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- PDB-4g91: CCAAT-binding complex from Aspergillus nidulans -

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Basic information

Entry
Database: PDB / ID: 4g91
TitleCCAAT-binding complex from Aspergillus nidulans
Components
  • HAPB protein
  • HapE
  • Transcription factor HapC (Eurofung)
KeywordsTRANSCRIPTION / transcription factor / nucleosome / minor groove binding / CCAAT-binding complex / histone fold motif / specific binding to the CCAAT-box / nucleus
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 ...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
HapE / Transcriptional activator HAP2 / Histone H2A/H2B/H3 domain-containing protein / Transcription factor HapC (Eurofung)
Similarity search - Component
Biological speciesEmericella nidulans (mold)
Aspergillus nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHuber, E.M. / Scharf, D.H. / Hortschansky, P. / Groll, M. / Brakhage, A.A.
CitationJournal: Structure / Year: 2012
Title: DNA Minor Groove Sensing and Widening by the CCAAT-Binding Complex.
Authors: Huber, E.M. / Scharf, D.H. / Hortschansky, P. / Groll, M. / Brakhage, A.A.
History
DepositionJul 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HAPB protein
B: Transcription factor HapC (Eurofung)
C: HapE


Theoretical massNumber of molelcules
Total (without water)31,9783
Polymers31,9783
Non-polymers00
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7330 Å2
ΔGint-55 kcal/mol
Surface area12010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.450, 60.700, 71.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HAPB protein


Mass: 7669.910 Da / Num. of mol.: 1 / Fragment: UNP residues 231-293 / Mutation: wild type
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Emericella nidulans (mold) / Gene: hapB / Production host: Escherichia coli (E. coli) / References: UniProt: P87249
#2: Protein Transcription factor HapC (Eurofung)


Mass: 10641.299 Da / Num. of mol.: 1 / Fragment: UNP residues 42-132 / Mutation: wild type
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus nidulans (mold) / Strain: FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139 / Gene: AN4034.2, ANIA_04034 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5B5Z6
#3: Protein HapE


Mass: 13666.752 Da / Num. of mol.: 1 / Fragment: UNP residues 47-164 / Mutation: wild type
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus nidulans (mold) / Strain: FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139 / Gene: AN6492.2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5AYY8, UniProt: C8V0B5*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O

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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: 1.96 Å3/Da / Density % sol: 37.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Tris, 20% PEG 6000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 2, 2010
RadiationMonochromator: LN2 cooled fixed-exit. Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→25 Å / Num. all: 20435 / Num. obs: 20415 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.9 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 24.4
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 6.2 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.6.0119refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1N1J

1n1j


Resolution: 1.9→10 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.95 / SU B: 6.563 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.422 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20223 1021 5 %RANDOM
Rwork0.17941 ---
obs0.18059 19393 99.89 %-
all-20414 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.617 Å2
Baniso -1Baniso -2Baniso -3
1-1.48 Å20 Å20 Å2
2---0.17 Å20 Å2
3----1.32 Å2
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1915 0 0 89 2004
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191948
X-RAY DIFFRACTIONr_angle_refined_deg0.9641.9542620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1335233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.20724.36294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.16515377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0631514
X-RAY DIFFRACTIONr_chiral_restr0.0750.2291
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211437
X-RAY DIFFRACTIONr_rigid_bond_restr2.64631948
X-RAY DIFFRACTIONr_sphericity_free15.253518
X-RAY DIFFRACTIONr_sphericity_bonded5.42151986
LS refinement shellResolution: 1.9→1.948 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 68 -
Rwork0.192 1231 -
obs--100 %
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)
13.8628-1.84312.06683.2672-0.70481.9796-0.0558-0.3516-0.33030.17010.12150.30140.1016-0.0503-0.06560.07620.02960.01050.06690.0380.05286.9050.23922.285
21.51870.0377-0.26541.64490.16631.5078-0.04190.07330.0503-0.05410.07470.045-0.0018-0.069-0.03280.00930.0037-0.00170.02280.00820.00416.60016.59986.4353
31.7356-0.5167-0.3741.22680.00051.6758-0.02220.1039-0.0277-0.09270.0357-0.02410.12960.0374-0.01340.0282-0.0087-0.00270.0197-0.0090.019511.2891.33912.4563
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A231 - 258
2X-RAY DIFFRACTION2B42 - 132
3X-RAY DIFFRACTION3C47 - 163

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