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Yorodumi- EMDB-14442: E. coli C-P lyase bound to PhnK/PhnL dual ABC dimer with AMPPNP a... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14442 | |||||||||
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Title | E. coli C-P lyase bound to PhnK/PhnL dual ABC dimer with AMPPNP and PhnK E171Q mutation | |||||||||
Map data | ||||||||||
Sample |
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Keywords | protein complex / transferase / ABC / hydrolase / lyase / carbon-phosphorus / SAM | |||||||||
Function / homology | Function and homology information alpha-D-ribose 1-methylphosphonate 5-phosphate C-P-lyase / alpha-D-ribose 1-methylphosphonate 5-phosphate C-P-lyase activity / alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase / alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase activity / alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase complex / carbon phosphorus lyase complex / organic phosphonate metabolic process / organic phosphonate transport / organic phosphonate catabolic process / peptide transport ...alpha-D-ribose 1-methylphosphonate 5-phosphate C-P-lyase / alpha-D-ribose 1-methylphosphonate 5-phosphate C-P-lyase activity / alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase / alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase activity / alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase complex / carbon phosphorus lyase complex / organic phosphonate metabolic process / organic phosphonate transport / organic phosphonate catabolic process / peptide transport / 4 iron, 4 sulfur cluster binding / lyase activity / protein homodimerization activity / ATP hydrolysis activity / ATP binding / identical protein binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.09 Å | |||||||||
Authors | Amstrup SK / Sofus N | |||||||||
Funding support | Denmark, 1 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structural remodelling of the carbon-phosphorus lyase machinery by a dual ABC ATPase. Authors: Søren K Amstrup / Sui Ching Ong / Nicholas Sofos / Jesper L Karlsen / Ragnhild B Skjerning / Thomas Boesen / Jan J Enghild / Bjarne Hove-Jensen / Ditlev E Brodersen / Abstract: In Escherichia coli, the 14-cistron phn operon encoding carbon-phosphorus lyase allows for utilisation of phosphorus from a wide range of stable phosphonate compounds containing a C-P bond. As part ...In Escherichia coli, the 14-cistron phn operon encoding carbon-phosphorus lyase allows for utilisation of phosphorus from a wide range of stable phosphonate compounds containing a C-P bond. As part of a complex, multi-step pathway, the PhnJ subunit was shown to cleave the C-P bond via a radical mechanism, however, the details of the reaction could not immediately be reconciled with the crystal structure of a 220 kDa PhnGHIJ C-P lyase core complex, leaving a significant gap in our understanding of phosphonate breakdown in bacteria. Here, we show using single-particle cryogenic electron microscopy that PhnJ mediates binding of a double dimer of the ATP-binding cassette proteins, PhnK and PhnL, to the core complex. ATP hydrolysis induces drastic structural remodelling leading to opening of the core complex and reconfiguration of a metal-binding and putative active site located at the interface between the PhnI and PhnJ subunits. #1: Journal: Biorxiv / Year: 2022 Title: Structural remodelling of the carbon-phosphorus lyase machinery by a dual ABC ATPase Authors: Amstrup SK / Sofos N / Karlsen JL / Skjerning RB / Boesen T / Enghild JJ / Hove-Jensen B / Brodersen DE | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14442.map.gz | 143.1 MB | EMDB map data format | |
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Header (meta data) | emd-14442-v30.xml emd-14442.xml | 30.2 KB 30.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14442_fsc.xml | 14.5 KB | Display | FSC data file |
Images | emd_14442.png | 179.1 KB | ||
Filedesc metadata | emd-14442.cif.gz | 8.8 KB | ||
Others | emd_14442_additional_1.map.gz emd_14442_half_map_1.map.gz emd_14442_half_map_2.map.gz | 4.9 MB 262.4 MB 262.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14442 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14442 | HTTPS FTP |
-Validation report
Summary document | emd_14442_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_14442_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_14442_validation.xml.gz | 22.2 KB | Display | |
Data in CIF | emd_14442_validation.cif.gz | 28.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14442 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14442 | HTTPS FTP |
-Related structure data
Related structure data | 7z16MC 7z15C 7z17C 7z18C 7z19C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_14442.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.9551 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Map filtered to local resolution
File | emd_14442_additional_1.map | ||||||||||||
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Annotation | Map filtered to local resolution | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A
File | emd_14442_half_map_1.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B
File | emd_14442_half_map_2.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : E. coli C-P lyase bound to PhnK/PhnL dual ABC dimer with AMPPNP a...
+Supramolecule #1: E. coli C-P lyase bound to PhnK/PhnL dual ABC dimer with AMPPNP a...
+Macromolecule #1: Phosphonate C-P lyase system protein PhnG
+Macromolecule #2: Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subuni...
+Macromolecule #3: Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subuni...
+Macromolecule #4: Alpha-D-ribose 1-methylphosphonate 5-phosphate C-P lyase
+Macromolecule #5: Putative phosphonates utilization ATP-binding protein PhnK
+Macromolecule #6: Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subuni...
+Macromolecule #7: ZINC ION
+Macromolecule #8: PHOSPHATE ION
+Macromolecule #9: MAGNESIUM ION
+Macromolecule #10: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
+Macromolecule #11: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.5 mg/mL | ||||||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: UltrAuFoil R0.6/1 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR / Details: 10 mA GloQube, Quorum | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: LEICA EM GP / Details: Blotting for 6-9 seconds before plunging. | ||||||||||||||||||
Details | Sample was monodisperse. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 5666 / Average electron dose: 62.0 e/Å2 Details: Images were collected in movie-mode with a total of 56 frames |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 135000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |