9JUS | pdb_00009jus

Structure of villin bound to an actin trimer

PDB DOI: https://doi.org/10.2210/pdb9JUS/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Gallus gallus, Paralvinella sulfincola
Expression System: Gallus gallus, Paralvinella sulfincola
Mutation(s): No

Deposited: 2024-10-08 Released: 2025-10-08
Deposition Author(s): Robinson, R.C.
Funding Organization(s): Other private, Human Frontier Science Program (HFSP)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.226 (Depositor), 0.228 (DCC)
R-Value Work:
0.196 (Depositor), 0.197 (DCC)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

The structure of a villin-stabilized actin nucleus

Robinson, R.C.

To be published.

Macromolecule Content

Total Structure Weight: 442.88 kDa
Atom Count: 30,576
Modeled Residue Count: 3,820
Deposited Residue Count: 3,908
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin, alpha skeletal muscle	A [auth p] B [auth f] C [auth g] E [auth P] F A [auth p], B [auth f], C [auth g], E [auth P], F, G	377	Gallus gallus	Mutation(s): 0 Gene Names: ACTA1, ACTA EC: 3.6.4
UniProt
Find proteins for P68139 (Gallus gallus) Explore P68139 Go to UniProtKB: P68139
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68139
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
villin	D [auth v], H [auth V]	823	Paralvinella sulfincola	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain BA [auth G] SDF format, chain I [auth p] SDF format, chain K [auth f] SDF format, chain M [auth g] SDF format, chain X [auth P] SDF format, chain Z [auth F] MOL2 format, chain BA [auth G] MOL2 format, chain I [auth p] MOL2 format, chain K [auth f] MOL2 format, chain M [auth g] MOL2 format, chain X [auth P] MOL2 format, chain Z [auth F] mmCIF format, chain BA [auth G] mmCIF format, chain I [auth p] mmCIF format, chain K [auth f] mmCIF format, chain M [auth g] mmCIF format, chain X [auth P] mmCIF format, chain Z [auth F]	BA [auth G] I [auth p] K [auth f] M [auth g] X [auth P] BA [auth G], I [auth p], K [auth f], M [auth g], X [auth P], Z [auth F]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain BA [auth G] Focus chain I [auth p] Focus chain K [auth f] Focus chain M [auth g] Focus chain X [auth P] Focus chain Z [auth F] Interactions & Density Focus chain BA [auth G] Focus chain I [auth p] Focus chain K [auth f] Focus chain M [auth g] Focus chain X [auth P] Focus chain Z [auth F]
SCN Query on SCN Download Ideal Coordinates CCD File SDF format, chain LA [auth V] MOL2 format, chain LA [auth V] mmCIF format, chain LA [auth V]	LA [auth V]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M		Interactions Focus chain LA [auth V] Interactions & Density Focus chain LA [auth V]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain DA [auth V] SDF format, chain EA [auth V] SDF format, chain FA [auth V] SDF format, chain GA [auth V] SDF format, chain HA [auth V] SDF format, chain IA [auth V] SDF format, chain JA [auth V] SDF format, chain KA [auth V] SDF format, chain O [auth v] SDF format, chain P [auth v] SDF format, chain Q [auth v] SDF format, chain R [auth v] SDF format, chain S [auth v] SDF format, chain T [auth v] SDF format, chain U [auth v] SDF format, chain V [auth v] MOL2 format, chain DA [auth V] MOL2 format, chain EA [auth V] MOL2 format, chain FA [auth V] MOL2 format, chain GA [auth V] MOL2 format, chain HA [auth V] MOL2 format, chain IA [auth V] MOL2 format, chain JA [auth V] MOL2 format, chain KA [auth V] MOL2 format, chain O [auth v] MOL2 format, chain P [auth v] MOL2 format, chain Q [auth v] MOL2 format, chain R [auth v] MOL2 format, chain S [auth v] MOL2 format, chain T [auth v] MOL2 format, chain U [auth v] MOL2 format, chain V [auth v] mmCIF format, chain DA [auth V] mmCIF format, chain EA [auth V] mmCIF format, chain FA [auth V] mmCIF format, chain GA [auth V] mmCIF format, chain HA [auth V] mmCIF format, chain IA [auth V] mmCIF format, chain JA [auth V] mmCIF format, chain KA [auth V] mmCIF format, chain O [auth v] mmCIF format, chain P [auth v] mmCIF format, chain Q [auth v] mmCIF format, chain R [auth v] mmCIF format, chain S [auth v] mmCIF format, chain T [auth v] mmCIF format, chain U [auth v] mmCIF format, chain V [auth v]	DA [auth V] EA [auth V] FA [auth V] GA [auth V] HA [auth V] DA [auth V], EA [auth V], FA [auth V], GA [auth V], HA [auth V], IA [auth V], JA [auth V], KA [auth V], O [auth v], P [auth v], Q [auth v], R [auth v], S [auth v], T [auth v], U [auth v], V [auth v]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain DA [auth V] Focus chain EA [auth V] Focus chain FA [auth V] Focus chain GA [auth V] Focus chain HA [auth V] Focus chain IA [auth V] Focus chain JA [auth V] Focus chain KA [auth V] Focus chain O [auth v] Focus chain P [auth v] Focus chain Q [auth v] Focus chain R [auth v] Focus chain S [auth v] Focus chain T [auth v] Focus chain U [auth v] Focus chain V [auth v] Interactions & Density Focus chain DA [auth V] Focus chain EA [auth V] Focus chain FA [auth V] Focus chain GA [auth V] Focus chain HA [auth V] Focus chain IA [auth V] Focus chain JA [auth V] Focus chain KA [auth V] Focus chain O [auth v] Focus chain P [auth v] Focus chain Q [auth v] Focus chain R [auth v] Focus chain S [auth v] Focus chain T [auth v] Focus chain U [auth v] Focus chain V [auth v]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain W [auth v] MOL2 format, chain W [auth v] mmCIF format, chain W [auth v]	W [auth v]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain W [auth v] Interactions & Density Focus chain W [auth v]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain CA [auth G] SDF format, chain J [auth p] SDF format, chain L [auth f] SDF format, chain N [auth g] SDF format, chain Y [auth P] MOL2 format, chain AA [auth F] MOL2 format, chain CA [auth G] MOL2 format, chain J [auth p] MOL2 format, chain L [auth f] MOL2 format, chain N [auth g] MOL2 format, chain Y [auth P] mmCIF format, chain AA [auth F] mmCIF format, chain CA [auth G] mmCIF format, chain J [auth p] mmCIF format, chain L [auth f] mmCIF format, chain N [auth g] mmCIF format, chain Y [auth P]	AA [auth F] CA [auth G] J [auth p] L [auth f] N [auth g] AA [auth F], CA [auth G], J [auth p], L [auth f], N [auth g], Y [auth P]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain CA [auth G] Focus chain J [auth p] Focus chain L [auth f] Focus chain N [auth g] Focus chain Y [auth P] Interactions & Density Focus chain AA [auth F] Focus chain CA [auth G] Focus chain J [auth p] Focus chain L [auth f] Focus chain N [auth g] Focus chain Y [auth P]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HIC Query on HIC	A [auth p] B [auth f] C [auth g] E [auth P] F A [auth p], B [auth f], C [auth g], E [auth P], F, G	L-PEPTIDE LINKING	C₇ H₁₁ N₃ O₂		HIS