Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 111.72 kDa 
• Atom Count: 4753 
• Modelled Residue Count: 570 
• Deposited Residue Count: 972 
• Unique protein chains: 1

3HAJ

Crystal structure of human PACSIN2 F-BAR domain (p212121 lattice)

• PDB DOI: 10.2210/pdb3HAJ/pdb

• Classification: ENDOCYTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-05-01 Released: 2009-06-16 
• Deposition Author(s): Wang, Q., Navarro, M.V.A.S., Peng, G., Rajashankar, K.R., Sondermann, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.78 Å
• R-Value Free: 0.274 
• R-Value Work: 0.224 
• R-Value Observed: 0.227 

Literature

Molecular mechanism of membrane constriction and tubulation mediated by the F-BAR protein Pacsin/Syndapin.

Wang, Q., Navarro, M.V., Peng, G., Molinelli, E., Lin Goh, S., Judson, B.L., Rajashankar, K.R., Sondermann, H.

(2009) Proc Natl Acad Sci U S A 106: 12700-12705

• PubMed: 19549836 
• DOI: 10.1073/pnas.0902974106
• Primary Citation of Related Structures:  
  3HAH, 3HAI, 3HAJ


• PubMed Abstract: 
  

Peripheral membrane proteins of the Bin/amphiphysin/Rvs (BAR) and Fer-CIP4 homology-BAR (F-BAR) family participate in cellular membrane trafficking and have been shown to generate membrane tubules. The degree of membrane bending appears to be encoded in the structure and immanent curvature of the particular protein domains, with BAR and F-BAR domains inducing high- and low-curvature tubules, respectively. In addition, oligomerization and the formation of ordered arrays influences tubule stabilization. Here, the F-BAR domain-containing protein Pacsin was found to possess a unique activity, creating small tubules and tubule constrictions, in addition to the wide tubules characteristic for this subfamily. Based on crystal structures of the F-BAR domain of Pacsin and mutagenesis studies, vesiculation could be linked to the presence of unique structural features distinguishing it from other F-BAR proteins. Tubulation was suppressed in the context of the full-length protein, suggesting that Pacsin is autoinhibited in solution. The regulated deformation of membranes and promotion of tubule constrictions by Pacsin suggests a more versatile function of these proteins in vesiculation and endocytosis beyond their role as scaffold proteins.

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Organizational Affiliation: 

Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
human PACSIN2 F-BAR	A, B	486	Homo sapiens	Mutation(s): 0  Gene Names: PACSIN2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UNF0 (Homo sapiens) Explore Q9UNF0  Go to UniProtKB:  Q9UNF0
PHAROS:  Q9UNF0 GTEx:  ENSG00000100266

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A], D [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.78 Å
• R-Value Free: 0.274 
• R-Value Work: 0.224 
• R-Value Observed: 0.227 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.295	α = 90
b = 88.395	β = 90
c = 357.722	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-05-01 
• Released Date: 2009-06-16 
Deposition Author(s): Wang, Q., Navarro, M.V.A.S., Peng, G., Rajashankar, K.R., Sondermann, H.

Revision History  

• Version 1.0: 2009-06-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description