4BNE | pdb_00004bne

Pacsin2 Interacts with Membranes and Actin-Filaments

• PDB DOI: https://doi.org/10.2210/pdb4BNE/pdb

• Classification: ENDOCYTOSIS
• Organism(s): Gallus gallus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2013-05-15 Released: 2014-05-14 
• Deposition Author(s): Kostan, J., Salzer, U., Orlova, A., Toeroe, I., Hodnik, V., Schreiner, C., Merilainen, J., Nikki, M., Virtanen, I., Lehto, V.-P., Anderluh, G., Egelman, E.H., Djinovic-Carugo, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.57 Å
• R-Value Free: 
  0.222 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Literature

Direct Interaction of Actin Filaments with F-Bar Protein Pacsin2.

Kostan, J., Salzer, U., Orlova, A., Toro, I., Hodnik, V., Senju, Y., Zou, J., Schreiner, C., Steiner, J., Merilainen, J., Nikki, M., Virtanen, I., Carugo, O., Rappsilber, J., Lappalainen, P., Lehto, V., Anderluh, G., Egelman, E.H., Djinovic-Carugo, K.

(2014) EMBO Rep 15: 1154

• PubMed: 25216944 
• DOI: https://doi.org/10.15252/embr.201439267
• Primary Citation Related Structures: 
  4BNE


• PubMed Abstract: 
  

  Two mechanisms have emerged as major regulators of membrane shape: BAR domain-containing proteins, which induce invaginations and protrusions, and nuclear promoting factors, which cause generation of branched actin filaments that exert mechanical forces on membranes. While a large body of information exists on interactions of BAR proteins with membranes and regulatory proteins of the cytoskeleton, little is known about connections between these two processes. Here, we show that the F-BAR domain protein pacsin2 is able to associate with actin filaments using the same concave surface employed to bind to membranes, while some other tested N-BAR and F-BAR proteins (endophilin, CIP4 and FCHO2) do not associate with actin. This finding reveals a new level of complexity in membrane remodeling processes.

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Organizational Affiliation: 
• Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria.
Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria Department of Medical Biochemistry, Medical University of Vienna, Vienna, Austria.
Department of Biochemistry and Molecular Genetics, University of Virginia Medical Center, Charlottesville, VA, USA.
Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.
Program in Cell and Molecular Biology, Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK.
Department of Pathology, Haartman Institute, University of Helsinki, Helsinki, Finland.
Institute of Biomedicine/Anatomy, University of Helsinki, Helsinki, Finland.
Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria Department of Chemistry, University of Pavia, Pavia, Italy.
Department of Pathology, Haartman Institute, University of Helsinki, Helsinki, Finland Department of Biotechnology, Technological University of Berlin, Berlin, Germany.
Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia National Institute of Chemistry, Ljubljana, Slovenia EN-FIST Centre of Excellence, Ljubljana, Slovena.
Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 106.78 kDa 
• Atom Count: 5,056 
• Modeled Residue Count: 579 
• Deposited Residue Count: 914 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN KINASE C AND CASEIN KINASE SUBSTRATE IN NEURONS PROTEIN 2	A, B	457	Gallus gallus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for O13154 (Gallus gallus) Explore O13154  Go to UniProtKB:  O13154

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	G [auth A], K [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
SO4	C [auth A], D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.57 Å
• R-Value Free:  0.222 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.06	α = 90
b = 105.5	β = 90
c = 125.95	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-05-14 
Deposition Author(s): Kostan, J., Salzer, U., Orlova, A., Toeroe, I., Hodnik, V., Schreiner, C., Merilainen, J., Nikki, M., Virtanen, I., Lehto, V.-P., Anderluh, G., Egelman, E.H., Djinovic-Carugo, K.

Revision History  

• Version 1.0: 2014-05-14
  Type: Initial release
  
• Version 1.1: 2014-09-24
  Changes: Database references
• Version 1.2: 2014-11-19
  Changes: Database references
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other