9JW0: N-terminal 3 domains (V1-V3) villin

Structure of the N-terminal 3 domains (V1-V3) villin bound to actin. Determined by X-ray diffraction at 2.69 Å resolution. Released 15 Oct 2025.

Method: X-ray diffraction
Resolution: 2.69 Å
Organisms: Paralvinella sulfincola, Gallus gallus
Chains: 2
Atoms: 5,731
Mol. weight: 88.05 kDa
Ligands: CA, ATP
Released: 15 Oct 2025

Explore 9JW0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9JW0 contains 40 α-helices and 43 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: 16 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	15-22	8	1
β-strand	25-28	4	1
α-helix	29-30	2
α-helix	31-33	3
β-strand	36-38	3	2
β-strand	42-51	10	1
β-strand	54-63	10	1
α-helix	69-85	17
β-strand	91-96	6	1
α-helix	102-106	5
β-strand	114-116	3	2
α-helix	120-122	3
β-strand	125	1	3
β-strand	134-139	6	4
β-strand	145-148	4	4
α-helix	154-156	3
β-strand	158	1	5
β-strand	162-166	5	4
β-strand	170-175	6	4
α-helix	176	1
α-helix	181-198	18
β-strand	202-207	6	4
α-helix	218-227	10
α-helix	233-236	4
β-strand	238	1	5
α-helix	239	1
α-helix	246-256	11
β-strand	258-263	6	6
β-strand	270-276	7	6
β-strand	280	1	7
α-helix	281-283	3
β-strand	289-293	5	6
α-helix	295-297	3
β-strand	299-303	5	6
α-helix	309-325	17
β-strand	334-338	5	6
α-helix	344-348	5
β-strand	352	1	7

Chain B: 24 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	8
β-strand	16-21	6	8
β-strand	22	1	3
β-strand	24	1	3
β-strand	29-32	4	8
β-strand	35-38	4	9
β-strand	53-54	2	9
α-helix	56-60	5
β-strand	65-68	4	9
β-strand	71-72	2	10
β-strand	75-76	2	10
α-helix	79-87	9
α-helix	88-94	7
α-helix	98-100	3
β-strand	103-107	5	8
α-helix	113-125	13
β-strand	131-136	6	8
α-helix	137-144	8
β-strand	150-155	6	11
β-strand	160-166	7	11
β-strand	169-170	2	11
α-helix	172-174	3
β-strand	176-178	3	11
α-helix	182-196	15
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	12
β-strand	247-250	4	12
α-helix	253-256	4
α-helix	258-261	4
α-helix	264-267	4
α-helix	272-273	2
α-helix	274-283	10
α-helix	287-289	3
α-helix	290-294	5
β-strand	297-300	4	11
α-helix	302-304	3
α-helix	309-320	12
α-helix	326-327	2
β-strand	329-330	2	11
α-helix	335-337	3
α-helix	338-348	11
α-helix	352-355	4
β-strand	357-358	2	8
α-helix	359-364	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Villin	A	protein	400	Paralvinella sulfincola
Actin, alpha skeletal muscle	B	protein	377	Gallus gallus	P68139 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9JW0_1 Villin (chains A)
TDPAFRSVPKGTPCFLIWRIENFQPVPVPKDQYGNFFEGDAYIILSQKDNKGILEQNLHF
WLGKNSSQDEQGTAALKTVELDDYLGGTPVQHRECQNNESKLFLSYFKNKSLKYLQGGVA
SGFNHVEHIVRRRLLSVKGKHTPRMEEKPEISWSQMNKGDVFILDLGEIIYVWNGELCSR
TERIKAMEIARGMRDDRGTGNIIVVEDGEETPDDMGEEEFEVFNEYLPVADKEASIKSAE
EGGADENFEKKKVAQLKLWKVAEEDGNLKITEEATAPLDKKMLDSNDCFIVDNGEDGIWV
WTGKKASPKERKESMNNAMAFLKQRNYSSQTRVTKVPEGGESSEFKSLFKTWEKTKLPGS
VKPYSVNKIAQTVQTKFDAMTLHNNPEVAKETGMVDDGSG

Sequence of entity 2 (B), FASTA

>9JW0_2 Actin, alpha skeletal muscle (chains B)
MCDEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEA
QSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREK
MTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRL
DLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEK
SYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNV
MSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWIT
KQEYDEAGPSIVHRKCF

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	5
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	1

Primary citation

The structure of an actin nucleus stabilized by villin. Robinson, R.C., Chongrungreang, T., Ponlachantra, K. et al. Sci Adv (2025) 11:eadw6915-eadw6915. DOI 10.1126/sciadv.adw6915 · PubMed

Other PDB entries of the same protein (UniProt P68139 (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)
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
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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