2VUS

Crystal structure of unliganded NmrA-AreA zinc finger complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.242 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural Analysis of the Recognition of the Negative Regulator Nmra and DNA by the Zinc Finger from the Gata-Type Transcription Factor Area.

Kotaka, M.Johnson, C.Lamb, H.K.Hawkins, A.R.Ren, J.Stammers, D.K.

(2008) J Mol Biol 381: 373

  • DOI: https://doi.org/10.1016/j.jmb.2008.05.077
  • Primary Citation of Related Structures:  
    2VUS, 2VUT, 2VUU

  • PubMed Abstract: 

    Amongst the most common protein motifs in eukaryotes are zinc fingers (ZFs), which, although largely known as DNA binding modules, also can have additional important regulatory roles in forming protein:protein interactions. AreA is a transcriptional activator central to nitrogen metabolism in Aspergillus nidulans. AreA contains a GATA-type ZF that has a competing dual recognition function, binding either DNA or the negative regulator NmrA. We report the crystal structures of three AreA ZF-NmrA complexes including two with bound NAD(+) or NADP(+). The molecular recognition of AreA ZF-NmrA involves binding of the ZF to NmrA via hydrophobic and hydrogen bonding interactions through helices alpha1, alpha6 and alpha11. Comparison with an earlier NMR solution structure of AreA ZF-DNA complex by overlap of the AreA ZFs shows that parts of helices alpha6 and alpha11 of NmrA are positioned close to the GATA motif of the DNA, mimicking the major groove of DNA. The extensive overlap of DNA with NmrA explains their mutually exclusive binding to the AreA ZF. The presence of bound NAD(+)/NADP(+) in the NmrA-AreaA ZF complex, however, causes minimal structural changes. Thus, any regulatory effects on AreA function mediated by the binding of oxidised nicotinamide dinucleotides to NmrA in the NmrA-AreA ZF complex appear not to be modulated via protein conformational rearrangements.


  • Organizational Affiliation

    Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NITROGEN METABOLITE REPRESSION REGULATOR NMRA
A, B, C, D, E
A, B, C, D, E, F, G, H
352Aspergillus nidulans FGSC A4Mutation(s): 0 
UniProt
Find proteins for Q5AU62 (Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139))
Explore Q5AU62 
Go to UniProtKB:  Q5AU62
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5AU62
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NITROGEN REGULATORY PROTEIN AREA
I, J, K, L, M
I, J, K, L, M, N, O, P
43Aspergillus nidulans FGSC A4Mutation(s): 0 
UniProt
Find proteins for P17429 (Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139))
Explore P17429 
Go to UniProtKB:  P17429
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17429
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth G]
DA [auth H]
Q [auth A]
S [auth B]
T [auth C]
AA [auth G],
DA [auth H],
Q [auth A],
S [auth B],
T [auth C],
V [auth D],
X [auth E],
Y [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
Query on ZN

Download Ideal Coordinates CCD File 
FA [auth I]
GA [auth J]
HA [auth K]
IA [auth L]
JA [auth M]
FA [auth I],
GA [auth J],
HA [auth K],
IA [auth L],
JA [auth M],
KA [auth N],
LA [auth O],
MA [auth P]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
BA [auth G]
CA [auth G]
EA [auth H]
R [auth A]
U [auth C]
BA [auth G],
CA [auth G],
EA [auth H],
R [auth A],
U [auth C],
W [auth D],
Z [auth F]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.242 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 228.788α = 90
b = 228.788β = 90
c = 222.296γ = 120
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-29
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.4: 2024-05-08
    Changes: Source and taxonomy