+Open data
-Basic information
Entry | Database: PDB / ID: 1n1j | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the NF-YB/NF-YC histone pair | ||||||
Components |
| ||||||
Keywords | DNA BINDING PROTEIN / HISTONE-LIKE PAIR | ||||||
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 / Activation of gene expression by SREBF (SREBP) / cellular response to leukemia inhibitory factor / 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 / Activation of gene expression by SREBF (SREBP) / cellular response to leukemia inhibitory factor / protein-DNA complex / PPARA activates gene expression / RNA polymerase II transcription regulator complex / protein folding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / DNA-binding transcription factor activity / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / 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 / MAD / Resolution: 1.67 Å | ||||||
Authors | Romier, C. / Cocchiarella, F. / Mantovani, R. / Moras, D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: The NF-YB/NF-YC structure gives insight into DNA binding and transcription regulation by CCAAT factor NF-Y Authors: Romier, C. / Cocchiarella, F. / Mantovani, R. / Moras, D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1n1j.cif.gz | 53.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1n1j.ent.gz | 37.4 KB | Display | PDB format |
PDBx/mmJSON format | 1n1j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n1/1n1j ftp://data.pdbj.org/pub/pdb/validation_reports/n1/1n1j | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 10722.289 Da / Num. of mol.: 1 / Fragment: NF-YB3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pACYC11b / Production host: Escherichia coli (E. coli) / References: UniProt: P25208 |
---|---|
#2: Protein | Mass: 11386.336 Da / Num. of mol.: 1 / Fragment: NF-YC2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: Q13952 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.34 % | |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 4000, magnesium acetate, sodium hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.920023 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 18, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.920023 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→50 Å / Num. all: 23068 / Num. obs: 22726 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 18.1 Å2 / Rsym value: 0.026 / Net I/σ(I): 43.8 |
Reflection shell | Resolution: 1.67→1.71 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 17.3 / Num. unique all: 1486 / Rsym value: 0.053 / % possible all: 99.6 |
Reflection | *PLUS Lowest resolution: 24 Å / % possible obs: 97.9 % / Num. measured all: 110854 / Rmerge(I) obs: 0.026 |
Reflection shell | *PLUS % possible obs: 99 % / Rmerge(I) obs: 0.053 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 1.67→24 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1171267.13 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 73.8335 Å2 / ksol: 0.393584 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.5 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.67→24 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.67→1.77 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 24 Å / Num. reflection obs: 21368 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|