2FXU | pdb_00002fxu

X-ray Structure of Bistramide A- Actin Complex at 1.35 A resolution.

• PDB DOI: https://doi.org/10.2210/pdb2FXU/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Oryctolagus cuniculus
• Mutation(s): Yes 


• Deposited: 2006-02-06 Released: 2006-03-07 
• Deposition Author(s): Rizvi, S.A., Tereshko, V., Kossiakoff, A.A., Kozmin, S.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 
  0.201 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

Literature

Structure of bistramide a-actin complex at a 1.35 A resolution

Rizvi, S.A., Tereshko, V., Kossiakoff, A.A., Kozmin, S.A.

(2006) J Am Chem Soc 128: 3882-3883

• PubMed: 16551075 
• DOI: https://doi.org/10.1021/ja058319c
• Primary Citation Related Structures: 
  2FXU


• PubMed Abstract: 
  

  Bistramide A is a highly potent antiproliferative marine natural product from Lissoclinum bistratum. We have previously established actin as the primary cellular receptor of bistramide A. We report herein the X-ray structure of bistramide A bound to monomeric actin at a resolution of 1.35 A. The most notable aspect of the bistramide A-actin structure is an extensive hydrogen-bonding network established upon a deep penetration of the central segment of bistramide A into the actin-binding cleft between subdomains 1 and 3. The structure presents the first insight into the observed ability of bistramide A to modulate G-actin polymerization. The structural information combined with our ability to chemically modify the bistramide framework provides the basis for rational development of a series of new synthetic analogues as useful probes for studying actin cytoskeleton and as potential therapeutic leads.

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Organizational Affiliation: 
• Department of Chemistry, University of Chicago, Chicago, Illinois 60637, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 43.25 kDa 
• Atom Count: 3,354 
• Modeled Residue Count: 361 
• Deposited Residue Count: 375 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin, alpha skeletal muscle	A	375	Oryctolagus cuniculus	Mutation(s): 1  EC: 3.6.4
UniProt
Find proteins for P68135 (Oryctolagus cuniculus) Explore P68135  Go to UniProtKB:  P68135

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BID	G [auth A]	BISTRAMIDE A C40 H68 N2 O8 HXZRMADPDYFMEB-CPBPHPDTSA-N
ATP	F [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
CA	B [auth A], C [auth A], D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-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: 1.35 Å
• R-Value Free:  0.201 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.125	α = 90
b = 56.513	β = 94.56
c = 101.652	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-03-07 
Deposition Author(s): Rizvi, S.A., Tereshko, V., Kossiakoff, A.A., Kozmin, S.A.

Revision History  

• Version 1.0: 2006-03-07
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary