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- PDB-5g49: Crystal structure of the Arabodopsis thaliana histone-fold dimer ... -

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Basic information

Entry
Database: PDB / ID: 5g49
TitleCrystal structure of the Arabodopsis thaliana histone-fold dimer L1L NF-YC3
Components
  • NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT B-6
  • NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT C-3
KeywordsTRANSCRIPTION / HISTONE-FOLD DOMAIN / NF-Y / TRANSCRIPTION FACTOR / CCAAT BOX- BINDING TRANSCRIPTION FACTOR
Function / homology
Function and homology information


positive regulation of photomorphogenesis / long-day photoperiodism, flowering / DNA-binding transcription factor binding => GO:0140297 / CCAAT-binding factor complex / gibberellic acid mediated signaling pathway / regulation of seed germination / abscisic acid-activated signaling pathway / transcription coregulator activity / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding ...positive regulation of photomorphogenesis / long-day photoperiodism, flowering / DNA-binding transcription factor binding => GO:0140297 / CCAAT-binding factor complex / gibberellic acid mediated signaling pathway / regulation of seed germination / abscisic acid-activated signaling pathway / 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, RNA polymerase II-specific / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / 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, subunit A / Histone, subunit A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold ...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, subunit A / Histone, subunit A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Nuclear transcription factor Y subunit B-6 / 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
AuthorsGnesutta, N. / Saad, D. / Chaves-Sanjuan, A. / Mantovani, R. / Nardini, M.
CitationJournal: Mol Plant / Year: 2017
Title: Crystal Structure of the Arabidopsis thaliana L1L/NF-YC3 Histone-fold Dimer Reveals Specificities of the LEC1 Family of NF-Y Subunits in Plants.
Authors: Gnesutta, N. / Saad, D. / Chaves-Sanjuan, A. / Mantovani, R. / Nardini, M.
History
DepositionMay 6, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Database references
Revision 1.2Apr 12, 2017Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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 B-6
B: NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT C-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8246
Polymers22,6072
Non-polymers2174
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-51.6 kcal/mol
Surface area10840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.344, 81.691, 95.998
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2023-

HOH

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Components

#1: Protein NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT B-6 / AT-L1L / ATNF-YB-6 / PROTEIN LEAFY COTYLEDON 1-LIKE


Mass: 11480.097 Da / Num. of mol.: 1 / Fragment: HISTONE-FOLD DOMAIN, RESIDUES 55-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q84W66
#2: Protein NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT C-3 / ATNF-YC-3 / AT-NF-YC3


Mass: 11126.929 Da / Num. of mol.: 1 / Fragment: HISTONE-FOLD DOMAIN, RESIDUES 55-148
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9ZVL3
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 3.57 Å3/Da / Density % sol: 65.5 % / Description: NONE
Crystal growDetails: 10% W/V PEG 8,000, 100 MM HEPES-NAOH PH 7.5, 200 MM CALCIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→52.42 Å / Num. obs: 12288 / % possible obs: 100 % / Observed criterion σ(I): 5.1 / Redundancy: 8.7 % / Biso Wilson estimate: 38.07 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 20.9
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 5.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CSR

4csr


Resolution: 2.3→40.845 Å / SU ML: 0.24 / σ(F): 1.19 / Phase error: 24.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2 1110 4.8 %
Rwork0.1617 --
obs0.1637 12245 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.46 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40.845 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1573 0 13 109 1695
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081629
X-RAY DIFFRACTIONf_angle_d0.9392192
X-RAY DIFFRACTIONf_dihedral_angle_d18.9071013
X-RAY DIFFRACTIONf_chiral_restr0.054245
X-RAY DIFFRACTIONf_plane_restr0.005285
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.40470.27451320.21652707X-RAY DIFFRACTION98
2.4047-2.53140.23931460.20662735X-RAY DIFFRACTION99
2.5314-2.690.21731100.19222760X-RAY DIFFRACTION100
2.69-2.89770.22871280.18552730X-RAY DIFFRACTION100
2.8977-3.18920.23251330.18462753X-RAY DIFFRACTION100
3.1892-3.65040.18621760.15412719X-RAY DIFFRACTION100
3.6504-4.59810.15831440.12872726X-RAY DIFFRACTION100
4.5981-40.85190.2031410.15292749X-RAY DIFFRACTION100
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)
11.1650.15050.35530.7317-0.35610.33660.47820.42290.2597-0.0593-0.3694-0.0057-0.3956-0.4460.00650.5166-0.13880.02810.49220.05650.4574-15.4499-20.7855-0.0118
21.37830.31210.91190.5115-0.1711.1581-00.2507-1.1375-0.1330.3237-0.21380.93450.36370.09330.56650.0184-0.07450.340.04510.52394.7997-28.50092.6701
32.12390.26121.04891.26971.27971.7991-0.1241-0.0999-0.10920.24810.16540.3449-0.2482-0.51890.00480.25220.01130.02190.37350.00670.3626-5.2806-11.7541-4.0053
40.897-0.14160.84523.65151.6312.71320.11340.20330.0498-0.2206-0.0391-0.1683-0.14930.32490.00110.2796-0.01020.00620.39670.05070.2724.6876-8.2569-14.762
51.0283-0.4196-0.41160.9061-0.59760.9565-0.00470.2688-0.7864-0.17090.2065-0.18561.0050.3907-0.00380.66910.0995-0.10990.6029-0.04730.638710.4051-24.5809-10.6269
60.76610.1486-0.19620.43180.0911.22420.19730.01560.345-0.185-0.10070.4712-0.0469-0.58170.00030.4053-0.0409-0.04480.4640.02650.4757-10.3763-13.5509-14.1187
71.3715-0.2409-0.30262.4196-0.75890.2880.0275-0.2386-0.24680.3646-0.0191-0.09040.0730.62430.00060.32660.004-0.02890.35650.05980.36675.6636-19.10413.051
80.0618-0.1194-0.02541.10070.65990.46310.5066-0.67850.16391.143-0.71630.5325-0.646-0.1067-0.01640.509-0.0471-0.0120.6420.07320.31871.5538-14.327311.9065
90.2168-0.11060.12480.52010.25680.3559-0.09-1.0035-0.08890.73960.1010.35350.1498-0.3113-0.00430.4144-0.03010.06360.42730.06810.4129-1.6007-8.95315.776
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 45 THROUGH 58 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 59 THROUGH 77 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 78 THROUGH 105 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 106 THROUGH 141 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 27 THROUGH 44 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 45 THROUGH 62 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 63 THROUGH 97 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 98 THROUGH 107 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 108 THROUGH 119 )

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