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Yorodumi- EMDB-2631: The Cryo-EM structure of the palindromic DNA-bound USP/EcR nuclea... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2631 | |||||||||
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Title | The Cryo-EM structure of the palindromic DNA-bound USP/EcR nuclear receptor reveals an asymmetric organization with allosteric domain positioning | |||||||||
Map data | - | |||||||||
Sample |
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Keywords | Nuclear receptor / 100kDa complex / transcription / ecdysone / USP / EcR / DNA response element / allostery / cryo electron microscopy | |||||||||
Function / homology | Function and homology information ecdysone binding / ecdysone receptor signaling pathway / bile acid signaling pathway / nuclear steroid receptor activity / negative regulation of inflammatory response / nuclear receptor activity / cell differentiation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II ...ecdysone binding / ecdysone receptor signaling pathway / bile acid signaling pathway / nuclear steroid receptor activity / negative regulation of inflammatory response / nuclear receptor activity / cell differentiation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleus Similarity search - Function | |||||||||
Biological species | Heliothis virescens (tobacco budworm) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 11.6 Å | |||||||||
Authors | Maletta M / Orlov I / Moras D / Billas IML / Klaholz BP | |||||||||
Citation | Journal: Nat Commun / Year: 2014 Title: The palindromic DNA-bound USP/EcR nuclear receptor adopts an asymmetric organization with allosteric domain positioning. Authors: Massimiliano Maletta / Igor Orlov / Pierre Roblin / Yannick Beck / Dino Moras / Isabelle M L Billas / Bruno P Klaholz / Abstract: Nuclear receptors (NRs) regulate gene expression through DNA- and ligand-binding and thus represent crucial therapeutic targets. The ultraspiracle protein/ecdysone receptor (USP/EcR) complex binds to ...Nuclear receptors (NRs) regulate gene expression through DNA- and ligand-binding and thus represent crucial therapeutic targets. The ultraspiracle protein/ecdysone receptor (USP/EcR) complex binds to half-sites with a one base pair spaced inverted repeat (IR1), a palindromic DNA response element (RE) reminiscent of IRs observed for vertebrate steroid hormone receptors. Here we present the cryo electron microscopy structure of the USP/EcR complex bound to an IR1 RE which provides the first description of a full IR-bound NR complex. The structure reveals that even though the DNA is almost symmetric, the complex adopts a highly asymmetric architecture in which the ligand-binding domains (LBDs) are positioned 5' off-centred. Additional interactions of the USP LBD with the 5'-flanking sequence trigger transcription activity as monitored by transfection assays. The comparison with DR-bound NR complexes suggests that DNA is the major allosteric driver in inversely positioning the LBDs, which serve as the main binding-site for transcriptional regulators. | |||||||||
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_2631.map.gz | 311.4 KB | EMDB map data format | |
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Header (meta data) | emd-2631-v30.xml emd-2631.xml | 11.4 KB 11.4 KB | Display Display | EMDB header |
Images | EMD-2631-USP-EcR-Image.png | 236.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2631 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2631 | HTTPS FTP |
-Validation report
Summary document | emd_2631_validation.pdf.gz | 188.1 KB | Display | EMDB validaton report |
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Full document | emd_2631_full_validation.pdf.gz | 187.3 KB | Display | |
Data in XML | emd_2631_validation.xml.gz | 5.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2631 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2631 | HTTPS FTP |
-Related structure data
Related structure data | 4ummMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_2631.map.gz / Format: CCP4 / Size: 3.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | - | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.7 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 : USP/EcR
Entire | Name: USP/EcR |
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Components |
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-Supramolecule #1000: USP/EcR
Supramolecule | Name: USP/EcR / type: sample / ID: 1000 / Oligomeric state: a heterodimer of USP and EcR bound to DNA / Number unique components: 3 |
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Molecular weight | Experimental: 100 KDa / Theoretical: 100 KDa |
-Macromolecule #1: ECR
Macromolecule | Name: ECR / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Recombinant expression: Yes |
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Source (natural) | Organism: Heliothis virescens (tobacco budworm) / Organelle: nucleus / Location in cell: nucleus |
Molecular weight | Experimental: 100 KDa / Theoretical: 100 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
-Macromolecule #3: USP
Macromolecule | Name: USP / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Recombinant expression: Yes |
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Source (natural) | Organism: Heliothis virescens (tobacco budworm) / Organelle: nucleus / Location in cell: nucleus |
Molecular weight | Experimental: 100 KDa / Theoretical: 100 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
-Macromolecule #2: DNA
Macromolecule | Name: DNA / type: dna / ID: 2 / Classification: DNA / Structure: SINGLE STRANDED / Synthetic?: Yes |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Experimental: 100 KDa / Theoretical: 100 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL |
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Buffer | Details: 10 mM TRIS pH 7.5, 100 mM NaCl, 10 mM MgCl2, 10 mM TCEP |
Grid | Details: Quantifoil 2/2.2 300 mesh |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK IV / Method: 2 seconds, force 4 |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Date | Nov 20, 2009 |
Image recording | Category: CCD / Film or detector model: FEI EAGLE (4k x 4k) / Number real images: 600 / Average electron dose: 20 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 100 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 64244 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder: FEI Polara cartrige / Specimen holder model: GATAN HELIUM |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Details | Imagic-V, angular reconstitution angles determination |
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CTF correction | Details: ccd images 4096x4096 |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 11.6 Å / Resolution method: OTHER / Software - Name: Imagic-V / Number images used: 50000 |
-Atomic model buiding 1
Initial model | PDB ID: |
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Details | The domains (USP/EcR LBD and DBD heterodimers respectively, PDB IDs 1R1K and 2HAN) were separately fitted by manual docking using program Pymol. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | PDB-4umm: |
-Atomic model buiding 2
Initial model | PDB ID: |
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Details | The domains (USP/EcR LBD and DBD heterodimers respectively, PDB IDs 1R1K and 2HAN) were separately fitted by manual docking using program Pymol. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | PDB-4umm: |