Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 57710.95 
• Atom Count: 4114 
• Residue Count: 503 
• Unique protein chains: 2

3CIP

Complex of Dictyostelium Discoideum Actin with Gelsolin

• DOI: 10.2210/pdb3CIP/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Homo sapiens, Dictyostelium discoideum
• Expression System: Escherichia coli


• Deposited: 2008-03-11 Released: 2008-08-19 
• Deposition Author(s): Baek, K., Dominguez, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.6 Å
• R-Value Free: 0.197 
• R-Value Work: 0.150 

Literature

Modulation of actin structure and function by phosphorylation of Tyr-53 and profilin binding.

Baek, K., Liu, X., Ferron, F., Shu, S., Korn, E.D., Dominguez, R.

(2008) Proc.Natl.Acad.Sci.Usa 105: 11748-11753

• PubMed: 18689676 
• DOI: 10.1073/pnas.0805852105
• Primary Citation of Related Structures:  
  3CI5, 3CHW


• PubMed Abstract: 
  

On starvation, Dictyostelium cells aggregate to form multicellular fruiting bodies containing spores that germinate when transferred to nutrient-rich medium. This developmental cycle correlates with the extent of actin phosphorylation at Tyr-53 (pY53-actin), which is low in vegetative cells but high in viable mature spores. Here we describe high-resolution crystal structures of pY53-actin and unphosphorylated actin in complexes with gelsolin segment 1 and profilin. In the structure of pY53-actin, the phosphate group on Tyr-53 makes hydrogen-bonding interactions with residues of the DNase I-binding loop (D-loop) of actin, resulting in a more stable conformation of the D-loop than in the unphosphorylated structures. A more rigidly folded D-loop may explain some of the previously described properties of pY53-actin, including its increased critical concentration for polymerization, reduced rates of nucleation and pointed end elongation, and weak affinity for DNase I. We show here that phosphorylation of Tyr-53 inhibits subtilisin cleavage of the D-loop and reduces the rate of nucleotide exchange on actin. The structure of profilin-Dictyostelium-actin is strikingly similar to previously determined structures of profilin-beta-actin and profilin-alpha-actin. By comparing this representative set of profilin-actin structures with other structures of actin, we highlight the effects of profilin on the actin conformation. In the profilin-actin complexes, subdomains 1 and 3 of actin close around profilin, producing a 4.7 degrees rotation of the two major domains of actin relative to each other. As a result, the nucleotide cleft becomes moderately more open in the profilin-actin complex, probably explaining the stimulation of nucleotide exchange on actin by profilin.

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Organizational Affiliation: 

Department of Physiology, 3700 Hamilton Walk, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6085, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Major actin	A	375	Dictyostelium discoideum	Mutation(s): 0  Gene Names: act1, act2, act4, act5, act6, act7, act8, act9, act11, act12, act13, act14, act15, act16, act19, act20, act21 (act1a, act2-1, actA8, actB1, actA1, actM6)
Find proteins for P07830 (Dictyostelium discoideum) Go to UniProtKB:  P07830

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Gelsolin	G	128	Homo sapiens	Mutation(s): 0  Gene Names: GSN
Find proteins for P06396 (Homo sapiens) Go to Gene View: GSN Go to UniProtKB:  P06396

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ATP	A	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
SO4	A, G	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	A, G	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	G	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HIC	A	L-PEPTIDE LINKING	C7 H11 N3 O2		HIS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.6 Å
• R-Value Free: 0.197 
• R-Value Work: 0.150 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 178.881	α = 90.00
b = 69.172	β = 104.36
c = 56.564	γ = 90.00

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data collection
SCALEPACK	data scaling
DENZO	data reduction
PDB_EXTRACT	data extraction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-03-11 
• Released Date: 2008-08-19 
• Deposition Author(s): Baek, K., Dominguez, R.

Revision History 

• Version 1.0: 2008-08-19
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Non-polymer description, Version format compliance
• Version 1.2: 2017-10-25
  Type: Refinement description