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- PDB-4csr: High resolution crystal structure of the histone fold dimer (NF-Y... -

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Basic information

Entry
Database: PDB / ID: 4csr
TitleHigh resolution crystal structure of the histone fold dimer (NF-YB)-(NF-YC)
Components
  • NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT BETA
  • NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT GAMMA
KeywordsTRANSCRIPTION / NF-Y / DNA-BINDING / CCAAT-BOX
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 / 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 / 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 / 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 DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Transcription factor, NFYB/HAP3, conserved site / Transcription factor NFYB/HAP3 / NF-YB/HAP3 subunit signature. / : / Transcription factor CBF/NF-Y/archaeal histone domain / Histone-like transcription factor (CBF/NF-Y) and archaeal histone / Histone, subunit A / Histone, subunit A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 ...Transcription factor, NFYB/HAP3, conserved site / Transcription factor NFYB/HAP3 / NF-YB/HAP3 subunit signature. / : / Transcription factor CBF/NF-Y/archaeal histone domain / Histone-like transcription factor (CBF/NF-Y) and archaeal histone / Histone, subunit A / Histone, subunit A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Nuclear transcription factor Y subunit beta / Nuclear transcription factor Y subunit gamma
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsGnesutta, N. / Cocolo, S. / Mantovani, R. / Bolognesi, M. / Nardini, M.
Citation
Journal: To be Published
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: Journal: Cell(Cambridge,Mass.) / Year: 2013
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
DepositionMar 9, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT BETA
B: NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT GAMMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2345
Polymers21,9582
Non-polymers2763
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-47.2 kcal/mol
Surface area9000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.670, 60.800, 61.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT BETA / CCAAT BOX DNA-BINDING PROTEIN SUBUNIT B / NUCLEAR TRANSCRIPTION FACTORY SUBUNIT B / NF-YB / NUCLEAR ...CCAAT BOX DNA-BINDING PROTEIN SUBUNIT B / NUCLEAR TRANSCRIPTION FACTORY SUBUNIT B / NF-YB / NUCLEAR TRANSCRIPTION FACTORY SUBUNIT B


Mass: 10853.485 Da / Num. of mol.: 1 / Fragment: RESIDUES 49-141
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P25208
#2: Protein NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT GAMMA / CCAAT BOX DNA-BINDING PROTEIN SUBUNIT C / NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT C / NF-YC / ...CCAAT BOX DNA-BINDING PROTEIN SUBUNIT C / NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT C / NF-YC / TRANSACTIVATOR HSM-1/2 / NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT C


Mass: 11104.061 Da / Num. of mol.: 1 / Fragment: RESIDUES 27-120
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q13952
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.6 % / Description: NONE
Crystal growpH: 8.2
Details: 28% PEG 4K, 100 MM TRIS PH 8.2, 200 MM MG(OAC)2, 100 MM NA(OAC)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N1J

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.
RfactorNum. reflection% reflectionSelection details
Rfree0.18432 1594 5 %RANDOM
Rwork0.14462 ---
obs0.1466 30042 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.426 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2---0.5 Å20 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.5→33.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1381 0 18 191 1590
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191496
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1161.9832027
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6555193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.04624.36671
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.48515302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2671512
X-RAY DIFFRACTIONr_chiral_restr0.0820.2235
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211104
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5331.616704
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.0382.433883
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8182.11792
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.92131496
X-RAY DIFFRACTIONr_sphericity_free28.155551
X-RAY DIFFRACTIONr_sphericity_bonded12.80851613
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 110 -
Rwork0.209 2186 -
obs--100 %

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