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- PDB-6qmq: NF-YB/C Heterodimer in Complex with NF-YA-derived Peptide Stabili... -

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Basic information

Entry
Database: PDB / ID: 6qmq
TitleNF-YB/C Heterodimer in Complex with NF-YA-derived Peptide Stabilized with C8-Hydrocarbon Linker
Components
  • Nuclear transcription factor Y subunit alpha
  • Nuclear transcription factor Y subunit beta
  • Nuclear transcription factor Y subunit gamma
KeywordsTRANSCRIPTION / stapled peptide histone fold transcription factor
Function / homology
Function and homology information


CCAAT-binding factor complex / ATF6 (ATF6-alpha) activates chaperone genes / ATF4 activates genes in response to endoplasmic reticulum stress / FOXO-mediated transcription of cell death genes / Activation of gene expression by SREBF (SREBP) / cellular response to leukemia inhibitory factor / PPARA activates gene expression / protein-DNA complex / RNA polymerase II transcription regulator complex / rhythmic process ...CCAAT-binding factor complex / ATF6 (ATF6-alpha) activates chaperone genes / ATF4 activates genes in response to endoplasmic reticulum stress / FOXO-mediated transcription of cell death genes / Activation of gene expression by SREBF (SREBP) / cellular response to leukemia inhibitory factor / PPARA activates gene expression / protein-DNA complex / RNA polymerase II transcription regulator complex / rhythmic process / protein folding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein heterodimerization activity / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / 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, subunit A / Histone, subunit A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Nuclear transcription factor Y subunit alpha / Nuclear transcription factor Y subunit beta / Nuclear transcription factor Y subunit gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKiehstaller, S. / Jeganathan, S. / Pearce, N.M. / Wendt, M. / Grossmann, T.N. / Hennig, S.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)678623European Union
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2019
Title: Constrained Peptides with Fine-Tuned Flexibility Inhibit NF-Y Transcription Factor Assembly.
Authors: Jeganathan, S. / Wendt, M. / Kiehstaller, S. / Brancaccio, D. / Kuepper, A. / Pospiech, N. / Carotenuto, A. / Novellino, E. / Hennig, S. / Grossmann, T.N.
History
DepositionFeb 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.2Nov 27, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0May 18, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_sites / audit_author / chem_comp / database_2 / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_audit_support / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_entity_src_syn / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_conf / struct_conn / struct_conn_type / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] ..._atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly.pdbx_strand_id / _entity_poly_seq.entity_id / _entity_poly_seq.mon_id / _entity_poly_seq.num / _entity_src_gen.entity_id / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _pdbx_audit_support.country / _pdbx_audit_support.funding_organization / _pdbx_contact_author.id / _pdbx_entity_src_syn.entity_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_poly_seq_scheme.asym_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.entity_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.ndb_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.seq_id / _pdbx_struct_assembly_prop.value / _pdbx_struct_sheet_hbond.range_1_label_asym_id / _pdbx_struct_sheet_hbond.range_2_label_asym_id / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_R_Free_selection_details / _refine.pdbx_diffrn_id / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_ion_probe_radii / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.cycle_id / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_hist.pdbx_number_residues_total / _struct_conn_type.id / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_db_isoform / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_asym_id / _struct_sheet_range.end_label_asym_id
Description: Ligand geometry
Details: Improved ligand description and more chemical meaningful positioning of crosslink
Provider: author / Type: Coordinate replacement
Revision 3.0Jul 13, 2022Group: Polymer sequence / Category: entity_poly / Item: _entity_poly.pdbx_seq_one_letter_code_can
Revision 3.1Jan 24, 2024Group: Data collection / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_conn
Item: _struct_conn.pdbx_leaving_atom_flag
Revision 3.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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 alpha
B: Nuclear transcription factor Y subunit beta
C: Nuclear transcription factor Y subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5284
Polymers24,5053
Non-polymers231
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, Fluorescence polarization assay
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6510 Å2
ΔGint-58 kcal/mol
Surface area9840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.010, 52.210, 72.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide Nuclear transcription factor Y subunit alpha / CAAT box DNA-binding protein subunit A / Nuclear transcription factor Y subunit A / NF-YA


Mass: 2369.926 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P23511, UniProt: P25208*PLUS
#2: Protein Nuclear transcription factor Y subunit beta / CAAT box DNA-binding protein subunit B / Nuclear transcription factor Y subunit B / NF-YB


Mass: 10876.456 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NFYB, HAP3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P25208, UniProt: Q13952*PLUS
#3: Protein Nuclear transcription factor Y subunit gamma / CAAT box DNA-binding protein subunit C / Nuclear transcription factor Y subunit C / NF-YC / ...CAAT box DNA-binding protein subunit C / Nuclear transcription factor Y subunit C / NF-YC / Transactivator HSM-1/2


Mass: 11258.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NFYC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13952, UniProt: P23511*PLUS
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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

Crystal growTemperature: 277.15 K / Method: vapor diffusion
Details: 0.1 M sodium cacodylate pH6.5 0.2 M calcium acetate 37% PEG600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97793 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97793 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 6325 / % possible obs: 99.6 % / Redundancy: 12.2 % / CC1/2: 0.997 / Net I/σ(I): 11.07
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 12.9 % / Mean I/σ(I) obs: 2.18 / Num. unique obs: 682 / CC1/2: 0.665 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
PDB-REDOrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CSR

4csr


Resolution: 2.5→19.89 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.936 / SU B: 27.001 / SU ML: 0.266 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.328 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2412 635 10.1 %RANDOM
Rwork0.1724 ---
obs0.1795 5661 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 140.62 Å2 / Biso mean: 66.721 Å2 / Biso min: 31.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å2-0 Å2
2--0.37 Å2-0 Å2
3---0.08 Å2
Refinement stepCycle: final / Resolution: 2.5→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1526 0 21 7 1554
Biso mean--40.35 49.78 -
Num. residues----187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0181573
X-RAY DIFFRACTIONr_bond_other_d0.0020.021591
X-RAY DIFFRACTIONr_angle_refined_deg1.6271.8892104
X-RAY DIFFRACTIONr_angle_other_deg1.1452.7173657
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6015182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.7921.30788
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.57215312
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1991514
X-RAY DIFFRACTIONr_chiral_restr0.0940.2238
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021724
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02364
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 42 -
Rwork0.248 402 -
all-444 -
obs--100 %
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)
13.87092.14540.54539.62640.6363.3727-0.0880.1232-0.2499-0.10580.15760.1350.2129-0.0199-0.06970.090.03830.01280.13670.00880.1206-11.8539.083-36.305
24.6974-0.4113-1.86683.62270.41775.9161-0.1379-0.0406-0.14480.18340.0984-0.16320.32140.27610.03950.0574-0.0079-0.01530.04860.03140.0727-0.9385.127-23.619
33.6273-3.3342-2.20076.64113.28046.8038-0.1341-0.1459-0.09290.40780.00620.11660.0768-0.11740.12790.0698-0.0625-0.010.12610.05680.0749-6.2826.923-20.09
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A301 - 319
2X-RAY DIFFRACTION2B57 - 143
3X-RAY DIFFRACTION3C36 - 119

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