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- PDB-6r0m: Histone fold domain of AtNF-YB2/NF-YC3 in P212121 -

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Basic information

Entry
Database: PDB / ID: 6r0m
TitleHistone fold domain of AtNF-YB2/NF-YC3 in P212121
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 / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / 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
(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: 2.3 Å
AuthorsChaves-Sanjuan, A. / Gnesutta, N. / Chiara, M. / Bernardini, A. / Fornara, F. / Horner, D. / 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 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id

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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
C: NF-YB2
D: NF-YC3


Theoretical massNumber of molelcules
Total (without water)44,5754
Polymers44,5754
Non-polymers00
Water2,126118
1
A: NF-YB2
B: NF-YC3


Theoretical massNumber of molelcules
Total (without water)22,2882
Polymers22,2882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-47 kcal/mol
Surface area9620 Å2
MethodPISA
2
C: NF-YB2
D: NF-YC3


Theoretical massNumber of molelcules
Total (without water)22,2882
Polymers22,2882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-46 kcal/mol
Surface area9780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.023, 74.980, 86.654
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 NF-YB2


Mass: 11160.813 Da / Num. of mol.: 2
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.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.55 Å3/Da / Density % sol: 51.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% PEG 3350, 0.1 M MES pH 6.5 and 0.3 M lithium citrate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1.010876 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.010876 Å / Relative weight: 1
ReflectionResolution: 2.3→44.07 Å / Num. obs: 20843 / % possible obs: 99.9 % / Redundancy: 12.7 % / Biso Wilson estimate: 47.1 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 13.5 % / Mean I/σ(I) obs: 3.6 / Num. unique obs: 2054 / CC1/2: 0.575 / Rpim(I) all: 0.215 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5G49

5g49


Resolution: 2.3→44.07 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.924 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.265 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.276 / SU Rfree Blow DPI: 0.21 / SU Rfree Cruickshank DPI: 0.209
RfactorNum. reflection% reflectionSelection details
Rfree0.241 967 4.64 %RANDOM
Rwork0.2 ---
obs0.202 20849 99.8 %-
Displacement parametersBiso mean: 63.91 Å2
Baniso -1Baniso -2Baniso -3
1--2.8816 Å20 Å20 Å2
2---1.4079 Å20 Å2
3---4.2895 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: 1 / Resolution: 2.3→44.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2848 0 0 118 2966
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0132906HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.963910HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1084SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes81HARMONIC2
X-RAY DIFFRACTIONt_gen_planes410HARMONIC5
X-RAY DIFFRACTIONt_it2906HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.07
X-RAY DIFFRACTIONt_other_torsion19.79
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion390SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3529SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.42 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.268 170 5.63 %
Rwork0.257 2848 -
all0.258 3018 -
obs--99.93 %
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)
12.69750.35960.85672.30880.46641.8987-0.26810.03870.21350.00730.1090.1145-0.2562-0.350.1592-0.00090.0316-0.0746-0.0481-0.0283-0.106514.630315.80079.7448
24.88750.75870.3322.23820.21683.6397-0.1066-0.11660.0360.0189-0.08970.2324-0.1817-0.54390.1963-0.00660.0807-0.0151-0.0151-0.0535-0.15567.842813.091811.4314
32.7692-0.98660.0772.8665-0.42673.47740.15620.09320.0563-0.0022-0.2861-0.2719-0.23290.12410.12990.0111-0.0204-0.0252-0.07790.0679-0.110133.39743.556232.0188
42.6713-0.6232-0.32874.0135-1.11653.15950.0258-0.10970.23730.1339-0.1065-0.0862-0.54420.04310.08070.0305-0.0273-0.0443-0.067-0.0158-0.140130.34489.908433.5496
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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