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- PDB-7aw7: CCAAT-binding complex and HapX bound to Aspergillus nidulans cccA DNA -

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Basic information

Entry
Database: PDB / ID: 7aw7
TitleCCAAT-binding complex and HapX bound to Aspergillus nidulans cccA DNA
Components
  • (DNA) x 2
  • BZIP domain-containing protein
  • CBFD_NFYB_HMF domain-containing protein
  • HapB
  • Transcription factor HapC (Eurofung)
KeywordsTRANSCRIPTION / transcription factor / histone fold / basic leucine zipper / heteropentamer / protein-DNA complex
Function / homology
Function and homology information


negative regulation of iron ion transport / : / CCAAT-binding factor complex / regulation of carbohydrate metabolic process / RNA polymerase II transcription regulator complex / nucleosome / DNA-binding transcription activator activity, RNA polymerase II-specific / intracellular iron ion homeostasis / sequence-specific DNA binding / transcription cis-regulatory region binding ...negative regulation of iron ion transport / : / CCAAT-binding factor complex / regulation of carbohydrate metabolic process / RNA polymerase II transcription regulator complex / nucleosome / DNA-binding transcription activator activity, RNA polymerase II-specific / intracellular iron ion homeostasis / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / protein heterodimerization activity / negative regulation of DNA-templated transcription / DNA-templated transcription / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / DNA binding / nucleus
Similarity search - Function
Hap4 transcription factor, heteromerisation domain / Minimal binding motif of Hap4 for binding to Hap2/3/5 / 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 ...Hap4 transcription factor, heteromerisation domain / Minimal binding motif of Hap4 for binding to Hap2/3/5 / 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 / Basic-leucine zipper (bZIP) domain signature. / basic region leucin zipper / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
DNA / DNA (> 10) / BZIP domain-containing protein / Transcriptional activator HAP2 / Histone H2A/H2B/H3 domain-containing protein / Transcription factor HapC (Eurofung)
Similarity search - Component
Biological speciesAspergillus nidulans FGSC A4 (mold)
Emericella nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsHuber, E.M. / Groll, M.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)GR 1861/8-1 Germany
German Research Foundation (DFG)SFB1309-325871075 Germany
CitationJournal: Structure / Year: 2022
Title: Structural insights into cooperative DNA recognition by the CCAAT-binding complex and its bZIP transcription factor HapX.
Authors: Huber, E.M. / Hortschansky, P. / Scheven, M.T. / Misslinger, M. / Haas, H. / Brakhage, A.A. / Groll, M.
History
DepositionNov 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: Database references / Category: citation
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 1.2Jul 20, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HapB
B: Transcription factor HapC (Eurofung)
C: CBFD_NFYB_HMF domain-containing protein
D: BZIP domain-containing protein
E: BZIP domain-containing protein
F: DNA
G: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,79310
Polymers77,7127
Non-polymers813
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23260 Å2
ΔGint-184 kcal/mol
Surface area35220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.150, 133.150, 199.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

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Protein , 4 types, 5 molecules ABCDE

#1: Protein HapB


Mass: 7669.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus nidulans FGSC A4 (mold) / Gene: ANIA_07545 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G5EAZ0
#2: Protein Transcription factor HapC (Eurofung)


Mass: 10641.299 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus nidulans FGSC A4 (mold) / Gene: ANIA_04034 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5B5Z6
#3: Protein CBFD_NFYB_HMF domain-containing protein / HapE


Mass: 13666.752 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus nidulans FGSC A4 (mold) / Gene: AN6492.2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5AYY8
#4: Protein BZIP domain-containing protein


Mass: 11479.957 Da / Num. of mol.: 2 / Mutation: C92K, C129S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (mold)
Strain: FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139 / Gene: ANIA_08251 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G5EAX9

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DNA chain , 2 types, 2 molecules FG

#5: DNA chain DNA /


Mass: 11426.298 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Aspergillus nidulans FGSC A4 (mold)
#6: DNA chain DNA /


Mass: 11347.332 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Aspergillus nidulans FGSC A4 (mold)

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Non-polymers , 2 types, 3 molecules

#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl

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Details

Has ligand of interestN

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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: 3.26 Å3/Da / Density % sol: 62.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium fluoride, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→47 Å / Num. obs: 14326 / % possible obs: 99.6 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 14.7
Reflection shellResolution: 3.4→3.5 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1166 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Y37, 5VPE
Resolution: 3.4→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.93 / SU B: 86.495 / SU ML: 0.574 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.627 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2966 716 5 %RANDOM
Rwork0.2521 ---
obs0.2544 13590 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 240.58 Å2 / Biso mean: 136.643 Å2 / Biso min: 84.92 Å2
Baniso -1Baniso -2Baniso -3
1--2.44 Å20 Å2-0 Å2
2--8.72 Å20 Å2
3----6.27 Å2
Refinement stepCycle: final / Resolution: 3.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3533 1517 3 0 5053
Biso mean--118.17 --
Num. residues----502
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0125382
X-RAY DIFFRACTIONr_bond_other_d0.0020.0184267
X-RAY DIFFRACTIONr_angle_refined_deg1.0221.497450
X-RAY DIFFRACTIONr_angle_other_deg1.1341.879921
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4055.527785
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.82720.256234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.69615697
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.8471546
X-RAY DIFFRACTIONr_chiral_restr0.1730.226752
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024880
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021193
LS refinement shellResolution: 3.4→3.487 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 52 -
Rwork0.358 990 -
all-1042 -
obs--99.9 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.299-0.32080.29170.3527-0.47643.46140.03420.08470.0008-0.0383-0.1416-0.010.11211.16010.10740.05680.00540.12050.4989-0.02970.2722-6.0006-49.8819-36.3841
20.7205-0.21170.93920.97190.17052.81020.03260.063-0.08040.0082-0.1023-0.0847-0.29610.28030.06970.3932-0.00990.10060.38480.00310.2418-17.9053-41.0851-30.7132
30.79860.19830.14820.43480.73681.5787-0.03170.0203-0.0436-0.0452-0.06660.0006-0.28150.0730.09820.47390.0660.0810.40670.00860.2663-21.0276-40.3394-37.7459
40.0721-0.16350.15590.8056-0.42730.49880.0170.00950.07320.0142-0.3197-0.17470.00090.29510.30280.3444-0.10.10170.58050.17040.2891-20.7045-12.0849-14.0288
50.09490.3051-0.22692.2053-1.76861.7409-0.14260.0334-0.1030.056-0.0454-0.4961-0.07520.11380.1880.3721-0.1690.03320.56730.18550.3596-7.5748-8.0451-13.1419
60.30010.16650.37331.51812.20753.47290.0782-0.0476-0.08990.1306-0.1260.00560.24840.04370.04780.39380.04670.05740.33270.06430.1634-19.2881-46.1575-10.7907
70.5739-0.10090.18990.92620.93552.57220.1822-0.1321-0.12990.1684-0.0369-0.26240.35160.0484-0.14530.34320.06620.04060.34260.09250.2251-17.8548-48.217-15.9251
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A233 - 290
2X-RAY DIFFRACTION2B41 - 132
3X-RAY DIFFRACTION3C48 - 164
4X-RAY DIFFRACTION4D38 - 130
5X-RAY DIFFRACTION5E61 - 128
6X-RAY DIFFRACTION6F1 - 37
7X-RAY DIFFRACTION7G1 - 37

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