9DUU

Cryo-EM structure of recombinant wildtype ACTA1 phalloidin-stabilized F-actin

PDB DOI: https://doi.org/10.2210/pdb9DUU/pdb
EM Map EMD-47179: EMDB EMDataResource

Classification: STRUCTURAL PROTEIN
Organism(s): Homo sapiens, Amanita phalloides
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2024-10-04 Released: 2024-10-23
Deposition Author(s): Garg, A., Greenberg, M.J., Zhang, R.
Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Leducq Foundation, Burroughs Wellcome Fund, Childrens Discovery Institute of Washington University and St. Louis Childrens Hospital

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.40 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Dilated cardiomyopathy-associated skeletal muscle actin (ACTA1) mutation R256H disrupts actin structure and function and causes cardiomyocyte hypocontractility

Garg, A., Jansen, S., Greenberg, L., Zhang, R., Lavine, K.J., Greenberg, M.J.

To be published.

Macromolecule Content

Total Structure Weight: 259.63 kDa
Atom Count: 17,953
Modelled Residue Count: 2,275
Deposited Residue Count: 2,299
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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	375	Homo sapiens	Mutation(s): 0 Gene Names: ACTA1, ACTA EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for P68133 (Homo sapiens) Explore P68133 Go to UniProtKB: P68133
PHAROS: P68133 GTEx: ENSG00000143632
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68133
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
phalloidin	G [auth M] H [auth N] I [auth O] J [auth P] K [auth Q] G [auth M], H [auth N], I [auth O], J [auth P], K [auth Q], L [auth R], M [auth S]	7	Amanita phalloides	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 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 N [auth A] SDF format, chain P [auth B] SDF format, chain R [auth C] SDF format, chain T [auth D] SDF format, chain V [auth E] SDF format, chain X [auth F] MOL2 format, chain N [auth A] MOL2 format, chain P [auth B] MOL2 format, chain R [auth C] MOL2 format, chain T [auth D] MOL2 format, chain V [auth E] MOL2 format, chain X [auth F] mmCIF format, chain N [auth A] mmCIF format, chain P [auth B] mmCIF format, chain R [auth C] mmCIF format, chain T [auth D] mmCIF format, chain V [auth E] mmCIF format, chain X [auth F]	N [auth A] P [auth B] R [auth C] T [auth D] V [auth E] N [auth A], P [auth B], R [auth C], T [auth D], V [auth E], X [auth F]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain N [auth A] Focus chain P [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain V [auth E] Focus chain X [auth F] Interactions & Density Focus chain N [auth A] Focus chain P [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain V [auth E] Focus chain X [auth F]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain Q [auth B] SDF format, chain S [auth C] SDF format, chain U [auth D] SDF format, chain W [auth E] SDF format, chain Y [auth F] MOL2 format, chain O [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth C] MOL2 format, chain U [auth D] MOL2 format, chain W [auth E] MOL2 format, chain Y [auth F] mmCIF format, chain O [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain S [auth C] mmCIF format, chain U [auth D] mmCIF format, chain W [auth E] mmCIF format, chain Y [auth F]	O [auth A] Q [auth B] S [auth C] U [auth D] W [auth E] O [auth A], Q [auth B], S [auth C], U [auth D], W [auth E], Y [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Focus chain Q [auth B] Focus chain S [auth C] Focus chain U [auth D] Focus chain W [auth E] Focus chain Y [auth F] Interactions & Density Focus chain O [auth A] Focus chain Q [auth B] Focus chain S [auth C] Focus chain U [auth D] Focus chain W [auth E] Focus chain Y [auth F]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HIC Query on HIC	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₇ H₁₁ N₃ O₂		HIS
HYP Query on HYP	G [auth M] H [auth N] I [auth O] J [auth P] K [auth Q] G [auth M], H [auth N], I [auth O], J [auth P], K [auth Q], L [auth R], M [auth S]	L-PEPTIDE LINKING	C₅ H₉ N O₃		PRO

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.40 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	3.4
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-10-23

Deposition Author(s):

Garg, A.

Greenberg, M.J.

Zhang, R.

Funding Organization	Location	Grant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	HL007081
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	HL007227
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	GM138448
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM138854
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	HL141086
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	HL141086
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	HL138466
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	HL139714
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	HL151078
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	HL161185
Leducq Foundation	France	20CVD02
Burroughs Wellcome Fund	United States	1014782
Childrens Discovery Institute of Washington University and St. Louis Childrens Hospital	United States	CH-II-2015-462
Childrens Discovery Institute of Washington University and St. Louis Childrens Hospital	United States	CH-II-2017-628
Childrens Discovery Institute of Washington University and St. Louis Childrens Hospital	United States	PM-LI-2019-829