4PKH

Complex of ADP-actin With the N-terminal Actin-Binding Domain of Tropomodulin

• PDB DOI:  https://doi.org/10.2210/pdb4PKH/pdb

• Classification: Contractile Protein/Actin-Binding Protein
• Organism(s): Oryctolagus cuniculus, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-05-14 Released: 2014-07-30 
• Deposition Author(s): Rao, J.N., Dominguez, R.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.326 
• R-Value Work: 0.274 
• R-Value Observed: 0.275 

Literature

Actin cytoskeleton. Mechanism of actin filament pointed-end capping by tropomodulin.

Rao, J.N., Madasu, Y., Dominguez, R.

(2014) Science 345: 463-467

• PubMed: 25061212 
• DOI: https://doi.org/10.1126/science.1256159
• Primary Citation of Related Structures:  
  4PKG, 4PKH, 4PKI


• PubMed Abstract: 
  

Proteins that cap the ends of the actin filament are essential regulators of cytoskeleton dynamics. Whereas several proteins cap the rapidly growing barbed end, tropomodulin (Tmod) is the only protein known to cap the slowly growing pointed end. The lack of structural information severely limits our understanding of Tmod's capping mechanism. We describe crystal structures of actin complexes with the unstructured amino-terminal and the leucine-rich repeat carboxy-terminal domains of Tmod. The structures and biochemical analysis of structure-inspired mutants showed that one Tmod molecule interacts with three actin subunits at the pointed end, while also contacting two tropomyosin molecules on each side of the filament. We found that Tmod achieves high-affinity binding through several discrete low-affinity interactions, which suggests a mechanism for controlled subunit exchange at the pointed end.

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Organizational Affiliation: 

Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 253.88 kDa 
• Atom Count: 16,459 
• Modelled Residue Count: 2,003 
• Deposited Residue Count: 2,252 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin, alpha skeletal muscle	A, C [auth D], E [auth F], G [auth I]	377	Oryctolagus cuniculus	Mutation(s): 0  Gene Names: ACTA1, ACTA
UniProt
Find proteins for P68135 (Oryctolagus cuniculus) Explore P68135  Go to UniProtKB:  P68135

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Gelsolin,Tropomodulin-1 chimera	B, D [auth E], F [auth G], H [auth J]	186	Homo sapiens	Mutation(s): 0  Gene Names: GSN, TMOD1, D9S57E, TMOD
UniProt & NIH Common Fund Data Resources
Find proteins for P28289 (Homo sapiens) Explore P28289  Go to UniProtKB:  P28289
PHAROS:  P28289
Find proteins for P06396 (Homo sapiens) Explore P06396  Go to UniProtKB:  P06396
PHAROS:  P06396
UniProt Groups	P28289P06396

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	I [auth A], M [auth D], Q [auth F], U [auth I]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
CA	J [auth A], K [auth A], L [auth B], N [auth D], O [auth D], P [auth E], R [auth F], S [auth F], T [auth G], V [auth I], W [auth I], X [auth J]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.326 
• R-Value Work: 0.274 
• R-Value Observed: 0.275 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.222	α = 90
b = 135.136	β = 94.41
c = 140.549	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2014-07-30 
Deposition Author(s): Rao, J.N., Dominguez, R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM073791

Revision History  

• Version 1.0: 2014-07-30
  Type: Initial release
  
• Version 1.1: 2014-08-06
  Changes: Database references
• Version 1.2: 2017-09-06
  Changes: Advisory, Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description