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- PDB-7aw9: CCAAT-binding complex and HapX bound to Aspergillus fumigatus cccA DNA -

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Basic information

Entry
Database: PDB / ID: 7aw9
TitleCCAAT-binding complex and HapX bound to Aspergillus fumigatus 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 / sequence-specific DNA binding / intracellular iron ion homeostasis / DNA-binding transcription factor activity, RNA polymerase II-specific / 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 / sequence-specific DNA binding / intracellular iron ion homeostasis / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / 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. ...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 / Basic-leucine zipper domain superfamily / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / 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)
Aspergillus fumigatus A1163 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 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)77,7448
Polymers77,7097
Non-polymers351
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22540 Å2
ΔGint-170 kcal/mol
Surface area34680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.840, 127.660, 198.980
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: 11507.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Aspergillus fumigatus A1163 (mold)
#6: DNA chain DNA


Mass: 11263.276 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Aspergillus fumigatus A1163 (mold)

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Non-polymers , 1 types, 1 molecules

#7: Chemical ChemComp-CL / CHLORIDE ION


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: 3.14 Å3/Da / Density % sol: 60.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Tris-HCl pH 8.5, 25 % PEG4000

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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: Mar 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→47 Å / Num. obs: 12478 / % possible obs: 97.9 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 18.5
Reflection shellResolution: 3.5→3.6 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.664 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 988 / % possible all: 99.1

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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: 7AW7

7aw7


Resolution: 3.5→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 101.093 / SU ML: 0.645 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.68 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2907 623 5 %RANDOM
Rwork0.2453 ---
obs0.2475 11837 97.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 316.22 Å2 / Biso mean: 172.965 Å2 / Biso min: 106.46 Å2
Baniso -1Baniso -2Baniso -3
1-1.72 Å20 Å2-0 Å2
2--4.97 Å20 Å2
3----6.69 Å2
Refinement stepCycle: final / Resolution: 3.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3495 1517 1 0 5013
Biso mean--169.57 --
Num. residues----498
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0125362
X-RAY DIFFRACTIONr_bond_other_d0.0010.0184249
X-RAY DIFFRACTIONr_angle_refined_deg1.0531.4897422
X-RAY DIFFRACTIONr_angle_other_deg1.1511.8739882
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.835.54785
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.07120.345232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.26515694
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.8021545
X-RAY DIFFRACTIONr_chiral_restr0.2220.226752
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024845
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021175
LS refinement shellResolution: 3.5→3.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 45 -
Rwork0.38 858 -
all-903 -
obs--99.01 %
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)
12.13961.02310.20551.4309-0.08132.80420.20870.2761-0.2989-0.1023-0.1326-0.94160.18040.8918-0.0760.07350.13740.13470.41730.1330.7342-6.8512-50.5042-35.7419
21.7364-0.79630.0142.67071.02295.04530.1224-0.0208-0.13340.07640.0029-0.3857-0.3380.1812-0.12530.23650.07760.10560.31550.06050.2278-17.7258-40.4039-30.2327
31.10550.53870.35932.66380.95433.66280.11810.0736-0.1037-0.193-0.26-0.0789-0.3266-0.08960.14190.29550.19640.14480.45310.05510.1526-20.8402-39.4616-37.2785
40.02570.05710.0130.5671-0.32850.51980.0936-0.05660.03580.203-0.3468-0.01610.02130.52530.25320.4867-0.17660.13280.870.23040.1778-20.7929-11.9423-13.7703
50.4171.9157-1.416311.0532-7.52075.5031-0.07290.0779-0.02160.30960.0784-0.1589-0.1763-0.0119-0.00550.2796-0.18060.01210.57750.23280.2931-7.6566-8.9086-11.9037
60.7841-0.3153-0.31952.4062.54633.12590.3311-0.1101-0.13110.3794-0.2137-0.38110.4187-0.0115-0.11740.44730.0023-0.0760.45010.26490.3115-19.8698-45.7203-10.3207
71.4279-0.1128-0.23462.37112.67234.23820.4148-0.3104-0.36050.4242-0.1963-0.42820.5262-0.1229-0.21850.45080.0371-0.04990.20720.2240.2896-18.3284-47.4129-15.2109
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A234 - 289
2X-RAY DIFFRACTION2B41 - 132
3X-RAY DIFFRACTION3C47 - 164
4X-RAY DIFFRACTION4D38 - 130
5X-RAY DIFFRACTION5E62 - 126
6X-RAY DIFFRACTION6F1 - 37
7X-RAY DIFFRACTION7G1 - 37

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