38KM | pdb_000038km

Cofilactin filament with two AIP1 bound to middle of the filament

PDB DOI: https://doi.org/10.2210/pdb38KM/pdb
EM Map EMD-78880: EMDB EMDataResource

Classification: STRUCTURAL PROTEIN
Organism(s): Oryctolagus cuniculus, Caenorhabditis elegans
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2026-08-31 Released: 2026-09-09
Deposition Author(s): Stukey, G.J., Dominguez, R.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.30 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 38KM

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

Literature

AIP1 Promotes Severing of Cofilin-Decorated Actin Filaments by Creating a Stress-Sensitive Rigid-Compliant Boundary

Stukey, G.J., Geng, S., Palmer, N.J., Saks, A., Vavylonis, D., Ono, S., Dominguez, R.

To be published.

Macromolecule Content

Total Structure Weight: 573.6 kDa
Atom Count: 40,460
Modeled Residue Count: 5,092
Deposited Residue Count: 5,150
Unique protein chains: 3

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin, alpha skeletal muscle	A, B, C, D, E A, B, C, D, E, F, G, H	377	Oryctolagus cuniculus	Mutation(s): 0 EC: 3.6.4
UniProt
Find proteins for P68135 (Oryctolagus cuniculus) Explore P68135 Go to UniProtKB: P68135
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P68135
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-interacting protein 1	I [auth X], J [auth Y]	611	Caenorhabditis elegans	Mutation(s): 0 Gene Names: unc-78, C04F6.4
UniProt
Find proteins for Q11176 (Caenorhabditis elegans) Explore Q11176 Go to UniProtKB: Q11176
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q11176
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cofilin	K [auth a] L [auth b] M [auth c] N [auth d] O [auth e] K [auth a], L [auth b], M [auth c], N [auth d], O [auth e], P [auth f]	152	Caenorhabditis elegans	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain CA [auth G] SDF format, chain EA [auth H] SDF format, chain Q [auth A] SDF format, chain S [auth B] SDF format, chain U [auth C] SDF format, chain W [auth D] SDF format, chain Y [auth E] MOL2 format, chain AA [auth F] MOL2 format, chain CA [auth G] MOL2 format, chain EA [auth H] MOL2 format, chain Q [auth A] MOL2 format, chain S [auth B] MOL2 format, chain U [auth C] MOL2 format, chain W [auth D] MOL2 format, chain Y [auth E] mmCIF format, chain AA [auth F] mmCIF format, chain CA [auth G] mmCIF format, chain EA [auth H] mmCIF format, chain Q [auth A] mmCIF format, chain S [auth B] mmCIF format, chain U [auth C] mmCIF format, chain W [auth D] mmCIF format, chain Y [auth E]	AA [auth F] CA [auth G] EA [auth H] Q [auth A] S [auth B] AA [auth F], CA [auth G], EA [auth H], Q [auth A], S [auth B], U [auth C], W [auth D], Y [auth E]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain AA [auth F] Focus chain CA [auth G] Focus chain EA [auth H] Focus chain Q [auth A] Focus chain S [auth B] Focus chain U [auth C] Focus chain W [auth D] Focus chain Y [auth E] Interactions & Density Focus chain AA [auth F] Focus chain CA [auth G] Focus chain EA [auth H] Focus chain Q [auth A] Focus chain S [auth B] Focus chain U [auth C] Focus chain W [auth D] Focus chain Y [auth E]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain DA [auth G] SDF format, chain FA [auth H] SDF format, chain R [auth A] SDF format, chain T [auth B] SDF format, chain V [auth C] SDF format, chain X [auth D] SDF format, chain Z [auth E] MOL2 format, chain BA [auth F] MOL2 format, chain DA [auth G] MOL2 format, chain FA [auth H] MOL2 format, chain R [auth A] MOL2 format, chain T [auth B] MOL2 format, chain V [auth C] MOL2 format, chain X [auth D] MOL2 format, chain Z [auth E] mmCIF format, chain BA [auth F] mmCIF format, chain DA [auth G] mmCIF format, chain FA [auth H] mmCIF format, chain R [auth A] mmCIF format, chain T [auth B] mmCIF format, chain V [auth C] mmCIF format, chain X [auth D] mmCIF format, chain Z [auth E]	BA [auth F] DA [auth G] FA [auth H] R [auth A] T [auth B] BA [auth F], DA [auth G], FA [auth H], R [auth A], T [auth B], V [auth C], X [auth D], Z [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth F] Focus chain DA [auth G] Focus chain FA [auth H] Focus chain R [auth A] Focus chain T [auth B] Focus chain V [auth C] Focus chain X [auth D] Focus chain Z [auth E] Interactions & Density Focus chain BA [auth F] Focus chain DA [auth G] Focus chain FA [auth H] Focus chain R [auth A] Focus chain T [auth B] Focus chain V [auth C] Focus chain X [auth D] Focus chain Z [auth E]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.30 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.7
MODEL REFINEMENT	PHENIX	1.21.2_5419

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-09-09

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM161161

Revision History (Full details and data files)

Version 1.0: 2026-09-09
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.