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- PDB-7c9p: Crystal structure of rice histone-fold dimer GHD8/OsNF-YC2 -

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Basic information

Entry
Database: PDB / ID: 7c9p
TitleCrystal structure of rice histone-fold dimer GHD8/OsNF-YC2
Components
  • Nuclear transcription factor Y subunit B-11
  • Nuclear transcription factor Y subunit C-2
KeywordsTRANSCRIPTION / photoperiodic flowering / CCT family / NF-CCT complex / specific DNA recognition
Function / homology
Function and homology information


positive regulation of unidimensional cell growth / negative regulation of long-day photoperiodism, flowering / CCAAT-binding factor complex / flower development / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / protein heterodimerization activity / regulation of transcription by RNA polymerase II / DNA binding ...positive regulation of unidimensional cell growth / negative regulation of long-day photoperiodism, flowering / CCAAT-binding factor complex / flower development / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / protein heterodimerization activity / regulation of transcription by RNA polymerase II / DNA binding / nucleus / cytoplasm
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 domain / Histone-fold
Similarity search - Domain/homology
Nuclear transcription factor Y subunit C-2 / Nuclear transcription factor Y subunit B-11
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsShen, C. / Liu, H. / Guan, Z. / Xing, Y. / Yin, P.
CitationJournal: Plant Cell / Year: 2020
Title: Structural Insight into DNA Recognition by CCT/NF-YB/YC Complexes in Plant Photoperiodic Flowering.
Authors: Shen, C. / Liu, H. / Guan, Z. / Yan, J. / Zheng, T. / Yan, W. / Wu, C. / Zhang, Q. / Yin, P. / Xing, Y.
History
DepositionJun 6, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Nov 29, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: Nuclear transcription factor Y subunit B-11
B: Nuclear transcription factor Y subunit C-2
C: Nuclear transcription factor Y subunit B-11
D: Nuclear transcription factor Y subunit C-2


Theoretical massNumber of molelcules
Total (without water)45,5144
Polymers45,5144
Non-polymers00
Water3,027168
1
A: Nuclear transcription factor Y subunit B-11
B: Nuclear transcription factor Y subunit C-2


Theoretical massNumber of molelcules
Total (without water)22,7572
Polymers22,7572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-44 kcal/mol
Surface area8480 Å2
MethodPISA
2
C: Nuclear transcription factor Y subunit B-11
D: Nuclear transcription factor Y subunit C-2


Theoretical massNumber of molelcules
Total (without water)22,7572
Polymers22,7572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-44 kcal/mol
Surface area9050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.267, 89.267, 81.341
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

#1: Protein Nuclear transcription factor Y subunit B-11 / OsNF-YB11 / Protein DAYS TO HEADING 8 / Protein HEADING DATE 5 / Transcriptional activator HAP3H / OsHAP3H


Mass: 10849.440 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: HD5, DTH8, GHD8, HAP3H, NFYB11, Os08g0174500, LOC_Os08g07740
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q0J7P4
#2: Protein Nuclear transcription factor Y subunit C-2 / OsNF-YC2 / Transcriptional activator HAP5C / OsHAP5C


Mass: 11907.627 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: NFYC2, HAP5C, Os03g0251350, LOC_Os03g14669 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A6BLW4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.06 Å3/Da / Density % sol: 40.16 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: PEG 3350, sodium malonate, sodium citrate tribasic dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2→45 Å / Num. obs: 25020 / % possible obs: 99.7 % / Redundancy: 10.8 % / Biso Wilson estimate: 26.86 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.026 / Rrim(I) all: 0.086 / Net I/σ(I): 21.2
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 5.3 / Num. unique obs: 1825 / CC1/2: 0.918 / Rpim(I) all: 0.181 / Rrim(I) all: 0.608

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Processing

Software
NameClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7C9O

7c9o


Resolution: 2→38.65 Å / SU ML: 0.1933 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.4282 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2146 1302 5.21 %
Rwork0.1706 23677 -
obs0.173 24979 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.29 Å2
Refinement stepCycle: LAST / Resolution: 2→38.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2731 0 0 168 2899
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00722780
X-RAY DIFFRACTIONf_angle_d0.85323743
X-RAY DIFFRACTIONf_chiral_restr0.0475426
X-RAY DIFFRACTIONf_plane_restr0.0051480
X-RAY DIFFRACTIONf_dihedral_angle_d26.77151072
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.080.24631510.20812589X-RAY DIFFRACTION98.63
2.08-2.170.24641600.19052597X-RAY DIFFRACTION100
2.17-2.290.23741170.19732660X-RAY DIFFRACTION100
2.29-2.430.25721170.18622657X-RAY DIFFRACTION100
2.43-2.620.25281750.18422617X-RAY DIFFRACTION100
2.62-2.880.22371360.17892646X-RAY DIFFRACTION100
2.88-3.30.21361240.17792653X-RAY DIFFRACTION99.96
3.3-4.150.18941660.15482626X-RAY DIFFRACTION99.93
4.15-38.650.19561560.15032632X-RAY DIFFRACTION98.13
Refinement TLS params.Method: refined / Origin x: -34.7707096507 Å / Origin y: 8.44159610158 Å / Origin z: 1.11804289245 Å
111213212223313233
T0.190454596081 Å2-0.0198314139621 Å20.00368850578249 Å2-0.155612750023 Å20.0242466932544 Å2--0.143383156795 Å2
L2.16925115546 °2-0.29874008259 °20.355149207407 °2-1.29306702512 °2-0.107788762023 °2--0.941761418974 °2
S0.0165919448917 Å °-0.0306361548828 Å °-0.254567722928 Å °-0.120216993423 Å °-0.00961421662924 Å °0.0102657853048 Å °0.0549414265558 Å °-0.0643634210345 Å °-0.000919132099689 Å °
Refinement TLS groupSelection details: all

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