8F8Q

Cryo-EM structure of the CapZ-capped barbed end of F-actin

PDB DOI: https://doi.org/10.2210/pdb8F8Q/pdb
EM Map EMD-28933: EMDB EMDataResource

Classification: STRUCTURAL PROTEIN
Organism(s): Oryctolagus cuniculus, Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-11-22 Released: 2023-06-07
Deposition Author(s): Carman, P.J., Barrie, K.R., Dominguez, R.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.79 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structures of the free and capped ends of the actin filament.

Carman, P.J., Barrie, K.R., Rebowski, G., Dominguez, R.

(2023) Science 380: 1287-1292

PubMed: 37228182 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1126/science.adg6812
Primary Citation of Related Structures:
8F8P, 8F8Q, 8F8R, 8F8S, 8F8T

PubMed Abstract:
The barbed and pointed ends of the actin filament (F-actin) are the sites of growth and shrinkage and the targets of capping proteins that block subunit exchange, including CapZ at the barbed end and tropomodulin at the pointed end. We describe cryo-electron microscopy structures of the free and capped ends of F-actin. Terminal subunits at the free barbed end adopt a "flat" F-actin conformation. CapZ binds with minor changes to the barbed end but with major changes to itself. By contrast, subunits at the free pointed end adopt a "twisted" monomeric actin (G-actin) conformation. Tropomodulin binding forces the second subunit into an F-actin conformation. The structures reveal how the ends differ from the middle in F-actin and how these differences control subunit addition, dissociation, capping, and interactions with end-binding proteins.

Organizational Affiliation

Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.

Macromolecule Content

Total Structure Weight: 319.59 kDa
Atom Count: 22,006
Modelled Residue Count: 2,778
Deposited Residue Count: 2,824
Unique protein chains: 3

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, B, C, D, E A, B, C, D, E, F	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68135
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
F-actin-capping protein subunit alpha-1	G	286	Homo sapiens	Mutation(s): 0 Gene Names: CAPZA1
UniProt & NIH Common Fund Data Resources
Find proteins for P52907 (Homo sapiens) Explore P52907 Go to UniProtKB: P52907
PHAROS: P52907 GTEx: ENSG00000116489
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P52907
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
F-actin-capping protein subunit beta	H	276	Homo sapiens	Mutation(s): 0 Gene Names: CAPZB
UniProt & NIH Common Fund Data Resources
Find proteins for P47756 (Homo sapiens) Explore P47756 Go to UniProtKB: P47756
PHAROS: P47756 GTEx: ENSG00000077549
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P47756
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 I [auth A] SDF format, chain K [auth B] SDF format, chain O [auth D] SDF format, chain S [auth F] SDF format, chain M [auth C] SDF format, chain Q [auth E] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain O [auth D] MOL2 format, chain S [auth F] MOL2 format, chain M [auth C] MOL2 format, chain Q [auth E] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain O [auth D] mmCIF format, chain S [auth F] mmCIF format, chain M [auth C] mmCIF format, chain Q [auth E]	I [auth A] K [auth B] M [auth C] O [auth D] Q [auth E] I [auth A], K [auth B], M [auth C], O [auth D], Q [auth E], S [auth F]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain S [auth F] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain S [auth F]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain T [auth F] SDF format, chain J [auth A] SDF format, chain P [auth D] SDF format, chain R [auth E] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain T [auth F] MOL2 format, chain J [auth A] MOL2 format, chain P [auth D] MOL2 format, chain R [auth E] mmCIF format, chain L [auth B] mmCIF format, chain N [auth C] mmCIF format, chain T [auth F] mmCIF format, chain J [auth A] mmCIF format, chain P [auth D] mmCIF format, chain R [auth E]	J [auth A] L [auth B] N [auth C] P [auth D] R [auth E] J [auth A], L [auth B], N [auth C], P [auth D], R [auth E], T [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain T [auth F] Interactions & Density Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain T [auth F]

Modified Residues 1 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

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.79 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC	4.0.0

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-06-07

Deposition Author(s):

Carman, P.J.

Barrie, K.R.

Dominguez, R.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM073791
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM136511
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	HL156431