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- PDB-4g92: CCAAT-binding complex from Aspergillus nidulans with DNA -

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Basic information

Entry
Database: PDB / ID: 4g92
TitleCCAAT-binding complex from Aspergillus nidulans with DNA
Components
  • (DNA) x 2
  • HAPB protein
  • HapE
  • Transcription factor HapC (Eurofung)
KeywordsTranscription/DNA / transcription factor / nucleosome / minor groove binding / CCAAT-binding complex / histone fold motif / specific binding to the CCAAT-box / DNA / nucleus / Transcription-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
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
DNA / DNA (> 10) / 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: 1.8 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 ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
D: DNA
E: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5257
Polymers47,3335
Non-polymers1922
Water9,602533
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14680 Å2
ΔGint-138 kcal/mol
Surface area20660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.040, 72.890, 145.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 protein


Mass: 7669.910 Da / Num. of mol.: 1 / Fragment: UNP residues 231-293
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
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
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

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DNA chain , 2 types, 2 molecules DE

#4: DNA chain DNA


Mass: 7574.896 Da / Num. of mol.: 1 / Source method: obtained synthetically
#5: DNA chain DNA


Mass: 7780.062 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 2 types, 535 molecules

#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 533 / 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: 3.2 Å3/Da / Density % sol: 61.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, 0.2 M (NH4)2SO4, 25% PEG3350, pH 7.5, 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: Jan 28, 2012
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: 1.8→40 Å / Num. all: 57233 / Num. obs: 54543 / % possible obs: 95.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 11.7
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 2.5 / % possible all: 96.8

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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 4G91

4g91


Resolution: 1.8→10 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / SU B: 4.956 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.19008 2728 5 %RANDOM
Rwork0.15674 ---
obs0.15843 49104 95.33 %-
all-51832 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.795 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å20 Å2
2---1.57 Å20 Å2
3---0.99 Å2
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2192 1025 10 533 3760
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0173389
X-RAY DIFFRACTIONr_angle_refined_deg1.0931.7444779
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2485267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.42223.333108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.14815429
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8481521
X-RAY DIFFRACTIONr_chiral_restr0.0710.2478
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212186
X-RAY DIFFRACTIONr_rigid_bond_restr2.63833389
X-RAY DIFFRACTIONr_sphericity_free31.4575124
X-RAY DIFFRACTIONr_sphericity_bonded14.75453637
LS refinement shellResolution: 1.8→1.845 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 182 -
Rwork0.22 3512 -
obs--97.08 %
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)
10.0915-0.0558-0.06740.2360.05670.0515-0.00220.0134-0.0091-0.0353-0.0016-0.01340.0011-0.01110.00380.0154-0.0045-0.00650.0104-0.00410.042838.0164-41.7644-42.7549
20.11530.0073-0.04620.2605-0.07610.07680.0074-0.0021-0.01970.0196-0.0091-0.036-0.0227-0.01470.00170.02310.0018-0.0060.01190.00250.046948.7101-39.6426-30.76
30.13760.02010.01850.2114-0.06060.1154-0.0032-0.0025-0.00790.0074-0.0068-0.0601-0.01-0.02230.010.0166-0.00060.00460.00680.00040.042654.0021-35.6625-35.4832
40.0787-0.0796-0.03360.1922-0.18660.49630.0121-0.0054-0.01090.01860.01550.0164-0.0486-0.0213-0.02760.01740.0025-0.00250.01490.00280.026233.5699-30.7684-31.1856
50.1296-0.03270.04690.1499-0.00220.01890.004-0.0161-0.0019-0.00010.00710.02080.0023-0.006-0.01110.02610.00740.00590.01680.00290.032933.5259-31.0419-36.2197
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A232 - 292
2X-RAY DIFFRACTION2B41 - 132
3X-RAY DIFFRACTION3C47 - 163
4X-RAY DIFFRACTION4D1 - 25
5X-RAY DIFFRACTION5E1 - 25

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