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- PDB-4umm: The Cryo-EM structure of the palindromic DNA-bound USP-EcR nuclea... -
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Basic information
Entry | Database: PDB / ID: 4umm | ||||||
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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 | ||||||
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![]() | NUCLEAR RECEPTOR / TRANSCRIPTION / ECDYSONE / USP-ECR / DNA RESPONSE ELEMENT / ALLOSTERY / CRYO ELECTRON MICROSCOPY | ||||||
Function / homology | ![]() 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 | ![]() SYNTHETIC CONSTRUCT (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 11.6 Å | ||||||
![]() | Maletta, M. / Orlov, I. / Moras, D. / Billas, I.M.L. / Klaholz, B.P. | ||||||
![]() | ![]() 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
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 168.2 KB | Display | ![]() |
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PDB format | ![]() | 123.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2631MC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 4 types, 4 molecules AEFG
#1: Protein | Mass: 9256.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#4: Protein | Mass: 10099.977 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#5: Protein | Mass: 29962.717 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#6: Protein | Mass: 30368.961 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-DNA chain , 2 types, 2 molecules CD
#2: DNA chain | Mass: 6148.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
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#3: DNA chain | Mass: 6117.979 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
-Non-polymers , 3 types, 10 molecules ![](data/chem/img/EPH.gif)
![](data/chem/img/P1A.gif)
![](data/chem/img/HOH.gif)
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![](data/chem/img/HOH.gif)
#7: Chemical | ChemComp-EPH / |
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#8: Chemical | ChemComp-P1A / |
#9: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: BRUNO P. KLAHOLZ / Type: COMPLEX |
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Buffer solution | Name: 10 MM TRIS PH 7.5, 100 MM NACL, 10 MM MGCL2, 10 MM TCEP pH: 7.5 Details: 10 MM TRIS PH 7.5, 100 MM NACL, 10 MM MGCL2, 10 MM TCEP |
Specimen | Conc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: CARBON |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 90, TEMPERATURE- 120, INSTRUMENT- FEI VITROBOT MARK IV, METHOD- 2 SECONDS, FORCE 4, |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai F30 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F30 / Date: Nov 20, 2009 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 59000 X / Calibrated magnification: 64244 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm / Cs: 2 mm |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: FEI EAGLE (4k x 4k) |
Image scans | Num. digital images: 600 |
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Processing
EM software | Name: IMAGIC / Version: 5 / Category: 3D reconstruction | ||||||||||||
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CTF correction | Details: CCD IMAGES 4096X4096 | ||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Method: CROSS-COMMON LINES / Resolution: 11.6 Å / Num. of particles: 50000 Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD -2631. (DEPOSITION ID: 12447). Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Details: METHOD--RIGID BODY | ||||||||||||
Atomic model building | PDB-ID: 1R1K Accession code: 1R1K / Source name: PDB / Type: experimental model | ||||||||||||
Refinement | Highest resolution: 11.6 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 11.6 Å
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