7W4Z: Fragmin domain-1

Crystal structure of fragmin domain-1 in complex with actin (AMPPNP-form). Determined by X-ray diffraction at 1.15 Å resolution. Released 26 Oct 2022.

Method: X-ray diffraction
Resolution: 1.15 Å
Organisms: Gallus gallus, Physarum polycephalum
Chains: 2
Atoms: 5,228
Mol. weight: 61.35 kDa
Ligands: PO4, CA, MG, ANP
Released: 26 Oct 2022

Explore 7W4Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7W4Z contains 35 α-helices and 30 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: 24 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	1
β-strand	16-21	6	1
β-strand	24	1	2
β-strand	29-32	4	1
β-strand	35-38	4	3
β-strand	53-54	2	3
α-helix	55-60	6
α-helix	62-64	3
β-strand	65-68	4	3
β-strand	71-72	2	4
β-strand	75-76	2	4
α-helix	79-87	9
α-helix	88-94	7
α-helix	98-100	3
β-strand	103-107	5	1
β-strand	112	1	5
α-helix	113-125	13
β-strand	131-136	6	1
α-helix	137-144	8
β-strand	150-155	6	6
β-strand	160-166	7	6
β-strand	169-170	2	6
α-helix	172-174	3
β-strand	176-178	3	6
α-helix	182-193	12
α-helix	194-196	3
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	7
β-strand	247-250	4	7
α-helix	253-262	10
α-helix	264-267	4
α-helix	274-283	10
α-helix	287-289	3
α-helix	290-294	5
β-strand	297-300	4	6
α-helix	302-305	4
α-helix	309-320	12
β-strand	329-330	2	6
α-helix	335-337	3
α-helix	338-346	9
α-helix	350-354	5
β-strand	357-358	2	1
α-helix	359-365	7
α-helix	369-373	5

Chain B: 11 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	9-11	3
β-strand	12	1	5
α-helix	20-30	11
α-helix	34-36	3
β-strand	44-51	8	8
β-strand	54-57	4	8
α-helix	58-59	2
α-helix	60-62	3
β-strand	65-67	3	9
β-strand	71-78	8	8
β-strand	88-95	8	8
α-helix	101-117	17
α-helix	122	1
β-strand	123-128	6	8
α-helix	134-137	4
β-strand	146-148	3	9
α-helix	152-154	3
α-helix	156	1
β-strand	157	1	2
α-helix	158-159	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Actin, alpha skeletal muscle	A	protein	377	Gallus gallus	P68139 (AlphaFold model)
Actin-binding protein fragmin P	B	protein	162	Physarum polycephalum	Q94707 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7W4Z_1 Actin, alpha skeletal muscle (chains A)
MCDEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEA
QSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREK
MTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRL
DLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEK
SYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNV
MSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWIT
KQEYDEAGPSIVHRKCF

Sequence of entity 2 (B), FASTA

>7W4Z_2 Actin-binding protein fragmin P (chains B)
GPMQKQKEYNIADSNIANLGTELEKKVKLEASQHEDAWKGAGKQVGVEIWRIQQFKVVPV
PKKHHGSFYTGDSYIVLSTYHPKTNPDKLAYDVHFWLGAFTTQDEAGTAAYKTVELDDYL
GGLPVQYREVQGYESERFLSLFPKGGLRILDGGVETGFHHVE

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	2
CA	Calcium ion	Ca	2
MG	Magnesium ion	Mg	1
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	1

Water and common crystallization additives (EDO) are not listed.

Primary citation

Structures and mechanisms of actin ATP hydrolysis. Kanematsu, Y., Narita, A., Oda, T. et al. Proc Natl Acad Sci U S A (2022) 119:e2122641119-e2122641119. DOI 10.1073/pnas.2122641119 · PubMed

Other PDB entries of the same protein (UniProt P68139 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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)
9L2N 1.7 Å, Crystal structure of Cytochalasin D bound to a filamentous conformation actin
7W52 2.0 Å, Crystal structure of fragmin domain-1 (15-160) in complex with actin
1MDU 2.2 Å, Crystal structure of the chicken actin trimer complexed with human gelsolin segment 1…
8D13 2.43 Å, Helical ADP-F-actin
8D14 2.51 Å, Helical ADP-Pi-F-actin
7R94 2.6 Å, T-Plastin-F-actin complex
8C4E 2.6 Å, F-actin decorated by SipA426-685
9JW0 2.69 Å, Structure of the N-terminal 3 domains (V1-V3) villin bound to actin
7YNE 2.7 Å, Crystal structure of fragmin domain-1 (1-160) in complex with G-form actin
8C4C 2.7 Å, F-actin decorated by SipA497-669

Browse structure collections

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