7X5G

Nrf2 (A510Y)-MafG heterodimer bound with CsMBE2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis of transcription regulation by CNC family transcription factor, Nrf2.

Sengoku, T.Shiina, M.Suzuki, K.Hamada, K.Sato, K.Uchiyama, A.Kobayashi, S.Oguni, A.Itaya, H.Kasahara, K.Moriwaki, H.Watanabe, C.Honma, T.Okada, C.Baba, S.Ohta, T.Motohashi, H.Yamamoto, M.Ogata, K.

(2022) Nucleic Acids Res 50: 12543-12557

  • DOI: https://doi.org/10.1093/nar/gkac1102
  • Primary Citation of Related Structures:  
    7X5E, 7X5F, 7X5G

  • PubMed Abstract: 

    Several basic leucine zipper (bZIP) transcription factors have accessory motifs in their DNA-binding domains, such as the CNC motif of CNC family or the EHR motif of small Maf (sMaf) proteins. CNC family proteins heterodimerize with sMaf proteins to recognize CNC-sMaf binding DNA elements (CsMBEs) in competition with sMaf homodimers, but the functional role of the CNC motif remains elusive. In this study, we report the crystal structures of Nrf2/NFE2L2, a CNC family protein regulating anti-stress transcriptional responses, in a complex with MafG and CsMBE. The CNC motif restricts the conformations of crucial Arg residues in the basic region, which form extensive contact with the DNA backbone phosphates. Accordingly, the Nrf2-MafG heterodimer has approximately a 200-fold stronger affinity for CsMBE than canonical bZIP proteins, such as AP-1 proteins. The high DNA affinity of the CNC-sMaf heterodimer may allow it to compete with the sMaf homodimer on target genes without being perturbed by other low-affinity bZIP proteins with similar sequence specificity.


  • Organizational Affiliation

    Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription factor MafG
A, E
104Homo sapiensMutation(s): 0 
Gene Names: MAFG
UniProt & NIH Common Fund Data Resources
Find proteins for O15525 (Homo sapiens)
Explore O15525 
Go to UniProtKB:  O15525
PHAROS:  O15525
GTEx:  ENSG00000197063 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15525
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear factor erythroid 2-related factor 2
B, F
113Homo sapiensMutation(s): 1 
Gene Names: NFE2L2NRF2
UniProt & NIH Common Fund Data Resources
Find proteins for Q16236 (Homo sapiens)
Explore Q16236 
Go to UniProtKB:  Q16236
PHAROS:  Q16236
GTEx:  ENSG00000116044 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16236
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*CP*TP*GP*CP*TP*GP*AP*GP*TP*CP*AP*CP*TP*GP*T)-3')
C, G
16synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*AP*CP*AP*GP*TP*GP*AP*CP*TP*CP*AP*GP*CP*AP*G)-3')
D, H
16synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download Ideal Coordinates CCD File 
I [auth C]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.222 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 246.022α = 90
b = 55.018β = 97.3
c = 86.152γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-09
    Type: Initial release
  • Version 1.1: 2022-12-14
    Changes: Database references
  • Version 1.2: 2022-12-28
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Refinement description