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Yorodumi- EMDB-5222: Nitrogen-Responsive Transcription Factor NrpR form Methanococcus ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5222 | |||||||||
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Title | Nitrogen-Responsive Transcription Factor NrpR form Methanococcus maripaludis in a 2OG-bound (inhibited) state | |||||||||
Map data | Reconstruction volume of 2OG-bound NrpR from Methanococcus maripaludis | |||||||||
Sample |
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Keywords | Nitrogen assimilation / Nitrogen regulation / Transcriptional regulation | |||||||||
Function / homology | NrpR regulatory domain Function and homology information | |||||||||
Biological species | Methanococcus maripaludis (archaea) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 22.0 Å | |||||||||
Authors | Wisedchaisri G / Dranow DM / Lie TJ / Bonanno JB / Patskovsky Y / Ozyurt SA / Sauder JM / Almo SC / Wasserman SR / Burley SK ...Wisedchaisri G / Dranow DM / Lie TJ / Bonanno JB / Patskovsky Y / Ozyurt SA / Sauder JM / Almo SC / Wasserman SR / Burley SK / Leigh JA / Gonen T | |||||||||
Citation | Journal: Structure / Year: 2010 Title: Structural underpinnings of nitrogen regulation by the prototypical nitrogen-responsive transcriptional factor NrpR. Authors: Goragot Wisedchaisri / David M Dranow / Thomas J Lie / Jeffrey B Bonanno / Yury Patskovsky / Sinem A Ozyurt / J Michael Sauder / Steven C Almo / Stephen R Wasserman / Stephen K Burley / John ...Authors: Goragot Wisedchaisri / David M Dranow / Thomas J Lie / Jeffrey B Bonanno / Yury Patskovsky / Sinem A Ozyurt / J Michael Sauder / Steven C Almo / Stephen R Wasserman / Stephen K Burley / John A Leigh / Tamir Gonen / Abstract: Plants and microorganisms reduce environmental inorganic nitrogen to ammonium, which then enters various metabolic pathways solely via conversion of 2-oxoglutarate (2OG) to glutamate and glutamine. ...Plants and microorganisms reduce environmental inorganic nitrogen to ammonium, which then enters various metabolic pathways solely via conversion of 2-oxoglutarate (2OG) to glutamate and glutamine. Cellular 2OG concentrations increase during nitrogen starvation. We recently identified a family of 2OG-sensing proteins--the nitrogen regulatory protein NrpR--that bind DNA and repress transcription of nitrogen assimilation genes. We used X-ray crystallography to determine the structure of NrpR regulatory domain. We identified the NrpR 2OG-binding cleft and show that residues predicted to interact directly with 2OG are conserved among diverse classes of 2OG-binding proteins. We show that high levels of 2OG inhibit NrpRs ability to bind DNA. Electron microscopy analyses document that NrpR adopts different quaternary structures in its inhibited 2OG-bound state compared with its active apo state. Our results indicate that upon 2OG release, NrpR repositions its DNA-binding domains correctly for optimal interaction with DNA thereby enabling gene repression. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_5222.map.gz | 308.1 KB | EMDB map data format | |
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Header (meta data) | emd-5222-v30.xml emd-5222.xml | 10 KB 10 KB | Display Display | EMDB header |
Images | emd_5222_1.jpg | 35.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5222 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5222 | HTTPS FTP |
-Validation report
Summary document | emd_5222_validation.pdf.gz | 78.6 KB | Display | EMDB validaton report |
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Full document | emd_5222_full_validation.pdf.gz | 77.7 KB | Display | |
Data in XML | emd_5222_validation.xml.gz | 492 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5222 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5222 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_5222.map.gz / Format: CCP4 / Size: 825.2 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction volume of 2OG-bound NrpR from Methanococcus maripaludis | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : NrpR from Methanococcus maripaludis
Entire | Name: NrpR from Methanococcus maripaludis |
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Components |
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-Supramolecule #1000: NrpR from Methanococcus maripaludis
Supramolecule | Name: NrpR from Methanococcus maripaludis / type: sample / ID: 1000 / Oligomeric state: Dimer / Number unique components: 1 |
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Molecular weight | Experimental: 600 KDa / Theoretical: 600 KDa |
-Macromolecule #1: NrpR
Macromolecule | Name: NrpR / type: protein_or_peptide / ID: 1 / Name.synonym: MMP0607 / Number of copies: 2 / Oligomeric state: Dimer / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Methanococcus maripaludis (archaea) / Strain: Mm500RC / Location in cell: Cytoplasm |
Molecular weight | Theoretical: 600 KDa |
Sequence | InterPro: NrpR regulatory domain |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.01 mg/mL |
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Buffer | pH: 7.5 Details: 100mM Tris HCl pH 7.5, 1M KCl and 5mM glycerol, 10mM 2-oxoglutarate |
Staining | Type: NEGATIVE Details: A 2 microlitre drop of NrpR was applied to a carbon-coated grid, washed 3 times with milliQ water and stained using 0.075% uranyl formate. |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI 12 |
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Image recording | Digitization - Scanner: NIKON SUPER COOLSCAN 9000 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 52000 |
Sample stage | Specimen holder: Eucentric / Specimen holder model: OTHER |
-Image processing
CTF correction | Details: Each particle |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 22.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider / Details: Random conical tilt followed by angular refinement / Number images used: 8498 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A |
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Software | Name: Chimera |
Details | PDBEntryID_givenInChain. Manual docking |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |