Biological Assembly 1  

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

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

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

Macromolecule Content

• Total Structure Weight: 75.41 kDa 
• Atom Count: 4057 
• Modelled Residue Count: 502 
• Deposited Residue Count: 674 
• Unique protein chains: 2

3TU5

Actin complex with Gelsolin Segment 1 fused to Cobl segment

• PDB DOI: 10.2210/pdb3TU5/pdb

• Classification: STRUCTURAL PROTEIN/ACTIN-BINDING PROTEIN
• Organism(s): Oryctolagus cuniculus, Homo sapiens, Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-09-15 Released: 2012-09-26 
• Deposition Author(s): Kudryashov, D.S., Sawaya, M.R., Durer, Z.A.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.204 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 

Literature

Structural States and dynamics of the d-loop in actin.

Durer, Z.A., Kudryashov, D.S., Sawaya, M.R., Altenbach, C., Hubbell, W., Reisler, E.

(2012) Biophys J 103: 930-939

• PubMed: 23009842 
• DOI: 10.1016/j.bpj.2012.07.030
• Primary Citation of Related Structures:  
  3TU5


• PubMed Abstract: 
  

Conformational changes induced by ATP hydrolysis on actin are involved in the regulation of complex actin networks. Previous structural and biochemical data implicate the DNase I binding loop (D-loop) of actin in such nucleotide-dependent changes. Here, we investigated the structural and conformational states of the D-loop (in solution) using cysteine scanning mutagenesis and site-directed labeling. The reactivity of D-loop cysteine mutants toward acrylodan and the mobility of spin labels on these mutants do not show patterns of an α-helical structure in monomeric and filamentous actin, irrespective of the bound nucleotide. Upon transition from monomeric to filamentous actin, acrylodan emission spectra and electron paramagnetic resonance line shapes of labeled mutants are blue-shifted and more immobilized, respectively, with the central residues (residues 43-47) showing the most drastic changes. Moreover, complex electron paramagnetic resonance line shapes of spin-labeled mutants suggest several conformational states of the D-loop. Together with a new (to our knowledge) actin crystal structure that reveals the D-loop in a unique hairpin conformation, our data suggest that the D-loop equilibrates in F-actin among different conformational states irrespective of the nucleotide state of actin.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin, alpha skeletal muscle	A	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,Protein cordon-bleu,Thymosin beta-4	B	297	Homo sapiens, Mus musculus	Mutation(s): 0  Gene Names: GSN, Cobl, Kiaa0633, TMSB4X, TB4X, THYB4, TMSB4
UniProt & NIH Common Fund Data Resources
Find proteins for Q5NBX1 (Mus musculus) Explore Q5NBX1  Go to UniProtKB:  Q5NBX1
Find proteins for P62328 (Homo sapiens) Explore P62328  Go to UniProtKB:  P62328
PHAROS:  P62328
Find proteins for P06396 (Homo sapiens) Explore P06396  Go to UniProtKB:  P06396
PHAROS:  P06396
UniProt Groups	P06396Q5NBX1P62328

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	D [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MPD	E [auth A], F [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
CA	C [auth A], G [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.204 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.184	α = 90
b = 71.184	β = 90
c = 222.244	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-09-15 
• Released Date: 2012-09-26 
Deposition Author(s): Kudryashov, D.S., Sawaya, M.R., Durer, Z.A.O.

Revision History  

• Version 1.0: 2012-09-26
  Type: Initial release
  
• Version 1.1: 2012-10-10
  Changes: Database references
• Version 1.2: 2017-06-07
  Changes: Database references