IITDFPGPKG QAVEKRGVKK FCSTAEMLGW WLQPENRLL DAKLYVHDMG RSVWEKPDDG HLIDATSAYY VVGTSLKGAM GASLASFAEE QDAKALAGMH GGRVLRFEEI D QALLQEAA ...String: MNALHRIGAG TLLAVLLAFG LTGCGEKEEV QQSLEPVAFH DSDECHVCGM IITDFPGPKG QAVEKRGVKK FCSTAEMLGW WLQPENRLL DAKLYVHDMG RSVWEKPDDG HLIDATSAYY VVGTSLKGAM GASLASFAEE QDAKALAGMH GGRVLRFEEI D QALLQEAA SMQHGGMHDH APNGAHNAHA GHWSHPQFEK |
-Macromolecule #5: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #6: COPPER (II) ION
Macromolecule | Name: COPPER (II) ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: CU |
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Molecular weight | Theoretical: 63.546 Da |
Chemical component information | ![]() ChemComp-CU: |
-Macromolecule #7: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 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 | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 420836 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |