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Yorodumi- EMDB-37375: Allosteric regulation of nitrate transporter NRT via the signalli... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37375 | |||||||||
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Title | Allosteric regulation of nitrate transporter NRT via the signalling protein PII | |||||||||
Map data | ||||||||||
Sample |
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Keywords | ATP-dependent transporter / ABC transporter / nitrate/nitrite transporter / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information nitrate transmembrane transporter activity / monoatomic ion transport / ATP hydrolysis activity / ATP binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Nostoc sp. PCC 7120 = FACHB-418 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Li B / Zhou CZ / Chen YX / Jiang YL | |||||||||
Funding support | China, 1 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2024 Title: Allosteric regulation of nitrate transporter NRT via the signaling protein PII. Authors: Bo Li / Xiao-Qian Wang / Qin-Yao Li / Da Xu / Jing Li / Wen-Tao Hou / Yuxing Chen / Yong-Liang Jiang / Cong-Zhao Zhou / Abstract: Coordinated carbon and nitrogen metabolism is crucial for bacteria living in the fluctuating environments. Intracellular carbon and nitrogen homeostasis is maintained by a sophisticated network, in ...Coordinated carbon and nitrogen metabolism is crucial for bacteria living in the fluctuating environments. Intracellular carbon and nitrogen homeostasis is maintained by a sophisticated network, in which the widespread signaling protein PII acts as a major regulatory hub. In cyanobacteria, PII was proposed to regulate the nitrate uptake by an ABC (ATP-binding cassette)-type nitrate transporter NrtABCD, in which the nucleotide-binding domain of NrtC is fused with a C-terminal regulatory domain (CRD). Here, we solved three cryoelectron microscopy structures of NrtBCD, bound to nitrate, ATP, and PII, respectively. Structural and biochemical analyses enable us to identify the key residues that form a hydrophobic and a hydrophilic cavity along the substrate translocation channel. The core structure of PII, but not the canonical T-loop, binds to NrtC and stabilizes the CRD, making it visible in the complex structure, narrows the substrate translocation channel in NrtB, and ultimately locks NrtBCD at an inhibited inward-facing conformation. Based on these results and previous reports, we propose a putative transport cycle driven by NrtABCD, which is allosterically inhibited by PII in response to the cellular level of 2-oxoglutarate. Our findings provide a distinct regulatory mechanism of ABC transporter via asymmetrically binding to a signaling protein. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_37375.map.gz | 3.6 MB | EMDB map data format | |
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Header (meta data) | emd-37375-v30.xml emd-37375.xml | 17.3 KB 17.3 KB | Display Display | EMDB header |
Images | emd_37375.png | 101.5 KB | ||
Filedesc metadata | emd-37375.cif.gz | 6.2 KB | ||
Others | emd_37375_half_map_1.map.gz emd_37375_half_map_2.map.gz | 23.3 MB 23.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37375 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37375 | HTTPS FTP |
-Related structure data
Related structure data | 8w9mMC 8wm7C 8wm8C 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_37375.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_37375_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_37375_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : nitrate transporter NrtBCD complexed with ATP
Entire | Name: nitrate transporter NrtBCD complexed with ATP |
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Components |
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-Supramolecule #1: nitrate transporter NrtBCD complexed with ATP
Supramolecule | Name: nitrate transporter NrtBCD complexed with ATP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria) |
-Macromolecule #1: Nitrate transport permease protein
Macromolecule | Name: Nitrate transport permease protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria) |
Molecular weight | Theoretical: 30.483053 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MTAVLGNRAR VRKSQKAINN FLWKKVVPPL VALGIFLVIW QLLCLNPNFK LPGPIETFSE TWDPFIINPF FDNGESDKGL GWQILSSLG RVGLGFSLAA IAGIILGILI GVNPLVYNAV DPIFQVLRTV PPLAWLPISL AAFQQANPSA IFVIFITSIW P ILLNTTVG ...String: MTAVLGNRAR VRKSQKAINN FLWKKVVPPL VALGIFLVIW QLLCLNPNFK LPGPIETFSE TWDPFIINPF FDNGESDKGL GWQILSSLG RVGLGFSLAA IAGIILGILI GVNPLVYNAV DPIFQVLRTV PPLAWLPISL AAFQQANPSA IFVIFITSIW P ILLNTTVG VQQIPQDYIN VAKVLRLKGV KYFFKIVFPA TVPYIFTGLR IGIGLSWLAI VAAEMLVGGV GIGSFIWDAY NT TTETNLS EIILALIYVG LVGLLLDRLV GFVASKVVAD QK UniProtKB: Nitrate transport permease protein |
-Macromolecule #2: Nitrate transport ATP-binding protein
Macromolecule | Name: Nitrate transport ATP-binding protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria) |
Molecular weight | Theoretical: 76.325156 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MPTFVEIDHV DRIFDLPNGG RYIALKNIEL KIKQGEFVSL IGHSGCGKST LLNIIAGLDR ASIGGVTLEG REIREPSPDR MVVFQNYSL LPWLTVRENV ALAVDEVYQG KSKGERRAII EEHIDMVGLR LAANKRPSEL SGGMKQRVAI ARALATRPKL L LLDQPFGA ...String: MPTFVEIDHV DRIFDLPNGG RYIALKNIEL KIKQGEFVSL IGHSGCGKST LLNIIAGLDR ASIGGVTLEG REIREPSPDR MVVFQNYSL LPWLTVRENV ALAVDEVYQG KSKGERRAII EEHIDMVGLR LAANKRPSEL SGGMKQRVAI ARALATRPKL L LLDQPFGA LDALTRGSLQ EQLMKICNEH QITCVMVTHD VDEALLLSDR VVMLTNGPEA HIGQILEVPI SRPRQRLEVV KH PSYYNLR NEIIYFLNQQ KLAKKRQTQQ ASAPLGTAKA VIEIGFMPLT DSAPLIVAKE KGFFAKYGLD NVILNRANNW QAI ATGVVT GKLDAAQMVA GMPIALTLGA GSQTPTPVIN ALNLSRNANA ITFSKRLYNQ GVRSLADLKA VIDSSPDQIL TLGV VHSAS MQNLILRYWL AAGGIDPDRD VSLTVIPPTQ MVSQLKAGNI DGYCAGEPWN YQAVHDDLGF VAATALEIWS GQPKK VLGV REDWAQKYPE TYLNLVKALI EACKYCDDLR NREEILEILC RPEYLDVNPA YVRSGFIDPY DRGDGTPPQQ LTAYNQ FYL NKTNYPNRTE ILWMITQMAR WGLTPFPKNW VEITERVCRT DIFGAAARDL GLLDIGEDDP IHLFDGKLFN PSEPIEY LK SLEIRRQIRI EEVFISSGDY KDHDGDYKDH DIDYKDDDDK UniProtKB: Nitrate transport ATP-binding protein |
-Macromolecule #3: Nitrate transport ATP-binding protein
Macromolecule | Name: Nitrate transport ATP-binding protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria) |
Molecular weight | Theoretical: 31.398152 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MQIINRNNQT NLKPQKTDNF LVVEGVSKIY PTPEGPYTVL DGIDLKVREG EFVCLIGHSG CGKSTLLNMI SGFNTPSEGV VLLQDKPIT EPGPDRMMVF QNYCLLPWLN VFENVYLAVD AVFPNKPQAE KRAIVREHLA MVGLTEAAEK KPSQISGGMK Q RVAIARAL ...String: MQIINRNNQT NLKPQKTDNF LVVEGVSKIY PTPEGPYTVL DGIDLKVREG EFVCLIGHSG CGKSTLLNMI SGFNTPSEGV VLLQDKPIT EPGPDRMMVF QNYCLLPWLN VFENVYLAVD AVFPNKPQAE KRAIVREHLA MVGLTEAAEK KPSQISGGMK Q RVAIARAL SIRPQVLILD QPFGALDAIT KEELQEELLQ IWSDHQVTVL MITHDIDEAL FLADRVVMMT NGPAAQIGEI LD IPFDRPR NRRRIMEDPK YYDLRNYALD FLFNRFAHNE UniProtKB: Nitrate transport ATP-binding protein |
-Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 8 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.5 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1222929 |