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- PDB-7ah8: NF-Y bound to suramin inhibitor -

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Basic information

Entry
Database: PDB / ID: 7ah8
TitleNF-Y bound to suramin inhibitor
Components
  • Isoform 6 of Nuclear transcription factor Y subunit gamma
  • Nuclear transcription factor Y subunit beta
KeywordsTRANSCRIPTION / Transcription factor / NF-Y / HFD / Inhibitor / Suramin
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 / 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 / DNA-binding transcription factor activity / protein heterodimerization 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
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 H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
CITRATE ANION / Chem-SVR / 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: 2.70001356517 Å
AuthorsNardone, V. / Chaves-Sanjuan, A. / Lapi, M. / Nardini, M.
Funding support Italy, 2items
OrganizationGrant numberCountry
Italian Association for Cancer ResearchIG-15267 Italy
Italian Ministry of Education2017SBFHLH Italy
CitationJournal: Cells / Year: 2020
Title: Structural Basis of Inhibition of the Pioneer Transcription Factor NF-Y by Suramin.
Authors: Nardone, V. / Chaves-Sanjuan, A. / Lapi, M. / Airoldi, C. / Saponaro, A. / Pasqualato, S. / Dolfini, D. / Camilloni, C. / Bernardini, A. / Gnesutta, N. / Mantovani, R. / Nardini, M.
History
DepositionSep 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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: Isoform 6 of Nuclear transcription factor Y subunit gamma
C: Nuclear transcription factor Y subunit beta
D: Isoform 6 of Nuclear transcription factor Y subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7207
Polymers39,1424
Non-polymers1,5783
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12240 Å2
ΔGint-133 kcal/mol
Surface area16920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.697, 61.213, 123.533
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLUGLUILEILE(chain 'B' and (resid 42 through 86 or resid 88 through 120))BB42 - 862 - 46
121THRTHRARGARG(chain 'B' and (resid 42 through 86 or resid 88 through 120))BB88 - 12048 - 80
231GLUGLUILEILE(chain 'D' and (resid 42 through 86 or resid 88 through 120))DD42 - 862 - 46
241THRTHRARGARG(chain 'D' and (resid 42 through 86 or resid 88 through 120))DD88 - 12048 - 80
152GLNGLNLYSLYS(chain 'A' and (resid 53 through 138 or resid 140))AA53 - 1382 - 87
162ARGARGARGARG(chain 'A' and (resid 53 through 138 or resid 140))AA14089
272GLNGLNLYSLYS(chain 'C' and (resid 53 through 138 or resid 140))CC53 - 1382 - 87
282ARGARGARGARG(chain 'C' and (resid 53 through 138 or resid 140))CC14089

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Nuclear transcription factor Y subunit beta / CAAT box DNA-binding protein subunit B / Nuclear transcription factor Y subunit B / NF-YB


Mass: 10201.729 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NFYB, HAP3 / Production host: Escherichia coli (E. coli) / References: UniProt: P25208
#2: Protein Isoform 6 of Nuclear transcription factor Y subunit gamma / CAAT box DNA-binding protein subunit C / Nuclear transcription factor Y subunit C / NF-YC / ...CAAT box DNA-binding protein subunit C / Nuclear transcription factor Y subunit C / NF-YC / Transactivator HSM-1/2


Mass: 9369.026 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NFYC / Production host: Escherichia coli (E. coli) / References: UniProt: Q13952

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Non-polymers , 4 types, 50 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#5: Chemical ChemComp-SVR / 8,8'-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFON IC ACID / SURAMIN / Suramin


Mass: 1297.280 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H40N6O23S6 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.21 Å3/Da / Density % sol: 44.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 200 mM Ammonium citrate pH 7.0, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.983998 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.983998 Å / Relative weight: 1
ReflectionResolution: 2.7→45.7 Å / Num. obs: 10061 / % possible obs: 100 % / Observed criterion σ(I): 3.5 / Redundancy: 12.1 % / Biso Wilson estimate: 52.115982668 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 16.2
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 12.8 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 1299 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDS0.68data reduction
Aimless1.12.2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N1J

1n1j


Resolution: 2.70001356517→43.4784980742 Å / SU ML: 0.362376274465 / Cross valid method: FREE R-VALUE / σ(F): 1.34531676701 / Phase error: 29.2425786086
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.274388484411 486 4.85078351133 %
Rwork0.222524196711 9533 -
obs0.225093115344 10019 99.9700658551 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.1247594228 Å2
Refinement stepCycle: LAST / Resolution: 2.70001356517→43.4784980742 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2724 0 105 47 2876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02596119249772902
X-RAY DIFFRACTIONf_angle_d1.324435037933924
X-RAY DIFFRACTIONf_chiral_restr0.0705678551305430
X-RAY DIFFRACTIONf_plane_restr0.0154024240879494
X-RAY DIFFRACTIONf_dihedral_angle_d24.32275557071101
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-3.09060.319896686691460.2613957486023105X-RAY DIFFRACTION99.9692496925
3.0906-3.89350.3161484562481500.2379274023913151X-RAY DIFFRACTION100
3.8935-43.470.2473589208091900.2029777136463277X-RAY DIFFRACTION99.9423464975

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