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- PDB-4csr: High resolution crystal structure of the histone fold dimer (NF-Y... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4csr | ||||||
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Title | High resolution crystal structure of the histone fold dimer (NF-YB)-(NF-YC) | ||||||
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![]() | TRANSCRIPTION / NF-Y / DNA-BINDING / CCAAT-BOX | ||||||
Function / homology | ![]() 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 ...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 / regulation of transcription by RNA polymerase II / chromatin / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gnesutta, N. / Cocolo, S. / Mantovani, R. / Bolognesi, M. / Nardini, M. | ||||||
![]() | ![]() Title: High Resolution Crystal Structure of the Histone Fold Dimer (NF-Yb)-(NF-Yc) Authors: Gnesutta, N. / Cocolo, S. / Mantovani, R. / Bolognesi, M. / Nardini, M. #1: ![]() Title: Sequence-Specific Transcription Factor NF-Y Displays Histone-Like DNA Binding and H2B-Like Ubiquitination. Authors: Nardini, M. / Gnesutta, N. / Donati, G. / Gatta, R. / Forni, C. / Fossati, A. / Vonrhein, C. / Moras, D. / Romier, C. / Bolognesi, M. / Mantovani, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 94.7 KB | Display | ![]() |
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PDB format | ![]() | 71.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1n1jS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 10853.485 Da / Num. of mol.: 1 / Fragment: RESIDUES 49-141 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Protein | Mass: 11104.061 Da / Num. of mol.: 1 / Fragment: RESIDUES 27-120 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.6 % / Description: NONE |
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Crystal grow | pH: 8.2 Details: 28% PEG 4K, 100 MM TRIS PH 8.2, 200 MM MG(OAC)2, 100 MM NA(OAC) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→33.18 Å / Num. obs: 31692 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1N1J Resolution: 1.5→33.18 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.998 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.426 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→33.18 Å
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Refine LS restraints |
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