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- PDB-4awl: The NF-Y transcription factor is structurally and functionally a ... -

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Basic information

Entry
Database: PDB / ID: 4awl
TitleThe NF-Y transcription factor is structurally and functionally a sequence specific histone
Components
  • (HSP70 PROMOTER ...) x 2
  • (NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT ...) x 3
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION-DNA COMPLEX / NF-Y / DNA-BINDING
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 / protein-DNA complex / PPARA activates gene expression / 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 / protein-DNA complex / PPARA activates gene expression / 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 / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2430 / 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. ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2430 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / 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: 3.08 Å
AuthorsNardini, M. / Gnesutta, N. / Donati, G. / Gatta, R. / Forni, C. / Fossati, A. / Vonrhein, C. / Moras, D. / Romier, C. / Mantovani, R. / Bolognesi, M.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2013
Title: Sequence-Specific Transcription Factor NF-Y Displays Histone-Like DNA Binding and H2B-Like Ubiquitination.
Authors: Nardini, M. / Gnesutta, N. / Donati, G. / Gatta, R. / Forni, C. / Fossati, A. / Vonrhein, C. / Moras, D. / Romier, C. / Bolognesi, M. / Mantovani, R.
History
DepositionJun 4, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval ..._exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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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
I: HSP70 PROMOTER FRAGMENT
J: HSP70 PROMOTER FRAGMENT


Theoretical massNumber of molelcules
Total (without water)46,6455
Polymers46,6455
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13030 Å2
ΔGint-94 kcal/mol
Surface area19380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.700, 62.560, 139.680
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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NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT ... , 3 types, 3 molecules ABC

#1: Protein NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT ALPHA / CCAAT BOX DNA-BINDING PROTEIN SUBUNIT A / CAAT BOX DNA-BINDING PROTEIN SUBUNIT A / NUCLEAR ...CCAAT BOX DNA-BINDING PROTEIN SUBUNIT A / CAAT BOX DNA-BINDING PROTEIN SUBUNIT A / NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT A / NF-YA


Mass: 9329.813 Da / Num. of mol.: 1 / Fragment: RESIDUES 233-303
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P23511
#2: Protein NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT BETA / CCAAT BOX DNA-BINDING PROTEIN SUBUNIT B / CAAT BOX DNA-BINDING PROTEIN SUBUNIT B / NUCLEAR ...CCAAT BOX DNA-BINDING PROTEIN SUBUNIT B / CAAT BOX DNA-BINDING PROTEIN SUBUNIT B / NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT B / NF-YB


Mass: 10853.485 Da / Num. of mol.: 1 / Fragment: RESIDUES 51-143
Source method: isolated from a genetically manipulated source
Details: FRAGMENT NUMBERING 49-141 IS THE NUMBERING DEFINED IN THE LITERATURE
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P25208
#3: Protein NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT GAMMA / CAAT BOX DNA-BINDING PROTEIN SUBUNIT C / CAAT BOX DNA-BINDING PROTEIN SUBUNIT C / NUCLEAR ...CAAT BOX DNA-BINDING PROTEIN SUBUNIT C / CAAT BOX DNA-BINDING PROTEIN SUBUNIT C / NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT C / NF-YC / TRANSACTIVATOR HSM-1/2


Mass: 11104.061 Da / Num. of mol.: 1 / Fragment: RESIDUES 27-120
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q13952

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HSP70 PROMOTER ... , 2 types, 2 molecules IJ

#4: DNA chain HSP70 PROMOTER FRAGMENT


Mass: 7618.924 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)
#5: DNA chain HSP70 PROMOTER FRAGMENT


Mass: 7738.997 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)

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Non-polymers , 1 types, 2 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsFOREIGN SEQUENCE PRESENT IN THE NF-YA RECOMBINANT PROTEIN THAT WERE ADDED FOR EXPRESSION- ...FOREIGN SEQUENCE PRESENT IN THE NF-YA RECOMBINANT PROTEIN THAT WERE ADDED FOR EXPRESSION-PURIFICATION PURPOSES N- TERMINAL MET C-TERMINAL GLY-SER-LEU-VAL-PRO-ARG FOREIGN SEQUENCE PRESENT IN THE NF-YB RECOMBINANT PROTEIN THAT WERE ADDED FOR EXPRESSION-PURIFICATION PURPOSES N- TERMINAL MET

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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: 2.56 Å3/Da / Density % sol: 51.99 %
Description: A 25 BP OLIGONUCLEOTIDE CUT FROM THE XENOPUS LAEVIS NUCLEOSOME, PDB ENTRY 1AOI, WAS USED AS THE SEARCH MODEL FOR THE DNA PART OF THE COMPLEX
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: VAPOUR DIFFUSION METHOD , HANGING DROP, 20-24% PEG3350, 100 MM MES OR CACODYLATE BUFFER, PH 6.5, 50 MM NAF. T ROOM.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9,1.0
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
211
ReflectionResolution: 3.08→62.56 Å / Num. obs: 8907 / % possible obs: 94.9 % / Observed criterion σ(I): 3 / Redundancy: 5.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.4
Reflection shellResolution: 3.08→3.25 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 4.4 / % possible all: 76.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N1J

1n1j


Resolution: 3.08→35.46 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.915 / SU B: 43.765 / SU ML: 0.413 / Cross valid method: THROUGHOUT / ESU R Free: 0.462 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE NF-YA MODEL COMPRISES RESIDUES 232-293. POOR DENSITY IS PRESENT FOR THE 232-235 SEGMENT, WHILE NO INTERPRETABLE ELECTRON DENSITY WAS ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE NF-YA MODEL COMPRISES RESIDUES 232-293. POOR DENSITY IS PRESENT FOR THE 232-235 SEGMENT, WHILE NO INTERPRETABLE ELECTRON DENSITY WAS PRESENT FOR THE 294-307 SEGMENT. NF-YB AND NF-YC COMPRISE RESIDUES 50-141 AND 40-119, RESPECTIVELY. FOR THE FIRST TWO NF-YB N-TERMINAL RESIDUES, THE FIRST THIRTEEN NF-YC N-TERMINAL RESIDUES AND THE LAST NF-YC C- TERMINAL RESIDUES NO ELECTRON DENSITY WAS AVAILABLE. FINAL STRUCTURE HAS NO RESIDUES IN THE DISALLOWED REGION OF THE RAMACHANDRAN PLOT AS DEFINED IN THE CCP4 PROCHECK PROGRAM.
RfactorNum. reflection% reflectionSelection details
Rfree0.24971 418 4.7 %RANDOM
Rwork0.19133 ---
obs0.19418 8448 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 79.475 Å2
Baniso -1Baniso -2Baniso -3
1-8.15 Å20 Å20 Å2
2---0.55 Å20 Å2
3----7.6 Å2
Refinement stepCycle: LAST / Resolution: 3.08→35.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1928 1019 0 2 2949
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223099
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7512.3824379
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8315231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.56822.9997
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.75615389
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4781521
X-RAY DIFFRACTIONr_chiral_restr0.0940.2482
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211979
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.421.51170
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.85321887
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.18331929
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9694.52492
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.081→3.161 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 29 -
Rwork0.241 454 -
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)
12.4211-0.6110.499410.1407-1.39384.7595-0.00330.0272-0.03090.18820.10260.8673-0.3645-0.6517-0.09930.0578-0.01780.06470.3199-0.02440.20374.7418-4.5547-11.0834
23.6264-1.18132.14376.8842-3.089211.102-0.1970.6290.5963-0.4932-0.2198-0.4506-1.19060.36930.41680.1914-0.05660.00480.12980.0820.328914.69845.4631-18.0178
33.0816-1.36054.45516.714-3.274921.2583-0.20230.14410.43270.3520.0613-0.212-1.2927-0.18260.1410.0391-0.1322-0.06540.05650.06920.271414.0244.3378-10.7036
42.1146-0.71631.46093.2313-1.32954.13450.07460.3310.0951-0.7381-0.1236-0.1930.89980.33270.0490.2283-0.07270.02540.2451-0.02550.234213.2061-12.3674-18.4462
51.4718-0.02972.71896.65981.21449.8097-0.0288-0.515-0.32391.0735-0.31960.18361.0613-0.47860.34840.2481-0.02940.07150.12160.08310.132314.1637-17.25824.8075
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A232 - 293
2X-RAY DIFFRACTION2B50 - 141
3X-RAY DIFFRACTION3C40 - 119
4X-RAY DIFFRACTION4I1 - 25
5X-RAY DIFFRACTION5J-10 - -1

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