6LJD: Fragmin F2-F3 domains

Crystal structure of fragmin F2-F3 domains (calcium condition). Determined by X-ray diffraction at 2.15 Å resolution. Released 1 Jan 2020.

Method: X-ray diffraction
Resolution: 2.15 Å
Organism: Physarum polycephalum
Chains: 1
Atoms: 1,809
Mol. weight: 23.64 kDa
Ligands: CA
Released: 1 Jan 2020

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

Secondary structure: helices and β-sheets

6LJD contains 11 α-helices and 12 β-strands across 1 chain. 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 C: 11 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	167-172	6	1
β-strand	178-182	5	1
α-helix	186-188	3
β-strand	190	1	2
β-strand	194-199	6	1
β-strand	202-207	6	1
α-helix	213-230	18
β-strand	235-240	6	1
α-helix	241-243	3
α-helix	246-252	7
α-helix	257-258	2
β-strand	259	1	2
α-helix	262-264	3
α-helix	267-273	7
β-strand	278-283	6	3
β-strand	290-296	7	3
α-helix	297-299	3
α-helix	302-304	3
β-strand	310-314	5	3
β-strand	319-323	5	3
α-helix	329-345	17
β-strand	354-358	5	3
α-helix	364-368	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Actin-binding protein fragmin P	C	protein	212	Physarum polycephalum	Q94707 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>6LJD_1 Actin-binding protein fragmin P (chains C)
GPDKYRTRLLHLKGKKHIRVHEVPKTYKSLNSGDVFVLDAGKTVIQWNGAKAGLLEKVKA
AELLQAIEGEREGIASGRVVAEADNDTEFFTLLGDKGPIADAAAGGSDLEADKKDQPAVL
LRLSDASGKFEFTEVARGLKVKRNLLDSNDVFVLYTGAEVFAWVGKHASVGEKKKALSFA
QEYVQKAGLPIHTPVARILEGGENEVFEDFFD

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	3

Water and common crystallization additives (MES, CL, GOL, SO4) are not listed.

Primary citation

Novel inter-domain Ca2+-binding site in the gelsolin superfamily protein fragmin. Takeda, S., Fujiwara, I., Sugimoto, Y. et al. J Muscle Res Cell Motil (2020) 41:153-162. DOI 10.1007/s10974-019-09571-5 · PubMed

Other PDB entries of the same protein (UniProt Q94707 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7W4Z 1.15 Å, Crystal structure of fragmin domain-1 in complex with actin (AMPPNP-form)
7W50 1.15 Å, Crystal structure of fragmin domain-1 in complex with actin (ADP-Pi-form)
7W51 1.2 Å, Crystal structure of fragmin domain-1 in complex with actin (ADP-form)
8GT1 1.35 Å, Crystal structure of human cardiac alpha actin A108G mutant (ADP-Pi state) in complex…
8GSW 1.4 Å, Crystal structure of human cardiac alpha actin A108G mutant (AMPPNP state) in complex…
8GT5 1.4 Å, Crystal structure of human cardiac alpha actin Q137A mutant (ADP-Pi state) in complex…
8GSU 1.5 Å, Crystal structure of human cardiac alpha actin (WT_ADP-Pi) in complex with fragmin F1…
8GT2 1.5 Å, Crystal structure of human cardiac alpha actin P109A mutant (AMPPNP state) in complex…
8GT3 1.5 Å, Crystal structure of human cardiac alpha actin P109A mutant (ADP-Pi state) in complex…
8GT4 1.55 Å, Crystal structure of human cardiac alpha actin Q137A mutant (AMPPNP state) in complex…
6KWZ 1.55 Å, Crystal structure of fragmin F3 domain with calcium ion
9L2N 1.7 Å, Crystal structure of Cytochalasin D bound to a filamentous conformation actin

Browse structure collections

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