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- PDB-6y36: CCAAT-binding complex from Aspergillus fumigatus with cccA DNA -

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Basic information

Entry
Database: PDB / ID: 6y36
TitleCCAAT-binding complex from Aspergillus fumigatus with cccA DNA
Components
  • (CCAAT-binding factor complex subunit ...) x 2
  • (DNA (25-MER)) x 2
  • CCAAT-binding transcription factor subunit HAPB
KeywordsTRANSCRIPTION / transcription factor / heterotrimer / histone fold / protein:DNA complex
Function / homology
Function and homology information


CCAAT-binding factor complex / regulation of aerobic respiration / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / regulation of transcription by RNA polymerase II / chromatin / DNA binding / nucleus
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2430 / 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2430 / 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 domain / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
SULFITE ION / DNA / DNA (> 10) / Transcription factor CBF/NF-Y/archaeal histone domain-containing protein / CCAAT-binding factor complex subunit HapE / Transcriptional activator HAP2
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
Aspergillus fumigatus A1163 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGroll, M. / Huber, E.M.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)GR 1861/8-1 Germany
German Research Foundation (DFG)SFB1309-325871075 Germany
CitationJournal: Life Sci Alliance / Year: 2020
Title: Structural basis of HapE P88L -linked antifungal triazole resistance in Aspergillus fumigatus .
Authors: Hortschansky, P. / Misslinger, M. / Morl, J. / Gsaller, F. / Bromley, M.J. / Brakhage, A.A. / Groll, M. / Haas, H. / Huber, E.M.
History
DepositionFeb 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 30, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CCAAT-binding transcription factor subunit HAPB
B: CCAAT-binding factor complex subunit HapC
C: CCAAT-binding factor complex subunit HapE
D: DNA (25-MER)
E: DNA (25-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4446
Polymers47,3645
Non-polymers801
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13830 Å2
ΔGint-97 kcal/mol
Surface area20120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.480, 83.740, 148.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CCAAT-binding transcription factor subunit HAPB


Mass: 7669.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (mold)
Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: AFUA_2G14720 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4X049

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CCAAT-binding factor complex subunit ... , 2 types, 2 molecules BC

#2: Protein CCAAT-binding factor complex subunit HapC


Mass: 10641.299 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus A1163 (mold) / Gene: Y699_06893 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A229Y8Y1*PLUS
#3: Protein CCAAT-binding factor complex subunit HapE


Mass: 13694.806 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (mold)
Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: AFUA_6G05300 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4WDM9

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DNA chain , 2 types, 2 molecules DE

#4: DNA chain DNA (25-MER)


Mass: 7801.016 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Aspergillus fumigatus A1163 (mold)
#5: DNA chain DNA (25-MER)


Mass: 7556.903 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Aspergillus fumigatus A1163 (mold)

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Non-polymers , 2 types, 69 molecules

#6: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O

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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: 3.38 Å3/Da / Density % sol: 63.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH 6.5, 25% PEG6000

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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 PILATUS 6M-F / Detector: PIXEL / Date: Sep 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→48 Å / Num. obs: 29239 / % possible obs: 99.7 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 21.2
Reflection shellResolution: 2.3→2.4 Å / Rmerge(I) obs: 0.589 / Num. unique obs: 3467

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G92

4g92


Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.955 / SU B: 12.634 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.167
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2109 1461 5 %RANDOM
Rwork0.1867 ---
obs0.188 27765 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 182.49 Å2 / Biso mean: 64.183 Å2 / Biso min: 28.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20 Å2
2--1.73 Å2-0 Å2
3----2.14 Å2
Refinement stepCycle: final / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2050 1025 4 68 3147
Biso mean--76.65 58.8 -
Num. residues----300
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0123262
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182589
X-RAY DIFFRACTIONr_angle_refined_deg1.0111.474605
X-RAY DIFFRACTIONr_angle_other_deg1.2551.8996030
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8925250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.5920.8125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.08615410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2271521
X-RAY DIFFRACTIONr_chiral_restr0.050.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022932
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02716
X-RAY DIFFRACTIONr_rigid_bond_restr0.735851
LS refinement shellResolution: 2.3→2.359 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 105 -
Rwork0.254 2009 -
all-2114 -
obs--99.81 %
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)
10.7058-0.32520.39991.68010.19731.24470.0980.11620.02370.1074-0.0564-0.05910.42190.3187-0.04150.16360.1479-0.01580.1883-0.02790.17920.419481.5674-6.1262
20.80040.22590.23651.36330.34011.43020.0226-0.0839-0.01540.06910.0132-0.0430.16220.0402-0.03590.05030.01180.00340.15080.01880.205211.144890.44042.3565
30.4742-0.00930.35211.58190.59820.970.01780.03-0.0611-0.0656-0.04080.10760.0766-0.00030.0230.03-0.0034-0.02730.14710.02740.18956.984790.7559-3.6532
40.4210.37250.74921.14850.39453.56640.1637-0.046-0.24850.07450.0706-0.16780.40960.0284-0.23440.22130.046-0.05980.05740.06130.178212.863373.44995.1148
50.75590.44240.811.38350.3953.55470.1089-0.0214-0.3010.08540.0617-0.1490.64260.1441-0.17060.20390.0597-0.03040.02550.01430.133113.375272.8517-0.4354
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A235 - 291
2X-RAY DIFFRACTION2B41 - 132
3X-RAY DIFFRACTION3C58 - 164
4X-RAY DIFFRACTION4D1 - 25
5X-RAY DIFFRACTION5E1 - 25

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