6H1F: Nanobody-stabilized gelsolin D187N variant

Structure of the nanobody-stabilized gelsolin D187N variant (second domain). Determined by X-ray diffraction at 1.9 Å resolution. Released 23 Jan 2019.

Method: X-ray diffraction
Resolution: 1.9 Å
Organisms: Lama glama, Homo sapiens
Chains: 2
Atoms: 1,896
Mol. weight: 28.49 kDa
Ligands: SCN
Released: 23 Jan 2019

Explore 6H1F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6H1F contains 5 α-helices and 16 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	10-12	3	2
β-strand	18-25	8	1
β-strand	33-39	7	2
β-strand	45-51	7	2
β-strand	58-60	3	2
β-strand	68-73	6	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-99	8	2
α-helix	111-113	3
β-strand	116-117	2	2
β-strand	121-125	5	2

Chain B: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	161-167	7	3
β-strand	171-176	6	3
α-helix	180-182	3
β-strand	188-192	5	3
β-strand	196-201	6	3
α-helix	207-224	18
β-strand	230-235	6	3
α-helix	241-247	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
gelsolin nanobody, Nb11	A	protein	140	Lama glama
Gelsolin	B	protein	119	Homo sapiens	P06396 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6H1F_1 gelsolin nanobody, Nb11 (chains A)
MQVQLQESGGGLVQAGGSLRLSCAASGRTFSSFVMGWFRQAPGKEREFVASISRSGSVTR
YADSAKGRFTISKDNAKNTVSLQMDNLNPDDTAVYYCAADLHRPYGPGSQRTDDYDTWGQ
GTQVTVSSLVPRGSHHHHHH

Sequence of entity 2 (B), FASTA

>6H1F_2 Gelsolin (chains B)
GSHHVVPNEVVVQRLFQVKGRRVVRATEVPVSWESFNNGNCFILDLGNNIHQWCGSNSNR
YERLKATQVSKGIRDNERSGRARVHVSEEGTEPEAMLQVLGPKPALPAGTEDTAKEDAA

Ligands and cofactors

ID	Name	Formula	Copies
SCN	Thiocyanate ion	C N S	1

Primary citation

Nanobody interaction unveils structure, dynamics and proteotoxicity of the Finnish-type amyloidogenic gelsolin variant. Giorgino, T., Mattioni, D., Hassan, A. et al. Biochim Biophys Acta Mol Basis Dis (2019) 1865:648-660. DOI 10.1016/j.bbadis.2019.01.010 · PubMed

Other PDB entries of the same protein (UniProt P06396 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5FAF 1.05 Å, N184K pathological variant of gelsolin domain 2 (orthorhombic form)
6QW3 1.3 Å, Calcium-bound gelsolin domain 2
6LJE 1.4 Å, Crystal structure of gelsolin G3 domain (calcium and magnesium condition)
6LJF 1.5 Å, Crystal structure of gelsolin G3 domain (calcium condition)
2FH1 1.55 Å, C-terminal half of gelsolin soaked in low calcium at pH 4.5
3CIP 1.6 Å, Complex of Dictyostelium Discoideum Actin with Gelsolin
1KCQ 1.65 Å, Human Gelsolin Domain 2 with a Cd2+ bound
3CI5 1.7 Å, Complex of Phosphorylated Dictyostelium Discoideum Actin with Gelsolin
5FAE 1.7 Å, N184K pathological variant of gelsolin domain 2 (trigonal form)
5O2Z 1.7 Å, Domain swap dimer of the G167R variant of gelsolin second domain
1D4X 1.75 Å, Crystal Structure of Caenorhabditis Elegans Mg-ATP Actin Complexed with Human Gelsolin…
1NLV 1.8 Å, Crystal Structure Of Dictyostelium Discoideum Actin Complexed With Ca ATP And Human…

Browse structure collections

About this viewer

MolViewer shows 6H1F directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.