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- PDB-8qu3: NF-YB/C Heterodimer in Complex with a 13-mer NF-YA-derived Peptid... -

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Basic information

Entry
Database: PDB / ID: 8qu3
TitleNF-YB/C Heterodimer in Complex with a 13-mer NF-YA-derived Peptide Stabilized with C8-Hydrocarbon Linker
Components(Nuclear transcription factor Y subunit ...) x 3
KeywordsTRANSCRIPTION / Peptidometic inhibitor
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 / PPARA activates gene expression / protein-DNA complex / RNA polymerase II transcription regulator complex / rhythmic process ...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 / PPARA activates gene expression / protein-DNA complex / 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 / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus
Similarity search - Function
CCAAT-binding factor, conserved site / NF-YA/HAP2 subunit signature. / Nuclear transcription factor Y subunit A / CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B / NF-YA/HAP2 family profile. / CCAAT-Binding transcription Factor / Transcription factor, NFYB/HAP3, conserved site / Transcription factor NFYB/HAP3 / NF-YB/HAP3 subunit signature. / : ...CCAAT-binding factor, conserved site / NF-YA/HAP2 subunit signature. / Nuclear transcription factor Y subunit A / CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B / NF-YA/HAP2 family profile. / CCAAT-Binding transcription Factor / 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 domain / Histone-fold
Similarity search - Domain/homology
FORMIC ACID / Nuclear transcription factor Y subunit alpha / 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: 1.41 Å
AuthorsArbore, F. / Durukan, C. / Klintrot, C.I.R. / Grossmann, T.N. / Hennig, S.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
Citation
Journal: Chembiochem / Year: 2024
Title: Binding Dynamics of a Stapled Peptide Targeting the Transcription Factor NF-Y.
Authors: Durukan, C. / Arbore, F. / Klintrot, R. / Bigiotti, C. / Ilie, I.M. / Vreede, J. / Grossmann, T.N. / Hennig, S.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionOct 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclear transcription factor Y subunit alpha
B: Nuclear transcription factor Y subunit beta
C: Nuclear transcription factor Y subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0515
Polymers23,8833
Non-polymers1682
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Fluorescence Polarization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6680 Å2
ΔGint-47 kcal/mol
Surface area9260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.750, 51.390, 72.560
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

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Components

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Nuclear transcription factor Y subunit ... , 3 types, 3 molecules ABC

#1: Protein/peptide Nuclear transcription factor Y subunit alpha / CAAT box DNA-binding protein subunit A / Nuclear transcription factor Y subunit A / NF-YA


Mass: 1748.177 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Stapled peptide inhibitor / Source: (synth.) Homo sapiens (human) / References: UniProt: P23511
#2: Protein Nuclear transcription factor Y subunit beta / CAAT box DNA-binding protein subunit B / Nuclear transcription factor Y subunit B / NF-YB


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 / Plasmid: pACYCDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P25208
#3: Protein 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: 11258.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NFYC / Plasmid: pACYCDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13952

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Non-polymers , 3 types, 130 molecules

#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 1.94 Å3/Da / Density % sol: 36.7 % / Description: Orthorombical 100x50 micron
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 100 mM Morpheus Buffer system 3 pH 9.0, 30% (v/v) Morpheus percipitant mix 1, 100 mM Morpheus carboxylic acids.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.41→41.94 Å / Num. obs: 31035 / % possible obs: 93.44 % / Redundancy: 24.8 % / Biso Wilson estimate: 20.75 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.06139 / Rpim(I) all: 0.01236 / Net I/σ(I): 26.1
Reflection shellResolution: 1.41→1.46 Å / Redundancy: 20.3 % / Rmerge(I) obs: 1.789 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2923 / CC1/2: 0.747 / CC star: 0.925 / Rpim(I) all: 0.4022 / % possible all: 89.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Cootmodel building
PHASERphasing
XSCALEdata scaling
XDSdata reduction
GDAdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.41→41.94 Å / SU ML: 0.1671 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.7465
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1991 1528 4.92 %
Rwork0.1655 29507 -
obs0.1672 31035 93.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.89 Å2
Refinement stepCycle: LAST / Resolution: 1.41→41.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1468 0 11 128 1607
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01351620
X-RAY DIFFRACTIONf_angle_d1.31952200
X-RAY DIFFRACTIONf_chiral_restr0.1168246
X-RAY DIFFRACTIONf_plane_restr0.0134290
X-RAY DIFFRACTIONf_dihedral_angle_d5.7516237
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.450.31531240.25442526X-RAY DIFFRACTION88.93
1.45-1.50.3181320.20862553X-RAY DIFFRACTION90.83
1.5-1.560.24071240.18942590X-RAY DIFFRACTION91.23
1.56-1.640.2311390.16432833X-RAY DIFFRACTION99.97
1.64-1.720.22711510.16592644X-RAY DIFFRACTION93.14
1.72-1.830.22921520.1642829X-RAY DIFFRACTION100
1.83-1.970.23431220.1732341X-RAY DIFFRACTION81.99
1.97-2.170.17361380.15482736X-RAY DIFFRACTION95.01
2.17-2.480.21141430.15872757X-RAY DIFFRACTION95.68
2.48-3.130.19851600.16432788X-RAY DIFFRACTION96.43
3.13-41.940.17411430.16292910X-RAY DIFFRACTION94.87

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