7AW9

CCAAT-binding complex and HapX bound to Aspergillus fumigatus cccA DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.247 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural insights into cooperative DNA recognition by the CCAAT-binding complex and its bZIP transcription factor HapX.

Huber, E.M.Hortschansky, P.Scheven, M.T.Misslinger, M.Haas, H.Brakhage, A.A.Groll, M.

(2022) Structure 30: 934

  • DOI: https://doi.org/10.1016/j.str.2022.04.001
  • Primary Citation of Related Structures:  
    7AW7, 7AW9

  • PubMed Abstract: 

    The heterotrimeric CCAAT-binding complex (CBC) is a fundamental eukaryotic transcription factor recognizing the CCAAT box. In certain fungi, like Aspergilli, the CBC cooperates with the basic leucine zipper HapX to control iron metabolism. HapX functionally depends on the CBC, and the stable interaction of both requires DNA. To study this cooperative effect, X-ray structures of the CBC-HapX-DNA complex were determined. Downstream of the CCAAT box, occupied by the CBC, a HapX dimer binds to the major groove. The leash-like N terminus of the distal HapX subunit contacts the CBC, and via a flexible polyproline type II helix mediates minor groove interactions that stimulate sequence promiscuity. In vitro and in vivo mutagenesis suggest that the structural and functional plasticity of HapX results from local asymmetry and its ability to target major and minor grooves simultaneously. The latter feature may also apply to related transcription factors such as yeast Hap4 and distinct Yap family members.


  • Organizational Affiliation

    Chair of Biochemistry, Center for Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, 85748 Garching, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HapB64Aspergillus nidulans FGSC A4Mutation(s): 0 
Gene Names: ANIA_07545
UniProt
Find proteins for G5EAZ0 (Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139))
Explore G5EAZ0 
Go to UniProtKB:  G5EAZ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG5EAZ0
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription factor HapC (Eurofung)92Aspergillus nidulans FGSC A4Mutation(s): 0 
Gene Names: 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
MoleculeChains Sequence LengthOrganismDetailsImage
CBFD_NFYB_HMF domain-containing protein119Aspergillus nidulans FGSC A4Mutation(s): 0 
Gene Names: AN6492.2
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
BZIP domain-containing protein
D, E
98Aspergillus nidulans FGSC A4Mutation(s): 2 
Gene Names: ANIA_08251
UniProt
Find proteins for G5EAX9 (Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139))
Explore G5EAX9 
Go to UniProtKB:  G5EAX9
Entity Groups  
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UniProt GroupG5EAX9
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA37Aspergillus fumigatus A1163
Sequence Annotations
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA37Aspergillus fumigatus A1163
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth C]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.247 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.84α = 90
b = 127.66β = 90
c = 198.98γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyGR 1861/8-1
German Research Foundation (DFG)GermanySFB1309-325871075

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-13
    Type: Initial release
  • Version 1.1: 2022-05-11
    Changes: Database references
  • Version 1.2: 2022-07-20
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Refinement description