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- PDB-6r2v: Arabidopsis NF-Y/CCAAT-box complex -

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Basic information

Entry
Database: PDB / ID: 6r2v
TitleArabidopsis NF-Y/CCAAT-box complex
Components
  • (FT (-5kb) CCAAT-box ...) x 2
  • NF-YB2
  • NF-YC3
  • Nuclear transcription factor Y subunit A-6
KeywordsTRANSCRIPTION / NF-Y / Transcription factor / arabidopsis / DNA-binding / Protein-DNA complex
Function / homology
Function and homology information


somatic embryogenesis / positive regulation of photomorphogenesis / long-day photoperiodism, flowering / CCAAT-binding factor complex / seed development / gibberellic acid mediated signaling pathway / regulation of seed germination / embryo development ending in seed dormancy / response to water deprivation / abscisic acid-activated signaling pathway ...somatic embryogenesis / positive regulation of photomorphogenesis / long-day photoperiodism, flowering / CCAAT-binding factor complex / seed development / gibberellic acid mediated signaling pathway / regulation of seed germination / embryo development ending in seed dormancy / 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
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
DNA / DNA (> 10) / (thale cress) hypothetical protein / (thale cress) hypothetical protein / Nuclear transcription factor Y subunit B-2 / Nuclear transcription factor Y subunit A-6 / Nuclear transcription factor Y subunit C-3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.503 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 19, 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: Nuclear transcription factor Y subunit A-6
B: NF-YB2
C: NF-YC3
I: FT (-5kb) CCAAT-box 5'
J: FT (-5kb) CCAAT-box 3'


Theoretical massNumber of molelcules
Total (without water)46,5095
Polymers46,5095
Non-polymers00
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13790 Å2
ΔGint-89 kcal/mol
Surface area20780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.446, 85.525, 130.305
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein Nuclear transcription factor Y subunit A-6 / AtNF-YA-6


Mass: 8866.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: NFYA6, At3g14020, MDC16.15 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9LVJ7
#2: 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
#3: 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

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FT (-5kb) CCAAT-box ... , 2 types, 2 molecules IJ

#4: DNA chain FT (-5kb) CCAAT-box 5'


Mass: 7552.899 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)
#5: DNA chain FT (-5kb) CCAAT-box 3'


Mass: 7802.058 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)

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Non-polymers , 1 types, 140 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 3.2 Å3/Da / Density % sol: 61.59 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 10% PEG 8000, 5% ethylene glycol, 0.1M MES pH 6.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.999998 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999998 Å / Relative weight: 1
ReflectionResolution: 2.5→41.32 Å / Num. obs: 11940 / % possible obs: 56.1 % / Observed criterion σ(I): 1.2 / Redundancy: 7.7 % / CC1/2: 0.99 / Rpim(I) all: 0.079 / Net I/σ(I): 7.6
Reflection shellResolution: 2.5→2.9 Å / Redundancy: 8.2 % / Num. unique obs: 271 / CC1/2: 0.678 / Rpim(I) all: 0.484 / % possible all: 8.5

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Processing

Software
NameVersionClassification
PHENIX(dev_3304: ???)refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4awl

4awl


Resolution: 2.503→41.322 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2469 624 5.23 %
Rwork0.1999 --
obs0.2024 11940 56.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.503→41.322 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2057 1019 0 140 3216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073244
X-RAY DIFFRACTIONf_angle_d0.894575
X-RAY DIFFRACTIONf_dihedral_angle_d33.4371326
X-RAY DIFFRACTIONf_chiral_restr0.057508
X-RAY DIFFRACTIONf_plane_restr0.008412
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5025-2.75430.3271110.3534260X-RAY DIFFRACTION5
2.7543-3.15270.3108880.30671451X-RAY DIFFRACTION29
3.1527-3.97160.25532470.21794483X-RAY DIFFRACTION89
3.9716-41.32720.2332780.17515122X-RAY DIFFRACTION98
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)
11.5512-0.871-0.28724.52350.92330.20510.7645-1.03040.0660.7938-0.2993-0.84562.12310.0135-0.29131.49610.2761-0.24411.0044-0.29770.804921.5166-6.7863-5.3106
24.2603-0.48831.7773.78661.59661.30330.07440.0777-0.1888-0.0688-0.05190.3106-0.0605-0.48630.00560.315300.00520.29980.04120.310211.5767-17.7111-38.783
30.67560.430.82370.2520.51411.0045-0.18160.63560.0938-0.58210.0671-0.1942-0.40790.5110.0640.57010.06040.0690.66070.25111.238310.66220.0718-35.4913
40.42710.19980.25620.1060.10820.1816-0.3775-0.10241.1946-0.16550.09990.0804-0.257-0.194900.35490.0103-0.10380.2958-0.07210.512722.012115.0601-28.0006
50.38490.58320.57471.15440.81790.9906-0.620.2374-0.1857-0.56450.8187-0.8641-0.31110.64790.11790.4524-0.0603-0.01010.29090.04140.470626.7964-4.9247-31.8844
61.19120.94690.42221.4242-0.46442.8958-0.4599-0.6595-0.1639-1.0122-0.3063-0.53860.4585-0.729-0.43690.19490.0718-0.00970.0967-0.01190.41218.2249-25.9001-35.0374
70.03910.0007-0.0289-0.00070.00280.0078-0.0706-0.2905-0.4851-0.3371-0.13760.46991.3353-0.748300.8922-0.10830.11660.9381-0.00241.37937.3517-37.1049-31.7529
86.8358-4.1313-3.31839.7826-5.40249.1228-0.3023-0.69150.919-0.015-0.1731-2.4926-0.54171.5147-0.65860.48470.0411-0.09770.2665-0.12960.564422.2224-4.6725-26.5606
94.2145-1.218-0.68612.8768-1.9723.461-0.102-0.09920.19320.03890.0017-0.0941-0.30840.1139-0.01290.04420.05640.02870.22770.02180.286810.45731.1656-29.6227
105.48281.326-0.91241.3998-0.16520.4656-0.1462-1.94941.4140.8136-0.1458-0.13780.09810.66660.23810.470.3023-0.10250.3821-0.40330.53419.415612.9171-15.6192
110.13820.06060.49061.62090.99323.1095-1.0762-2.3141-0.41281.63020.24381.20090.6562-0.8673-0.39420.90230.14580.28021.26120.17940.962-0.89424.2503-15.3296
120.1028-0.0240.12340.0106-0.03190.1386-0.4047-1.9430.27010.47091.0244-0.2528-0.4899-1.84820.00760.8090.1280.10741.69770.32491.3417-19.6687-23.7807-26.2792
132.994-3.45175.10233.9952-5.88438.65050.45561.207-1.9699-0.55-0.27972.52550.6968-2.83540.44890.53780.29140.0121.517-0.58120.94452.4207-11.9526-23.2302
143.2434-0.9812-2.1483.76620.39752.44950.05-0.30780.72380.078-0.34930.05860.2684-0.1109-0.0370.29670.09620.04270.20680.01490.24579.82762.3565-25.2699
156.1152.51891.33576.42294.62413.70070.05730.64221.2906-1.4581-0.55980.4572-0.9745-0.5688-0.45780.4904-0.01760.02680.41310.11990.44918.42466.0309-41.4321
161.738-0.13661.42469.4691.93151.58860.61510.7519-0.2784-0.979-0.3694-0.9536-0.15770.5940.57410.33290.1421-0.02590.5530.10590.316512.1447-14.0348-48.8948
172.84830.7866-0.85162.23350.2182.62090.071-1.00150.06581.3919-0.24590.1534-0.0764-0.7110.01631.02180.0619-0.0250.36110.08130.276816.4046-16.4724-16.9402
181.2339-0.5513-0.34676.18360.62930.14330.5787-0.10050.16770.6827-0.3574-0.8962-0.32390.7796-0.08311.26580.18490.04430.9504-0.10230.550923.57747.96211.8399
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'J' and (resid -25 through -16 )
2X-RAY DIFFRACTION2chain 'J' and (resid -15 through -1 )
3X-RAY DIFFRACTION3chain 'A' and (resid 172 through 179 )
4X-RAY DIFFRACTION4chain 'A' and (resid 180 through 195 )
5X-RAY DIFFRACTION5chain 'A' and (resid 196 through 208 )
6X-RAY DIFFRACTION6chain 'A' and (resid 209 through 226 )
7X-RAY DIFFRACTION7chain 'A' and (resid 227 through 233 )
8X-RAY DIFFRACTION8chain 'B' and (resid 24 through 33 )
9X-RAY DIFFRACTION9chain 'B' and (resid 34 through 81 )
10X-RAY DIFFRACTION10chain 'B' and (resid 82 through 100 )
11X-RAY DIFFRACTION11chain 'B' and (resid 101 through 116 )
12X-RAY DIFFRACTION12chain 'C' and (resid 54 through 63 )
13X-RAY DIFFRACTION13chain 'C' and (resid 64 through 72 )
14X-RAY DIFFRACTION14chain 'C' and (resid 73 through 118 )
15X-RAY DIFFRACTION15chain 'C' and (resid 119 through 148 )
16X-RAY DIFFRACTION16chain 'I' and (resid 3 through 7 )
17X-RAY DIFFRACTION17chain 'I' and (resid 8 through 22 )
18X-RAY DIFFRACTION18chain 'I' and (resid 23 through 27 )

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