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- PDB-6y39: HapE-P88L mutant CCAAT-binding complex from Aspergillus nidulans ... -

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Basic information

Entry
Database: PDB / ID: 6y39
TitleHapE-P88L mutant CCAAT-binding complex from Aspergillus nidulans with cycA 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 / DNA-binding transcription factor activity / protein heterodimerization activity / negative regulation of DNA-templated transcription / 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 / 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
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 ...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 / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / 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: 2.3 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: HapB
B: Transcription factor HapC (Eurofung)
C: CBFD_NFYB_HMF domain-containing protein
D: HapB
E: Transcription factor HapC (Eurofung)
F: CBFD_NFYB_HMF domain-containing protein
G: HapB
H: Transcription factor HapC (Eurofung)
I: CBFD_NFYB_HMF domain-containing protein
J: DNA (25 mer)
K: DNA (25 mer)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,40813
Polymers111,33711
Non-polymers712
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27770 Å2
ΔGint-236 kcal/mol
Surface area43420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.150, 103.500, 159.710
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, 9 molecules ADGBEHCFI

#1: Protein HapB


Mass: 7669.910 Da / Num. of mol.: 3
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.: 3
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: 13682.795 Da / Num. of mol.: 3 / Mutation: P88L
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 JK

#4: DNA chain DNA (25 mer)


Mass: 7574.896 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Aspergillus nidulans FGSC A4 (mold)
#5: DNA chain DNA (25 mer)


Mass: 7780.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Aspergillus nidulans FGSC A4 (mold)

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Non-polymers , 2 types, 61 molecules

#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 3.07 Å3/Da / Density % sol: 59.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 175 mM di-ammonium phosphate, 19% 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: Aug 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→49 Å / Num. obs: 52851 / % possible obs: 98 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.5
Reflection shellResolution: 2.3→2.4 Å / Rmerge(I) obs: 0.598 / Num. unique obs: 6281

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Processing

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

4g92


Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.945 / SU B: 19.401 / SU ML: 0.207 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.284 / ESU R Free: 0.22
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.254 2641 5 %RANDOM
Rwork0.2209 ---
obs0.2225 50185 97.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 147.8 Å2 / Biso mean: 68.217 Å2 / Biso min: 40.64 Å2
Baniso -1Baniso -2Baniso -3
1--1.22 Å20 Å20 Å2
2--3.87 Å2-0 Å2
3----2.66 Å2
Refinement stepCycle: final / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5725 1025 2 59 6811
Biso mean--88.31 61.74 -
Num. residues----755
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0126969
X-RAY DIFFRACTIONr_bond_other_d0.0020.0186152
X-RAY DIFFRACTIONr_angle_refined_deg1.3311.5579598
X-RAY DIFFRACTIONr_angle_other_deg1.2621.71614295
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6035696
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.88722.253324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.31151126
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2671544
X-RAY DIFFRACTIONr_chiral_restr0.0640.2925
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026978
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021453
LS refinement shellResolution: 2.3→2.359 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 193 -
Rwork0.315 3663 -
all-3856 -
obs--98.32 %
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)
10.76111.7904-0.4094.5848-2.15965.1574-0.0402-0.0998-0.221-0.2252-0.096-0.48250.33360.12960.13610.0416-0.0383-0.05250.3021-0.00850.576113.773424.4356-29.1004
22.39860.95471.1951.54990.43123.03740.1652-0.4150.09490.2194-0.18840.01140.1877-0.01020.02320.0533-0.06210.0120.2819-0.05990.4197-2.533226.1818-22.9981
32.78740.72790.47391.41960.01640.86930.0422-0.18380.37270.0527-0.00630.00940.1166-0.0088-0.03590.0271-0.03060.00530.2222-0.04670.4376-5.565828.3522-28.982
42.69781.08561.31154.24432.04036.1894-0.1188-0.34720.1884-0.2775-0.00020.3069-0.5889-0.08920.11890.0705-0.02520.04350.27610.03880.584-49.8969-11.897-45.7417
52.6182-0.1522-1.10772.0522-0.49912.54190.1066-0.3188-0.17170.2582-0.04410.0752-0.24610.0043-0.06250.0598-0.05860.02020.2540.08620.4184-33.747-14.4151-40.1304
62.56330.1313-0.28611.71730.11611.05460.1323-0.2164-0.396-0.0146-0.05340.0777-0.16990.1012-0.07890.0321-0.03320.01660.2350.05690.4324-30.3256-16.6821-45.4511
71.55980.4539-0.20090.2046-0.09117.2847-0.1058-0.1199-0.1134-0.0248-0.1139-0.18760.58310.18530.21970.12580.001-0.00020.4250.12290.400913.798320.2532-71.9498
81.28760.59530.68782.20160.452.83290.09530.02250.17340.3531-0.10590.00990.06070.11610.01060.0571-0.0180.01310.38830.09180.3502-2.557525.882-69.8487
91.77740.1910.49441.5504-0.1263.17580.03220.20390.18950.099-0.06430.03580.1161-0.05570.03210.012-0.01870.01180.40690.09370.3025-5.639624.4329-75.7533
100.2171-0.18270.11550.86651.77856.05870.10870.06190.0098-0.0850.0959-0.07270.0588-0.0969-0.20460.3749-0.08080.04060.3478-0.00730.1958-18.94321.3758-68.2492
110.177-0.3079-0.14711.35421.54483.90480.12470.10920.0052-0.13060.0491-0.0429-0.18760.0188-0.17380.3631-0.10560.020.4232-0.03620.1746-17.76691.5666-62.1541
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A231 - 258
2X-RAY DIFFRACTION2B43 - 132
3X-RAY DIFFRACTION3C47 - 164
4X-RAY DIFFRACTION4D231 - 259
5X-RAY DIFFRACTION5E44 - 130
6X-RAY DIFFRACTION6F47 - 163
7X-RAY DIFFRACTION7G231 - 261
8X-RAY DIFFRACTION8H44 - 130
9X-RAY DIFFRACTION9I47 - 164
10X-RAY DIFFRACTION10J-5 - 19
11X-RAY DIFFRACTION11K8 - 32

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