Crystal structure of an H-NOX protein from Nostoc sp. PCC 7120

Experimental Data Snapshot

  • Resolution: 2.13 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

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Tunnels modulate ligand flux in a heme nitric oxide/oxygen binding (H-NOX) domain.

Winter, M.B.Herzik, M.A.Kuriyan, J.Marletta, M.A.

(2011) Proc Natl Acad Sci U S A 108: E881-E889

  • DOI: https://doi.org/10.1073/pnas.1114038108
  • Primary Citation of Related Structures:  
    3TF0, 3TF1, 3TF8, 3TF9, 3TFA, 3TFD, 3TFE, 3TFF, 3TFG

  • PubMed Abstract: 

    Interior topological features, such as pockets and channels, have evolved in proteins to regulate biological functions by facilitating the diffusion of biomolecules. Decades of research using the globins as model heme proteins have clearly highlighted the importance of gas pockets around the heme in controlling the capture and release of O(2). However, much less is known about how ligand migration contributes to the diverse functions of other heme protein scaffolds. Heme nitric oxide/oxygen binding (H-NOX) domains are a conserved family of gas-sensing heme proteins with a divergent fold that are critical to numerous signaling pathways. Utilizing X-ray crystallography with xenon, a tunnel network has been shown to serve as a molecular pathway for ligand diffusion. Structure-guided mutagenesis results show that the tunnels have unexpected effects on gas-sensing properties in H-NOX domains. The findings provide insights on how the flux of biomolecules through protein scaffolds modulates protein chemistry.

  • Organizational Affiliation

    Department of Chemistry, California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alr2278 protein
A, B
189Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Gene Names: alr2278
Find proteins for Q8YUQ7 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Explore Q8YUQ7 
Go to UniProtKB:  Q8YUQ7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8YUQ7
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.13 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.696α = 90
b = 123.696β = 90
c = 123.696γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-11-09
    Type: Initial release
  • Version 1.1: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description