4G92

CCAAT-binding complex from Aspergillus nidulans with DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

DNA Minor Groove Sensing and Widening by the CCAAT-Binding Complex.

Huber, E.M., Scharf, D.H., Hortschansky, P., Groll, M., Brakhage, A.A.

(2012) Structure 20: 1757-1768

  • DOI: https://doi.org/10.1016/j.str.2012.07.012
  • Primary Citation of Related Structures:  
    4G91, 4G92

  • PubMed Abstract: 

    • The CCAAT box is a frequent element of eukaryotic promoters, and its specific recognition by the conserved heterotrimeric CCAAT-binding complex (CBC) constitutes a key step in promoter organization and regulation of transcription. Here, we report the crystal structures of the CBC from Aspergillus nidulans in the absence and in complex with double-stranded DNA at 1 ...

    The CCAAT box is a frequent element of eukaryotic promoters, and its specific recognition by the conserved heterotrimeric CCAAT-binding complex (CBC) constitutes a key step in promoter organization and regulation of transcription. Here, we report the crystal structures of the CBC from Aspergillus nidulans in the absence and in complex with double-stranded DNA at 1.8 Å resolution. The histone-like subunits HapC and HapE induce nucleosome-like DNA bending by interacting with the sugar-phosphate backbone. Minor groove sensing and widening by subunit HapB tightly anchor the CBC to the CCAAT box, as shown by structural and biochemical data. Furthermore, crucial interactions of the DNA duplex with subunit HapB provide an explanation for the sequence specificity of the CBC. The herein-described mode of transcription factor binding answers the question of how histone proteins gained sequence specificity for the CCAAT box.

    Organizational Affiliation: 

    Center for Integrated Protein Science, Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, Garching 85747, Germany.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HAPB proteinA64Aspergillus nidulansMutation(s): 0 
Gene Names: hapB
UniProt
Find proteins for P87249 (Emericella nidulans)
Explore P87249 
Go to UniProtKB:  P87249
Entity Groups  
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UniProt GroupP87249
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription factor HapC (Eurofung)B92Aspergillus nidulans FGSC A4Mutation(s): 0 
Gene Names: AN4034.2, ANIA_04034
UniProt
Find proteins for Q5B5Z6 (Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139))
Explore Q5B5Z6 
Go to UniProtKB:  Q5B5Z6
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UniProt GroupQ5B5Z6
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
HapEC119Aspergillus nidulans FGSC A4Mutation(s): 0 
Gene Names: AN6492.2, ANIA_06492
UniProt
Find proteins for C8V0B5 (Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139))
Explore C8V0B5 
Go to UniProtKB:  C8V0B5
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UniProt GroupC8V0B5
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Entity ID: 4
MoleculeChainsLengthOrganismImage
DNAD25N/A
Protein Feature View
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNAE25N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
F [auth B],
G [auth C]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.04α = 90
b = 72.89β = 90
c = 145.89γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-31
    Type: Initial release