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Four crystal structures of human LLT1, a ligand of human NKR-P1, in varied glycosylation and oligomerization states.

Skálová T, Bláha J, Harlos K, Dušková J, Koval' T, Stránský J, Hašek J, Vaněk O, Dohnálek J - Acta Crystallogr. D Biol. Crystallogr. (2015)

Bottom Line: The monomeric form keeps the same fold with the exception of the position of an outer part of the long loop region.The hexamer of glycosylated LLT1 consists of three classical dimers.The hexameric packing may indicate a possible mode of interaction of C-type lectin-like proteins in the glycosylated form.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Biotechnology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, 142 20 Praha 4, Czech Republic.

ABSTRACT
Human LLT1 is a C-type lectin-like ligand of NKR-P1 (CD161, gene KLRB1), a C-type lectin-like receptor of natural killer cells. Using X-ray diffraction, the first experimental structures of human LLT1 were determined. Four structures of LLT1 under various conditions were determined: monomeric, dimeric deglycosylated after the first N-acetylglucosamine unit in two forms and hexameric with homogeneous GlcNAc2Man5 glycosylation. The dimeric form follows the classical dimerization mode of human CD69. The monomeric form keeps the same fold with the exception of the position of an outer part of the long loop region. The hexamer of glycosylated LLT1 consists of three classical dimers. The hexameric packing may indicate a possible mode of interaction of C-type lectin-like proteins in the glycosylated form.

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(a) Electron-density OMIT maps for the flexible loop (residues 147–160) placed in an unusual position in the monomeric structure of LLT1 (LLT1_mono). 2mFo − DFc (blue, 0.8σ) and mFo − DFc (green, 2.5 σ) Fourier maps are drawn up to a distance of 1.6 Å from the atoms of residues 147–160. The residues are better localized in the middle of the loop, where they are stabilized by the nearby α-helix of a neighbouring molecule in the crystal (green). The loop is not modelled in the deposited structure because weak signal in this region causes unstable refinement. (b) Two neighbouring hexamers in the crystal of LLT1_glyco are connected by weak electron density belonging to the glycan chains. The glycosylated residues and GlcNAc units are shown as spheres. 2mFo − DFc (blue, 0.7σ) and mFo − DFc (green, 1.8σ) Fourier maps are shown.
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fig3: (a) Electron-density OMIT maps for the flexible loop (residues 147–160) placed in an unusual position in the monomeric structure of LLT1 (LLT1_mono). 2mFo − DFc (blue, 0.8σ) and mFo − DFc (green, 2.5 σ) Fourier maps are drawn up to a distance of 1.6 Å from the atoms of residues 147–160. The residues are better localized in the middle of the loop, where they are stabilized by the nearby α-helix of a neighbouring molecule in the crystal (green). The loop is not modelled in the deposited structure because weak signal in this region causes unstable refinement. (b) Two neighbouring hexamers in the crystal of LLT1_glyco are connected by weak electron density belonging to the glycan chains. The glycosylated residues and GlcNAc units are shown as spheres. 2mFo − DFc (blue, 0.7σ) and mFo − DFc (green, 1.8σ) Fourier maps are shown.

Mentions: In LLT1_mono, residues 147–160 (the outer loop of the long loop region) are poorly visible and were not built in the deposited structure. However, the approximate position of the loop is apparent in the electron density and differs significantly from its position in LLT1 in its dimeric form (Figs. 2 ▶c and 3 ▶a). The structure of LLT1_mono with the approximate position of the loop is available from the authors upon request.


Four crystal structures of human LLT1, a ligand of human NKR-P1, in varied glycosylation and oligomerization states.

Skálová T, Bláha J, Harlos K, Dušková J, Koval' T, Stránský J, Hašek J, Vaněk O, Dohnálek J - Acta Crystallogr. D Biol. Crystallogr. (2015)

(a) Electron-density OMIT maps for the flexible loop (residues 147–160) placed in an unusual position in the monomeric structure of LLT1 (LLT1_mono). 2mFo − DFc (blue, 0.8σ) and mFo − DFc (green, 2.5 σ) Fourier maps are drawn up to a distance of 1.6 Å from the atoms of residues 147–160. The residues are better localized in the middle of the loop, where they are stabilized by the nearby α-helix of a neighbouring molecule in the crystal (green). The loop is not modelled in the deposited structure because weak signal in this region causes unstable refinement. (b) Two neighbouring hexamers in the crystal of LLT1_glyco are connected by weak electron density belonging to the glycan chains. The glycosylated residues and GlcNAc units are shown as spheres. 2mFo − DFc (blue, 0.7σ) and mFo − DFc (green, 1.8σ) Fourier maps are shown.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4356368&req=5

fig3: (a) Electron-density OMIT maps for the flexible loop (residues 147–160) placed in an unusual position in the monomeric structure of LLT1 (LLT1_mono). 2mFo − DFc (blue, 0.8σ) and mFo − DFc (green, 2.5 σ) Fourier maps are drawn up to a distance of 1.6 Å from the atoms of residues 147–160. The residues are better localized in the middle of the loop, where they are stabilized by the nearby α-helix of a neighbouring molecule in the crystal (green). The loop is not modelled in the deposited structure because weak signal in this region causes unstable refinement. (b) Two neighbouring hexamers in the crystal of LLT1_glyco are connected by weak electron density belonging to the glycan chains. The glycosylated residues and GlcNAc units are shown as spheres. 2mFo − DFc (blue, 0.7σ) and mFo − DFc (green, 1.8σ) Fourier maps are shown.
Mentions: In LLT1_mono, residues 147–160 (the outer loop of the long loop region) are poorly visible and were not built in the deposited structure. However, the approximate position of the loop is apparent in the electron density and differs significantly from its position in LLT1 in its dimeric form (Figs. 2 ▶c and 3 ▶a). The structure of LLT1_mono with the approximate position of the loop is available from the authors upon request.

Bottom Line: The monomeric form keeps the same fold with the exception of the position of an outer part of the long loop region.The hexamer of glycosylated LLT1 consists of three classical dimers.The hexameric packing may indicate a possible mode of interaction of C-type lectin-like proteins in the glycosylated form.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Biotechnology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, 142 20 Praha 4, Czech Republic.

ABSTRACT
Human LLT1 is a C-type lectin-like ligand of NKR-P1 (CD161, gene KLRB1), a C-type lectin-like receptor of natural killer cells. Using X-ray diffraction, the first experimental structures of human LLT1 were determined. Four structures of LLT1 under various conditions were determined: monomeric, dimeric deglycosylated after the first N-acetylglucosamine unit in two forms and hexameric with homogeneous GlcNAc2Man5 glycosylation. The dimeric form follows the classical dimerization mode of human CD69. The monomeric form keeps the same fold with the exception of the position of an outer part of the long loop region. The hexamer of glycosylated LLT1 consists of three classical dimers. The hexameric packing may indicate a possible mode of interaction of C-type lectin-like proteins in the glycosylated form.

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