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- PDB-6y35: CCAAT-binding complex from Aspergillus fumigatus with cycA DNA -

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Basic information

Entry
Database: PDB / ID: 6y35
TitleCCAAT-binding complex from Aspergillus fumigatus with cycA 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: 2.6 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)47,4436
Polymers47,3635
Non-polymers801
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13900 Å2
ΔGint-98 kcal/mol
Surface area20290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.570, 75.510, 142.940
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: 7695.956 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Aspergillus fumigatus A1163 (mold)
#5: DNA chain DNA (25-MER)


Mass: 7660.978 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Aspergillus fumigatus A1163 (mold)

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Non-polymers , 2 types, 25 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.: 24 / 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: 2.94 Å3/Da / Density % sol: 58.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH 6.5 25 % PEG8000

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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: 2.6→48 Å / Num. obs: 17526 / % possible obs: 98.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 19
Reflection shellResolution: 2.6→2.7 Å / Rmerge(I) obs: 0.509 / Num. unique obs: 1862

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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: 2.6→30 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.944 / SU B: 23.018 / SU ML: 0.209 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.267
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2316 876 5 %RANDOM
Rwork0.1919 ---
obs0.1939 16636 98.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 158.5 Å2 / Biso mean: 64.025 Å2 / Biso min: 36.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.88 Å20 Å2-0 Å2
2---1.5 Å20 Å2
3----1.38 Å2
Refinement stepCycle: final / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2069 1025 4 24 3122
Biso mean--90.96 57.48 -
Num. residues----302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0123269
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182608
X-RAY DIFFRACTIONr_angle_refined_deg0.9911.4714612
X-RAY DIFFRACTIONr_angle_other_deg1.1921.8986071
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7385250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.84120.635126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.05315414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6591522
X-RAY DIFFRACTIONr_chiral_restr0.0440.2427
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022930
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02715
X-RAY DIFFRACTIONr_rigid_bond_restr0.28735877
LS refinement shellResolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 63 -
Rwork0.34 1194 -
all-1257 -
obs--99.52 %
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)
11.9107-0.7716-0.12376.4481-1.7951.21040.0991-0.14440.00130.4752-0.02070.8550.0966-0.1909-0.07840.1833-0.11330.1180.2051-0.05460.1784-22.3371-4.1286.2265
20.46670.06780.19931.9056-0.15631.03360.0250.0260.0473-0.0446-0.0002-0.08890.1091-0.0758-0.02470.01530.0138-0.00560.15680.02310.2354-12.08884.7209-2.4
30.60060.49890.58042.4029-0.37470.96530.112-0.0647-0.06570.3052-0.1189-0.21820.022-0.11230.0070.0554-0.0167-0.07510.17110.01920.2164-7.92974.963.6162
40.1303-0.02080.61421.5527-0.40573.17810.04310.0237-0.0585-0.030.17630.03580.09940.0145-0.21940.0728-0.0157-0.00610.20720.0160.1161-13.7198-11.9254-4.9292
50.4642-0.01390.89860.9637-0.22263.13480.01950.0474-0.00610.0408-0.09440.02770.087-0.00090.07490.0857-0.04740.03160.13470.00850.1247-14.2723-12.61520.2431
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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