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- EMDB-14813: ABC transporter complex NosDFYL in GDN -

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Basic information

Entry
Database: EMDB / ID: EMD-14813
TitleABC transporter complex NosDFYL in GDN
Map data
Sample
  • Complex: Hetero-hexameric complex of NosDF2Y2L
    • Protein or peptide: Probable ABC transporter ATP-binding protein NosF
    • Protein or peptide: Probable ABC transporter permease protein NosY
    • Protein or peptide: Probable ABC transporter binding protein NosD
    • Protein or peptide: Copper-binding lipoprotein NosL
  • Ligand: MAGNESIUM ION
  • Ligand: COPPER (II) ION
  • Ligand: ZINC ION
KeywordsATP-binding-cassette transporter complex NosDFYL / MEMBRANE PROTEIN
Function / homology
Function and homology information


ABC-type transporter activity / periplasmic space / ATP hydrolysis activity / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
Nitrous oxide reductase accessory protein NosL / NosL / Nitrous oxide reductase family maturation protein NosD / : / ABC-2 family transporter protein / ABC-2 family transporter protein / Parallel beta-helix repeat-2 / Periplasmic copper-binding protein NosD, beta helix domain / Carbohydrate-binding/sugar hydrolysis domain / Domain present in carbohydrate binding proteins and sugar hydrolses ...Nitrous oxide reductase accessory protein NosL / NosL / Nitrous oxide reductase family maturation protein NosD / : / ABC-2 family transporter protein / ABC-2 family transporter protein / Parallel beta-helix repeat-2 / Periplasmic copper-binding protein NosD, beta helix domain / Carbohydrate-binding/sugar hydrolysis domain / Domain present in carbohydrate binding proteins and sugar hydrolses / Periplasmic copper-binding protein (NosD) / Parallel beta-helix repeat / Parallel beta-helix repeats / Pectin lyase fold / Pectin lyase fold/virulence factor / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / Prokaryotic membrane lipoprotein lipid attachment site profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Probable ABC transporter binding protein NosD / Probable ABC transporter ATP-binding protein NosF / Probable ABC transporter permease protein NosY / Copper-binding lipoprotein NosL
Similarity search - Component
Biological speciesPseudomonas stutzeri ATCC 14405 = CCUG 16156 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsZhang L / Mueller C / Zipfel S / Chami M / Einsle O
Funding supportEuropean Union, Germany, 3 items
OrganizationGrant numberCountry
European Research Council (ERC)310656European Union
German Research Foundation (DFG)403222702 Germany
German Research Foundation (DFG)192904750 Germany
CitationJournal: 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
DepositionApr 21, 2022-
Header (metadata) releaseAug 3, 2022-
Map releaseAug 3, 2022-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14813.png

Downloads & links

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Map

FileDownload / File: emd_14813.map.gz / Format: CCP4 / Size: 83.7 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 280 pix.
= 229.6 Å		0.82 Å/pix.
x 280 pix.
= 229.6 Å		0.82 Å/pix.
x 280 pix.
= 229.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.22473334 - 0.48916355
Average (Standard dev.)0.0005792819 (±0.018391235)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 229.59999 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14813_msk_1.map
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Additional map: #1

Fileemd_14813_additional_1.map
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Half map: #1

Fileemd_14813_half_map_1.map
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Half map: #2

Fileemd_14813_half_map_2.map
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Sample components

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Entire : Hetero-hexameric complex of NosDF2Y2L

EntireName: Hetero-hexameric complex of NosDF2Y2L
Components
  • Complex: Hetero-hexameric complex of NosDF2Y2L
    • Protein or peptide: Probable ABC transporter ATP-binding protein NosF
    • Protein or peptide: Probable ABC transporter permease protein NosY
    • Protein or peptide: Probable ABC transporter binding protein NosD
    • Protein or peptide: Copper-binding lipoprotein NosL
  • Ligand: MAGNESIUM ION
  • Ligand: COPPER (II) ION
  • Ligand: ZINC ION

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Supramolecule #1: Hetero-hexameric complex of NosDF2Y2L

SupramoleculeName: Hetero-hexameric complex of NosDF2Y2L / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Pseudomonas stutzeri ATCC 14405 = CCUG 16156 (bacteria)
Molecular weightTheoretical: 192 KDa

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Macromolecule #1: Probable ABC transporter ATP-binding protein NosF

MacromoleculeName: Probable ABC transporter ATP-binding protein NosF / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas stutzeri ATCC 14405 = CCUG 16156 (bacteria)
Molecular weightTheoretical: 33.821703 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

UniProtKB: Probable ABC transporter ATP-binding protein NosF

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Macromolecule #2: Probable ABC transporter permease protein NosY

MacromoleculeName: Probable ABC transporter permease protein NosY / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas stutzeri ATCC 14405 = CCUG 16156 (bacteria)
Molecular weightTheoretical: 29.449203 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

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Macromolecule #3: Probable ABC transporter binding protein NosD

MacromoleculeName: Probable ABC transporter binding protein NosD / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas stutzeri ATCC 14405 = CCUG 16156 (bacteria)
Molecular weightTheoretical: 48.2585 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

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Macromolecule #4: Copper-binding lipoprotein NosL

MacromoleculeName: Copper-binding lipoprotein NosL / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas stutzeri ATCC 14405 = CCUG 16156 (bacteria)
Molecular weightTheoretical: 21.512299 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

UniProtKB: Copper-binding lipoprotein NosL

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION

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Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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: 8
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: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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 modelType of model: PDB ENTRY
PDB model - PDB ID:

7osg

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 420836
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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