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- PDB-8qu4: NF-YB/C Heterodimer in Complex with a 13-mer NF-YA-derived Peptid... -

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Basic information

Entry
Database: PDB / ID: 8qu4
TitleNF-YB/C Heterodimer in Complex with a 13-mer NF-YA-derived Peptide Stabilized with C8-Hydrocarbon Linker in an alternative binding pose
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 / 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 / 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 / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / 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. / Transcription factor CBF/NF-Y/archaeal histone domain ...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 / Histone-fold
Similarity search - Domain/homology
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: 1.38 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

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


Theoretical massNumber of molelcules
Total (without water)24,0675
Polymers23,8833
Non-polymers1842
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: FP assay
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6460 Å2
ΔGint-43 kcal/mol
Surface area9610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.450, 51.400, 71.910
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 / 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
Details: GP is a carryover. / Source: (gene. exp.) Homo sapiens (human) / Gene: NFYB, HAP3 / 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
Details: GP is a carryover from the Precission cleavage site
Source: (gene. exp.) Homo sapiens (human) / Gene: NFYC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13952

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Non-polymers , 3 types, 92 molecules

#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 1.64 Å3/Da / Density % sol: 25.3 % / Description: 100x50 micron rod-like crystal.
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 100 mM Morpheus buffer system 3 pH 9, 30% Morpheus precipitant 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 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.38→41.82 Å / Num. obs: 32648 / % possible obs: 94.69 % / Redundancy: 24.5 % / Biso Wilson estimate: 20.29 Å2 / CC1/2: 1 / CC star: 1 / Rpim(I) all: 0.01089 / Net I/σ(I): 28.52
Reflection shellResolution: 1.38→1.43 Å / Redundancy: 20.6 % / Mean I/σ(I) obs: 1.76 / Num. unique obs: 3329 / CC1/2: 0.784 / CC star: 0.937 / Rpim(I) all: 0.3004 / % possible all: 98.14

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.38→41.82 Å / SU ML: 0.1376 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.3902
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1936 1596 4.9 %
Rwork0.1699 30991 -
obs0.1711 32587 94.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.65 Å2
Refinement stepCycle: LAST / Resolution: 1.38→41.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1462 0 16 90 1568
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00461587
X-RAY DIFFRACTIONf_angle_d0.7542149
X-RAY DIFFRACTIONf_chiral_restr0.0698241
X-RAY DIFFRACTIONf_plane_restr0.007280
X-RAY DIFFRACTIONf_dihedral_angle_d5.3656232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.430.26431460.21452868X-RAY DIFFRACTION97.95
1.43-1.480.23971110.19812486X-RAY DIFFRACTION84.13
1.48-1.540.25031370.1822710X-RAY DIFFRACTION92.65
1.54-1.610.22461490.16512942X-RAY DIFFRACTION100
1.61-1.690.20671480.14982934X-RAY DIFFRACTION99.97
1.69-1.80.2021570.1552802X-RAY DIFFRACTION94.81
1.8-1.940.18311450.15582662X-RAY DIFFRACTION90.4
1.94-2.130.19321490.15272724X-RAY DIFFRACTION91.94
2.13-2.440.1761470.15992887X-RAY DIFFRACTION96.65
2.44-3.070.171550.17782946X-RAY DIFFRACTION97.39
3.07-41.820.20261520.17573030X-RAY DIFFRACTION95.56

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