RCSB entry 5KIZ
NMR structure of an engineered HIF-2α PAS-B protein shows that replacement of native water stabilized core with a more conventional mix of amino acid-based hydrophobic and hydrophilic interactions have minimal impact on protein topology. Single point mutations show that internal protein-water hydrogen bond network is essential for the stability of protein tertiary fold. Successful repacking requires the combination of simultaneous and multi-site mutations. These mutations remove allosteric small molecule binding site while keeping heterodimerization with ARNT PAS-B unchanged.

structure: CorrĂȘa et al., Structure, 24(2016): 1918-1927. ( Abstract and full text )

RCSB entry 2N9U
Combining an NMR structure and biochemistry data of EL_PhyR, a stress-related response regulator protein from Erythrobacter litoralis, we show that interactions between sensory (REC) and output domains establish mutually inhibited conformations in both domains. Notably, removal of output domain stabilizes the REC active conformation, which is marked by extensive structural and backbone dynamic changes at regions adjacent (α4 helix) or distant (α3 helix) to the domain/domain interface. Additional data showed that minor perturbations, such as the extension of linker connecting domains, are enough to induce similar effects.

structure: Correa and Gardner Cell Chem. Biol. 23(2016): 945-954. ( Abstract and full text )

RCSB entry 4XT2
Crystal structure (4XT2) of a second HTS-identified, medicinal chemistry-optimized scaffold of small molecule HIF-2α antagonists in a ternary complex with the C-terminal PAS domains from the HIF-2α and ARNT subunits. Complementing earlier achiral compounds, this structure reveals that a more complex ligand with two stereocenters can bind within a cavity inside of HIF-2α PAS-B, interfering with HIF-2 function.

structure: Scheuermann et al. J. Med. Chem. 58(2015): 5930-5941. ( Abstract and full text )

RCSB entries 4LPZ, 4PKY
Crystal structures of ARNT PAS-B domain with the TACC domain (C-terminal region) of TACC3, showing interaction of TACC3 helices with ARNT PAS-B beta-sheet. Despite different constructs and conditions being used for crystallization, these two structures reveal very comparable binding modes that agree well with solution binding data.

structures: Guo et al. J. Biol. Chem. 290(2015): 7707-7721. ( Abstract and full text )

RCSB entry 2MSW
NMR structure and spectroscopic data of EL_LovR, a single domain response regulator (SDRR) protein from E. litoralis that exhibits significant ligand-dependent folding effects. The apo protein, free of Mg2+ cation and phosphorylation, is chiefly unfolded; addition of Mg2+ induces partial folding of most of the proper secondary structure. Phosphorylation induces full and proper folding, underscoring the importance of examining structure in multiple signaling states.

structure: Ocasio et al. Biochemistry 54(2015): 1353-1363. ( Abstract and full text )

RCSB entries 4R38, 4R39, 4R3A.
Crystal structure of a full-length sensor histidine kinase sensitive to blue light. Unusually, this structure reveals how a SHK can function as a monomer, using intramolecular interactions between the sensory LOV domain and the regulatory DHp domain. Structures include the full length protein (4R3A), the isolated LOV domain (4R38) and isolated DHp/CA catalytic constructs (4R39).

structures: Rivera-Cancel et al. Proc. Natl. Acad. Sci. USA 111(2014): 17839-17844. ( Abstract and full text )

RCSB entry 4GHI
Crystal structure (4GHI) of a HTS-identified, medicinal chemistry-optimized small molecule antagonist in a ternary complex with the C-terminal PAS domains from the HIF-2α and ARNT subunits. Compound binding within a cavity inside of HIF-2α specifically disrupts the heterodimerization of full-length, endogenous HIF-2 heterodimers, reducing HIF-2 DNA-binding and transcription activity, while not affecting the similar HIF-1 homolog.

Statistics on the prevalence of cavities within protein structures were generated with the following in-house script: cavfinder.py.

structure: Scheuermann et al. Nat. Chem. Biol. 9(2013): 271-276. ( Abstract and full text )

RCSB entry 4GS9
Crystal structure (4GS9) of the heterodimer of the HIF-2 C-terminal PAS domains in complex with an inactive analogue of the compound present in the 4GHI structure. The associated manuscript details the medicinal chemistry optimization of benzoxadiazole-containing HIF-2 ligands to a Kd < 100 nM antagonist of transcription factor activity in cells.

structure: Rogers, Bayeh, Scheuermann et al. J. Med. Chem. 56(2013): 1739-1747. ( Abstract and full text )

RCSB entry 4EQ1
Crystal structure (4EQ1) of a homodimer of the ARNT C-terminal PAS-B domains, showing the locations of internal cavities suitable for small molecule binding.

structure: Guo et al. ACS Chem. Biol. 8(2013): 626-635. ( Abstract and full text )

RCSB entry 2LRU
WNK1-AI, the autoinhibitory domain of serine/threonine protein kinase WNK1, is a small regulatory subunit located C-terminal to the kinase domain. The solution structure shows that this protein is a circularly-permuted variant of the OSR1-PF2 domain. Despite this difference, both types of domain bind to peptides containing RFXV motifs.

structure: Moon, Correa et al. J. Mol. Biol. 425(2013): 1245-1252. ( Abstract and full text )

RCSB entry 3P7N
EL222, a LOV-HTH protein from E litoralis HTCC2594 provides a nice example of how LOV domains can regulate diverse effectors. In this case, a DNA-binding helix-turn-helix (HTH) domain is inhibited in the dark state by interactions with the LOV domain analogously to the Jα helix in AsLOV2 as shown by the crystal structure reported in this work. Photoactivation leads to enhanced DNA binding, as predicted by this structure and the AsLOV2 signaling model.

structure: Nash, McNulty et al. Proc. Natl. Acad. Sci. 108(2011): 9449-9454. ( Abstract and full text )

Partch/Gardner PNAS 2011 Supporting Information
Ternary complex of TACC3 coiled coil in association of the PAS-B domains of human HIF-2α and ARNT. Complex is assembled using HADDOCK data-driven docking of the TACC3 segment onto the HIF-2α/ARNT PAS-B complex, not de novo structure determination, and thus is not deposited in RCSB - but remains highly useful for analyzing this complex as detailed in the accompanying article.

structure: Partch and Gardner Proc. Natl. Acad. Sci. 108(2011): 7739-7744. ( Abstract and full text )

RCSB entry 2KB2
K. pneumoniae BlrP1 BLUF domain. A blue light sensory domain, binds an FAD chromophore and regulates downstream effector EAL domain's phosphodiesterase activity.

structure: Wu and Gardner Biochemistry 48(2009): 2620-2629. ( Abstract and full text )

RCSB entry 2K7S
ARNT PAS-B domain containing point mutations which enable a second conformation (with +3 register shift in Iβ strand) to exist in equilibrium with the wildtype conformation.

structure: Evans et al. Proc. Natl. Acad. Sci. 106(2009): 2617-2622. ( Abstract and full text )

RCSB entries 3F1N, 3F1O, 3F1P, 3H7W, 3H82
Five crystal structures of the HIF2α/ARNT PAS-B heterodimer (similar to 2a24, see below). The HIF2α half of this complex (blue ribbon) contains a 290 A3 cavity, which accommodates either eight ordered water molecules (3F1P), two ethylene glycol molecules (3F1N) or artificial small molecule (3F1O, 3H7W, 3H82) identified from an NMR-based compound library screen.

structures: Scheuermann et al. Proc. Natl. Acad. Sci. 106(2009): 450-455. ( Abstract and full text ) ; Key et al, J. Am. Chem. Soc. 131(2009): 17647-17654. ( Abstract and full text ).
review:Scheuermann et al. Meth. Enz. 435(2007): 3-24. ( Abstract and full text )

RCSB entry 2VLG
B. subtilis sporulation kinase KinA, N-terminal PAS domain.

structure: Lee et al. Biochemistry 47(2008): 4051-4064. ( Abstract and full text )

RCSB entries 2X0O,
2A24
Human ARNT, C-terminal PAS ("PAS B") domain. Binds HIF-2α PAS-B domain (and PAS domains from other bHLH/PAS proteins) within heterodimeric transcriptional activator complexes via a solvent-exposed β sheet surface. 2X0O = monomer, 2A24 = HADDOCK model of HIF-2α/ARNT PAS-B heterodimer (see also 3F1[NOP] entries).

structures: Card et al. J. Mol. Biol. 353(2005): 664-677. ( Abstract and full text )
review:Scheuermann et al. Meth. Enz. 435(2007): 3-24. ( Abstract and full text )

RCSB entry 1P97
Human HIF2α, C-terminal PAS ("PAS B") domain. Binds ARNT PAS-B domain within the heterodimeric hypoxia inducible factor (HIF) transcritpional activator complex via a solvent-exposed β sheet surface.

structure: Erbel et al. Proc. Natl. Acad. Sci. 100(2003): 15504-15509. ( Abstract and full text )
biological validation:Yang et al. J. Biol. Chem. 280(2005): 36047-36054. ( Abstract and full text )
review:Scheuermann et al. Meth. Enz. 435(2007): 3-24. ( Abstract and full text )

RCSB entry 1LL8
Human PAS kinase, N-terminal PAS domain. Binds small organic compounds internally and regulates kinase activity, potentially linking sensing with enzymatic regulation.

structure: Amezcua et al. Structure 10(2002): 1349-1361. ( Abstract and full text )
biological context: Rutter et al. Proc. Natl. Acad. Sci. 98(2001): 8991-8996. ( Abstract and full text )

RCSB entry 1CLD

Cd2LAC9(61), the DNA-binding domain of the K. lactis LAC9 protein. A member of the Zn2Cys6 family of fungal DNA-binding proteins, the two native zinc atoms were replaced with NMR-active 113Cd to facilitate a variety of heteronuclear NMR experiments to examine the metal-protein interactions.


structure: Gardner, K.H. et al. Nat. Struct. Biol. 2(1995): 898-905.
113Cd relaxation: Schweitzer, B.I. et al. J. Biomol. NMR 6(1995): 180-188.
113Cd-1H heteroTOCSY: Gardner, K.H. and Coleman, J.E. J. Biomol. NMR 4(1994): 761-774.

RCSB entries 170D (araC-substituted), 171D (native)

Dickerson DNA dodecamer, native and araC-substituted. Both structures were determined by Barry Schweitzer and colleagues to examine the effects of arabinosyl cytosine (araC, red DNA) incorporation on standard B-form DNA structure (blue DNA).


structures: Schweitzer, B.I. et al. Biochem 33(1994): 11460-11475.
31P relaxation: Schweitzer, B.I. et al. J. Biomol. NMR 6(1995): 180-188.