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- PDB-6r0n: Histone fold domain of AtNF-YB2/NF-YC3 in I2 -

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Basic information

Entry
Database: PDB / ID: 6r0n
TitleHistone fold domain of AtNF-YB2/NF-YC3 in I2
Components
  • NF-YB2
  • NF-YC3
KeywordsTRANSCRIPTION / NF-Y / Transcription factor / arabidopsis
Function / homology
Function and homology information


positive regulation of photomorphogenesis / long-day photoperiodism, flowering / CCAAT-binding factor complex / gibberellic acid mediated signaling pathway / regulation of seed germination / response to water deprivation / abscisic acid-activated signaling pathway / plastid / transcription coregulator activity / DNA-binding transcription activator activity, RNA polymerase II-specific ...positive regulation of photomorphogenesis / long-day photoperiodism, flowering / CCAAT-binding factor complex / gibberellic acid mediated signaling pathway / regulation of seed germination / response to water deprivation / abscisic acid-activated signaling pathway / plastid / transcription coregulator activity / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity / protein heterodimerization activity / DNA binding / nucleus
Similarity search - Function
Transcription factor, NFYB/HAP3, conserved site / NF-YB/HAP3 subunit signature. / Transcription factor NFYB/HAP3 / : / 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
(thale cress) hypothetical protein / (thale cress) hypothetical protein / Nuclear transcription factor Y subunit B-2 / Nuclear transcription factor Y subunit C-3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsChaves-Sanjuan, A. / Gnesutta, N. / Bernardini, A. / Fornara, F. / Nardini, M. / Mantovani, R.
CitationJournal: Plant J. / Year: 2021
Title: Structural determinants for NF-Y subunit organization and NF-Y/DNA association in plants.
Authors: Chaves-Sanjuan, A. / Gnesutta, N. / Gobbini, A. / Martignago, D. / Bernardini, A. / Fornara, F. / Mantovani, R. / Nardini, M.
History
DepositionMar 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NF-YB2
B: NF-YC3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5645
Polymers22,2882
Non-polymers2763
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-47 kcal/mol
Surface area9050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.194, 57.416, 97.827
Angle α, β, γ (deg.)90.000, 99.364, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Components on special symmetry positions
IDModelComponents
11A-336-

HOH

21A-339-

HOH

31B-203-

HOH

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Components

#1: Protein NF-YB2


Mass: 11160.813 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AXX17_At5g46140 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A178UPH7, UniProt: Q9FGJ3*PLUS
#2: Protein NF-YC3


Mass: 11126.929 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AXX17_At1g49320 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A178WGU5, UniProt: Q9ZVL3*PLUS
#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.: 58 / Source method: isolated from a natural source / Formula: H2O
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: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 277 K / Method: microdialysis / pH: 8 / Details: 100 mM NaCl, 50 mM Tris-HCl pH 8.0 and 2 mM DTT

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.999996 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999996 Å / Relative weight: 1
ReflectionResolution: 2.1→49.4 Å / Num. obs: 11924 / % possible obs: 99.6 % / Observed criterion σ(I): 2.3 / Redundancy: 6.7 % / Biso Wilson estimate: 46.9 Å2 / CC1/2: 1 / Rpim(I) all: 0.018 / Net I/σ(I): 13.9
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 958 / CC1/2: 0.86 / Rpim(I) all: 0.351 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5G49

5g49


Resolution: 2.1→49.35 Å / SU ML: 0.2136 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 30.1963
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2073 577 4.85 %
Rwork0.1928 11321 -
obs0.1935 11898 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.11 Å2
Refinement stepCycle: LAST / Resolution: 2.1→49.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1389 0 18 58 1465
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01421441
X-RAY DIFFRACTIONf_angle_d1.34511934
X-RAY DIFFRACTIONf_chiral_restr0.0703217
X-RAY DIFFRACTIONf_plane_restr0.0078247
X-RAY DIFFRACTIONf_dihedral_angle_d28.2565568
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.310.32771440.31772796X-RAY DIFFRACTION98.43
2.31-2.650.25291300.24212813X-RAY DIFFRACTION99.12
2.65-3.330.26161430.23752836X-RAY DIFFRACTION99.67
3.33-49.350.17321600.15872876X-RAY DIFFRACTION99.77
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.221664547026-0.309788475076-0.175484886420.6653555475860.3536286669210.185922046614-0.09212846394351.209581701760.46120691563-0.6605937948320.03845422161172.08672061527-1.10483271496-1.3102614103-0.003679625485571.11099701792-0.107772908950.01419180904571.037931778520.2610691208971.16233006003-0.596988197379-22.290746060515.3619852595
20.4612673565740.04751033772870.1780892642160.1188224904740.1621316486740.528010744289-0.05043702566110.382324755161-1.87633038919-0.3030431157160.569024432069-0.2014650880391.907178143770.3095240856870.01349020490440.718057290573-0.0763241773161-0.02280072839620.6210162296620.08308817852720.73379887391211.5737484368-27.908949261322.4150617515
32.56698491299-0.8533978933541.247942196542.312573118090.1804139590361.84079295503-0.222643872907-0.0548915471671-0.007380459228910.4332824434080.278205776344-0.138612396416-0.552062554123-0.4263247808051.54434170653E-70.4163887190790.036335345475-0.006358170676770.4631922056190.0537661682890.47670641641710.718228009-12.183651448315.8735166785
41.625429631950.6879043889470.2570536891591.06969002634-0.6780735261080.808234988717-0.408306016208-0.2648348985530.06228160585670.368532930316-0.179470435364-0.4739405299670.08794917170642.17506553137-0.01655081391540.5463055330720.0257063178068-0.06786800267750.7481582924580.117529760540.57990131389825.1186984949-15.109220104811.3344488624
52.276895182991.50581791632-0.1014469611681.777972433921.108910331082.150177819250.3047301781960.579450348585-0.229261397501-0.198952448866-0.4318510621850.278766416550.123976900077-0.405643022756-2.70759913418E-60.488160032637-0.0279515464887-0.0008667450215710.5420221669470.005377369213820.5753407595016.94108631145-16.13929938766.36862938148
62.338672490810.6135441265991.701550916872.58914361608-0.7512174124781.677010635740.0868042937494-0.721591344342-0.1780581498120.7942342109450.01032404600320.173939484697-0.342467932542-0.0170901936974-7.81273775727E-70.6134411943310.08642114784070.01220306509720.5650249577790.07976850459160.49499525743412.7496620143-18.746407462628.1869185919
70.107738152545-0.107555440176-0.06478240706750.100999018360.02918106536820.191802586722-0.270966178067-2.272219748881.02626598861.278081054230.2839303221430.437103199107-0.987432322597-0.2165454118195.14427180731E-61.334168946170.2893651129040.05693258486311.07346047195-0.02269499433750.7983671065536.05958287468-8.9857539804328.0997241451
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 26 through 33 )
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 43 )
3X-RAY DIFFRACTION3chain 'A' and (resid 44 through 100 )
4X-RAY DIFFRACTION4chain 'A' and (resid 101 through 116 )
5X-RAY DIFFRACTION5chain 'B' and (resid 69 through 90 )
6X-RAY DIFFRACTION6chain 'B' and (resid 91 through 135 )
7X-RAY DIFFRACTION7chain 'B' and (resid 136 through 148 )

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