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- PDB-6y37: CCAAT-binding complex from Aspergillus nidulans with cccA DNA -

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Basic information

Entry
Database: PDB / ID: 6y37
TitleCCAAT-binding complex from Aspergillus nidulans with cccA DNA
Components
  • (DNA (25-MER)) x 2
  • CBFD_NFYB_HMF domain-containing protein
  • HapB
  • Transcription factor HapC (Eurofung)
KeywordsTRANSCRIPTION / transcription factor / heterotrimer / histone fold / protein:DNA complex
Function / homology
Function and homology information


CCAAT-binding factor complex / regulation of carbohydrate metabolic process / nucleosome / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / 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 / negative regulation of DNA-templated transcription ...CCAAT-binding factor complex / regulation of carbohydrate metabolic process / nucleosome / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / 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 / 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
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 ...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 / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcriptional activator HAP2 / Histone H2A/H2B/H3 domain-containing protein / Transcription factor HapC (Eurofung)
Similarity search - Component
Biological speciesAspergillus nidulans FGSC A4 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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: HapB
B: Transcription factor HapC (Eurofung)
C: CBFD_NFYB_HMF domain-containing protein
D: DNA (25-MER)
E: DNA (25-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4286
Polymers47,3365
Non-polymers921
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14450 Å2
ΔGint-97 kcal/mol
Surface area20320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.680, 72.010, 148.450
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 , 3 types, 3 molecules ABC

#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 (E. coli) / 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 (E. coli) / 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 (E. coli) / References: UniProt: Q5AYY8

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DNA chain , 2 types, 2 molecules DE

#4: DNA chain DNA (25-MER)


Mass: 7622.892 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Aspergillus nidulans FGSC A4 (mold)
#5: DNA chain DNA (25-MER)


Mass: 7735.029 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Aspergillus nidulans FGSC A4 (mold)

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Non-polymers , 2 types, 124 molecules

#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 3.71 Å3/Da / Density % sol: 66.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium acetate, 0.1 M HEPES pH 7.5, 25 % 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 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: 2.2→48 Å / Num. obs: 36047 / % possible obs: 98.7 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 16
Reflection shellResolution: 2.2→2.3 Å / Rmerge(I) obs: 0.565 / Num. unique obs: 4419

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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: 2.2→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.951 / SU B: 11.873 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.402 / ESU R Free: 0.153
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2178 1802 5 %RANDOM
Rwork0.1955 ---
obs0.1966 34232 98.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 147.72 Å2 / Biso mean: 55.544 Å2 / Biso min: 32.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20 Å2
2--2.13 Å2-0 Å2
3----1.8 Å2
Refinement stepCycle: final / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2193 1025 6 123 3347
Biso mean--60.18 58.17 -
Num. residues----319
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0123399
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182714
X-RAY DIFFRACTIONr_angle_refined_deg1.0331.4774792
X-RAY DIFFRACTIONr_angle_other_deg1.1961.8846322
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1575268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.68820.985132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.59615431
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.131522
X-RAY DIFFRACTIONr_chiral_restr0.0470.2441
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023089
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02742
X-RAY DIFFRACTIONr_rigid_bond_restr0.37136113
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 131 -
Rwork0.274 2487 -
all-2618 -
obs--99.24 %
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)
10.6455-1.0574-0.0941.83690.03780.27750.1510.04440.1865-0.1836-0.127-0.2399-0.08210.1748-0.0240.11160.00690.0070.151-0.00290.240919.07074.5013-39.3506
20.56280.0306-0.10880.65310.33320.8884-0.0321-0.03530.05080.0940.02810.02670.01860.10160.00410.13920.01630.0080.01450.00340.13837.41710.8374-29.9898
30.53570.00650.12880.83070.25510.4893-0.03050.0150.03020.010.03760.14070.02190.0615-0.00710.12710.0115-0.00460.00850.00280.14163.5267-2.1052-35.6319
40.1121-0.0650.1530.69320.72522.63680.005-0.00730.00980.09660.0434-0.10430.19930.17-0.04840.08310.0243-0.0160.079-0.00440.068122.8051-7.5029-27.4783
50.3022-0.05590.07690.5331-0.29750.1986-0.00490.0034-0.0534-0.04730.0028-0.05920.05790.05940.0020.10280.0653-0.00320.1461-0.04220.11323.543-8.0057-32.962
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A231 - 290
2X-RAY DIFFRACTION2B42 - 132
3X-RAY DIFFRACTION3C47 - 164
4X-RAY DIFFRACTION4D1 - 25
5X-RAY DIFFRACTION5E1 - 25

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