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Yorodumi- PDB-6qms: NF-YB/C Heterodimer in Complex with NF-YA-derived Peptide Stabili... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qms | |||||||||
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Title | NF-YB/C Heterodimer in Complex with NF-YA-derived Peptide Stabilized with C11-Hydrocarbon Linker | |||||||||
Components |
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Keywords | TRANSCRIPTION / stapled peptide histone fold transcription factor | |||||||||
Function / homology | Function and homology information : / CCAAT-binding factor complex / ATF6 (ATF6-alpha) activates chaperone genes / ATF4 activates genes in response to endoplasmic reticulum stress / FOXO-mediated transcription of cell death genes / cellular response to leukemia inhibitory factor / Activation of gene expression by SREBF (SREBP) / protein-DNA complex / PPARA activates gene expression / RNA polymerase II transcription regulator complex ...: / CCAAT-binding factor complex / ATF6 (ATF6-alpha) activates chaperone genes / ATF4 activates genes in response to endoplasmic reticulum stress / FOXO-mediated transcription of cell death genes / cellular response to leukemia inhibitory factor / Activation of gene expression by SREBF (SREBP) / protein-DNA complex / PPARA activates gene expression / RNA polymerase II transcription regulator complex / rhythmic process / protein folding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein heterodimerization activity / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Kiehstaller, S. / Jeganathan, S. / Pearce, N.M. / Wendt, M. / Grossmann, T.N. / Hennig, S. | |||||||||
Funding support | European Union, 1items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2019 Title: Constrained Peptides with Fine-Tuned Flexibility Inhibit NF-Y Transcription Factor Assembly. Authors: Jeganathan, S. / Wendt, M. / Kiehstaller, S. / Brancaccio, D. / Kuepper, A. / Pospiech, N. / Carotenuto, A. / Novellino, E. / Hennig, S. / Grossmann, T.N. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qms.cif.gz | 96.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qms.ent.gz | 70.1 KB | Display | PDB format |
PDBx/mmJSON format | 6qms.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qm/6qms ftp://data.pdbj.org/pub/pdb/validation_reports/qm/6qms | HTTPS FTP |
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-Related structure data
Related structure data | 6qmpC 6qmqC 4csrS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 2436.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P23511, UniProt: P25208*PLUS |
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#2: Protein | Mass: 10876.456 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NFYB, HAP3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P25208, UniProt: Q13952*PLUS |
#3: Protein | Mass: 11258.227 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NFYC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13952, UniProt: P23511*PLUS |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.84 Å3/Da / Density % sol: 33.17 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / Details: 0.1 M Tris pH8.5 0.2 M MgCl2 18% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97797 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 25, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97797 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→19.06 Å / Num. obs: 17408 / % possible obs: 99.4 % / Redundancy: 12.4 % / CC1/2: 0.999 / Net I/σ(I): 20.16 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 12.8 % / Mean I/σ(I) obs: 2.15 / Num. unique obs: 2544 / CC1/2: 0.895 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4CSR Resolution: 1.8→19.06 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.961 / SU B: 9.07 / SU ML: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 114.37 Å2 / Biso mean: 48.716 Å2 / Biso min: 18.5 Å2
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Refinement step | Cycle: final / Resolution: 1.8→19.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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