PDB-9jvt: Structure of the C-terminal 4 domains (V4-V6-HP) villin bound to ...

ID or keywords:

Entry

Database: PDB / ID: 9jvt

Title

Structure of the C-terminal 4 domains (V4-V6-HP) villin bound to an actin

Components

Actin, alpha skeletal muscle
Villin

Keywords

STRUCTURAL PROTEIN / Villin actin

Function / homology

Function and homology information

Striated Muscle Contraction / striated muscle thin filament / skeletal muscle thin filament assembly / skeletal muscle fiber development / stress fiber / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / actin cytoskeleton / hydrolase activity / ATP binding
Similarity search - Function

Biological species

Paralvinella sulfincola (invertebrata)

Gallus gallus (chicken)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.29 Å

Authors

Robinson, R.C.

Funding support

United States,

France, 2items

Citation

Journal: To Be Published
Title: The structure of a villin-stabilized actin nucleus
Authors: Robinson, R.C.

History

Deposition	Oct 9, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 15, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9jvt.cif.gz	635 KB	Display	PDBx/mmCIF format
PDB format	pdb9jvt.ent.gz	525.2 KB	Display	PDB format
PDBx/mmJSON format	9jvt.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9jvt_validation.pdf.gz	3.1 MB	Display	wwPDB validaton report
Full document	9jvt_full_validation.pdf.gz	3.1 MB	Display
Data in XML	9jvt_validation.xml.gz	59.6 KB	Display
Data in CIF	9jvt_validation.cif.gz	76.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jv/9jvt ftp://data.pdbj.org/pub/pdb/validation_reports/jv/9jvt	HTTPS FTP

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Related structure data

Related structure data	9jusSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#19 - Jul 2001 Actin similarity (8) #18 - Jun 2001 Myosin similarity (8) #241 - Jan 2020 Twenty Years of Molecules similarity (3)

Deposited unit

v: Villin

g: Actin, alpha skeletal muscle

V: Villin

G: Actin, alpha skeletal muscle

hetero molecules

195 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

v: Villin

g: Actin, alpha skeletal muscle

hetero molecules

defined by author&software
97.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

V: Villin

G: Actin, alpha skeletal muscle

hetero molecules

defined by author&software
97.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	131.122, 97.689, 134.308
Angle α, β, γ (deg.)	90.00, 103.95, 90.00
Int Tables number	5
Space group name H-M	C121
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

#1: Protein	Villin Mass: 54901.398 Da / Num. of mol.: 2 / Fragment: C-terminal 4 domains Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paralvinella sulfincola (invertebrata) / Production host: Escherichia coli (E. coli)
#2: Protein	Actin, alpha skeletal muscle / Alpha-actin-1 Mass: 42109.973 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: ACTA1, ACTA / Production host: Escherichia coli (E. coli) / References: UniProt: P68139
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
Has ligand of interest	Y
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.15 Å³/Da / Density % sol: 42.83 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M Tris, pH 8.0 50% PEG 400 0.2 M Li2SO4 1 mM CaCl2

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.29→46.62 Å / Num. obs: 24970 / % possible obs: 99.5 % / Redundancy: 3.5 % / B_iso Wilson estimate: 98.27 Å² / R_merge(I) obs: 0.124 / R_pim(I) all: 0.077 / R_rim(I) all: 0.146 / Net I/σ(I): 7.6
Reflection shell	Resolution: 3.29→3.52 Å / R_merge(I) obs: 0.991 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2432 / CC_1/2: 0.57 / R_pim(I) all: 0.605 / R_rim(I) all: 1.163

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Processing

Software

Name	Version	Classification
PHENIX	(1.17.1_3660: ???)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 9JUS

9jus

Resolution: 3.29→46.62 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.82 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2682	1997	8.01 %
R_work	0.2411	-	-
obs	0.2433	24931	99.37 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 3.29→46.62 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12038	0	64	0	12102

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	12361
X-RAY DIFFRACTION	f_angle_d	0.588	16722
X-RAY DIFFRACTION	f_dihedral_angle_d	23.184	4578
X-RAY DIFFRACTION	f_chiral_restr	0.045	1792
X-RAY DIFFRACTION	f_plane_restr	0.005	2163

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
3.29-3.38	0.436	136	0.395	1554	X-RAY DIFFRACTION	94
3.38-3.47	0.4221	140	0.3506	1606	X-RAY DIFFRACTION	100
3.47-3.57	0.3537	144	0.34	1657	X-RAY DIFFRACTION	100
3.57-3.68	0.3069	142	0.3087	1632	X-RAY DIFFRACTION	100
3.68-3.82	0.3555	141	0.3019	1623	X-RAY DIFFRACTION	100
3.82-3.97	0.3067	145	0.2852	1656	X-RAY DIFFRACTION	100
3.97-4.15	0.3078	141	0.2666	1630	X-RAY DIFFRACTION	100
4.15-4.37	0.2835	142	0.2315	1629	X-RAY DIFFRACTION	100
4.37-4.64	0.2314	143	0.2222	1642	X-RAY DIFFRACTION	100
4.64-5	0.262	144	0.2112	1644	X-RAY DIFFRACTION	100
5-5.5	0.2832	144	0.2219	1667	X-RAY DIFFRACTION	100
5.5-6.3	0.2474	143	0.2336	1635	X-RAY DIFFRACTION	100
6.3-7.92	0.2254	144	0.2278	1665	X-RAY DIFFRACTION	100
7.93-46.62	0.2033	148	0.1841	1694	X-RAY DIFFRACTION	99

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	2.1899	-0.5668	-0.2301	0.1655	-0.0509	3.5225	-0.778	0.4548	-0.3723	0.361	0.2788	-0.7703	-2.1286	1.3676	-0.121	1.7981	-0.9534	0.3738	1.5285	-0.2175	1.279	45.031	-10.111	25.149
2	1.3859	0.0698	0.5327	1.7642	-1.2411	3.3333	-0.0179	-0.3369	-0.1365	0.9881	0.2346	-0.2894	-1.2131	0.588	-0.0002	1.7325	-0.2381	0.2766	0.9768	-0.188	0.9616	32.376	-18.324	47.588
3	0.8863	-0.3781	1.5091	0.2629	-0.1456	3.0255	-0.0689	-0.5607	0.1924	0.2927	0.6689	0.1979	-1.5194	-0.2194	0.0114	1.8778	0.0602	0.6028	0.8078	0.0479	1.0662	18.625	-14.62	37.423
4	0.8232	1.3839	-0.7565	2.2784	-0.8814	0.845	-0.1147	1.6152	0.5616	-0.23	0.6585	1.7663	-2.2362	-0.7178	0.0825	1.8801	-0.5381	0.1235	1.5179	-0.0664	0.9526	36.445	-8.571	13.223
5	1.037	0.9126	0.8772	0.1036	0.262	0.2593	-0.6066	0.3655	-0.4096	-0.166	0.185	-0.1679	-0.297	1.1121	-0.0006	1.2714	0.1803	0.1713	1.3788	-0.0161	0.9397	-15.828	-24.867	24.172
6	3.2956	-0.4576	-1.3104	3.0911	-1.0526	4.0071	-0.0104	0.1837	0.1126	-1.0084	0.0265	-0.1306	0.796	1.1077	-0.0009	1.1671	0.2045	-0.0912	0.9461	-0.1604	0.7282	-28.692	-22.375	12.854
7	1.4023	-0.0068	0.6452	3.4663	-1.3083	3.1926	0.272	0.0433	0.3952	-0.1151	-0.2528	-0.5495	-0.1943	0.6994	-0.0001	0.6178	-0.0308	-0.0036	1.1026	-0.1147	1.079	-20.293	-1.785	22.411
8	0.4884	0.7144	-0.9973	2.3505	-0.4928	1.5949	1.5215	-2.342	1.5389	0.4385	-0.7611	-0.3825	-1.1174	0.5753	0.1019	1.1026	-0.6156	-0.1204	1.928	-0.179	0.9463	-18.996	-2.595	44.178
9	-0.479	0.1008	-0.6737	-0.2466	0.4169	2.9255	0.1726	-0.1527	-0.2155	0.633	-0.0164	0.0154	-0.017	0.2847	-0.0002	1.2939	-0.1999	0.0163	1.3042	-0.0284	1.2542	-36.08	0.261	58.08
10	2.7169	-1.3157	-1.5016	2.8472	1.7229	1.2451	1.727	-0.5196	-0.1141	-0.2253	0.3763	0.5632	0.8763	-1.5249	0.1692	1.048	-0.2914	-0.3173	1.2389	0.2357	1.1836	-56.65	-22.843	19.402
11	1.6687	-1.1982	-0.0866	0.692	-0.0059	0.5691	-0.8303	-0.2002	0.157	-0.0298	1.6544	0.4997	1.4798	-1.724	0.0328	1.6959	-0.7527	-0.2723	1.7122	0.6139	1.6876	-66.146	-31.838	32.027
12	2.3395	0.23	-0.4072	1.9169	-0.9538	6.0736	-0.0618	-0.2083	-0.198	0.1576	0.2701	1.0138	1.7073	-0.8261	-0.0013	1.1201	-0.2153	-0.2832	0.8225	0.1351	1.0249	-52.312	-30.622	32.279
13	1.7098	0.7057	-1.1264	1.727	-1.2961	5.1053	0.1363	-0.2139	0.0407	0.085	0.132	0.2055	0.999	0.1861	0.0112	1.0926	0.0565	-0.2319	0.8153	-0.0313	0.6416	-42.39	-26.601	38.626
14	1.5318	0.6361	-1.2478	1.2513	-0.5734	0.9297	-0.4617	0.6954	-3.0512	0.2756	-0.6936	-2.4209	2.2199	0.4786	-0.0865	1.3274	-0.1795	-0.3551	2.1432	-0.0906	1.9799	-15.611	-18.436	48.404
15	2.6615	-0.6193	1.8752	2.7821	-1.466	5.4317	0.3201	0.624	-0.5557	-0.5287	0.1487	1.0891	-0.4863	-0.5386	0.0003	0.8062	-0.0219	0.003	0.8794	-0.0761	1.2832	12.658	-20.929	12.274
16	0.5911	-0.5634	-0.0688	5.9457	-0.1723	2.8851	0.4872	0.0592	-0.0699	0.5004	0.3799	1.9358	0.4598	-0.415	0.0429	0.6905	-0.1511	0.1682	0.9371	0.2121	2.0942	6.03	-42.25	27.305
17	1.4497	-0.667	1.565	3.0813	-1.2151	1.6788	0.6605	-0.1362	-0.0429	-0.2586	0.3791	0.0705	-2.9906	3.229	0.1716	1.2233	-0.5613	0.3546	1.152	-0.4329	1.1672	41.014	-20.48	21.38
18	2.2206	-1.9895	-0.4392	1.6962	0.2328	1.3994	-0.452	0.4867	-0.1109	0.6714	-0.0333	-0.0564	-0.2783	1.7071	-1.0474	2.2986	-1.3735	-0.3824	1.7744	-0.2933	0.5641	53.599	-16.529	35.613

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN G AND RESID 61:145 )	G	61 - 145
2	X-RAY DIFFRACTION	2	( CHAIN G AND RESID 146:273 )	G	146 - 273
3	X-RAY DIFFRACTION	3	( CHAIN G AND RESID 274:337 )	G	274 - 337
4	X-RAY DIFFRACTION	4	( CHAIN G AND RESID 338:374 )	G	338 - 374
5	X-RAY DIFFRACTION	5	( CHAIN v AND RESID 376:409 )	v	376 - 409
6	X-RAY DIFFRACTION	6	( CHAIN v AND RESID 410:495 )	v	410 - 495
7	X-RAY DIFFRACTION	7	( CHAIN v AND RESID 496:673 )	v	496 - 673
8	X-RAY DIFFRACTION	8	( CHAIN v AND RESID 674:716 )	v	674 - 716
9	X-RAY DIFFRACTION	9	( CHAIN v AND RESID 717:824 )	v	717 - 824
10	X-RAY DIFFRACTION	10	( CHAIN g AND RESID 1:28 )	g	1 - 28
11	X-RAY DIFFRACTION	11	( CHAIN g AND RESID 29:92 )	g	29 - 92
12	X-RAY DIFFRACTION	12	( CHAIN g AND RESID 93:216 )	g	93 - 216
13	X-RAY DIFFRACTION	13	( CHAIN g AND RESID 217:368 )	g	217 - 368
14	X-RAY DIFFRACTION	14	( CHAIN V AND RESID 370:389 )	V	370 - 389
15	X-RAY DIFFRACTION	15	( CHAIN V AND RESID 390:495 )	V	390 - 495
16	X-RAY DIFFRACTION	16	( CHAIN V AND RESID 496:750 )	V	496 - 750
17	X-RAY DIFFRACTION	17	( CHAIN G AND RESID 3:28 )	G	3 - 28
18	X-RAY DIFFRACTION	18	( CHAIN G AND RESID 29:60 )	G	29 - 60

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