Biological Assembly 1  

 3D View: Structure | Electron Density

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: 45.63 kDa 
• Atom Count: 3518 
• Residue Count: 421 
• Unique protein chains: 2

2G60

Structure of anti-FLAG M2 Fab domain

• DOI: 10.2210/pdb2G60/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Mutation(s): No 


• Deposited: 2006-02-23 Released: 2006-09-12 
• Deposition Author(s): Roosild, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.278 
• R-Value Work: 0.235 
• R-Value Observed: 0.237 

Literature

Structure of anti-FLAG M2 Fab domain and its use in the stabilization of engineered membrane proteins.

Roosild, T.P., Castronovo, S., Choe, S.

(2006) Acta Crystallogr Sect F Struct Biol Cryst Commun 62: 835-839

• PubMed: 16946459 
• DOI: 10.1107/S1744309106029125
• Primary Citation of Related Structures:  
  2G60


• PubMed Abstract: 
  

The inherent difficulties of stabilizing detergent-solubilized integral membrane proteins for biophysical or structural analysis demand the development of new methodologies to improve success rates. One proven strategy is the use of antibody fragments to increase the ;soluble' portion of any membrane protein, but this approach is limited by the difficulties and expense associated with producing monoclonal antibodies to an appropriate exposed epitope on the target protein. Here, the stabilization of a detergent-solubilized K(+) channel protein, KvPae, by engineering a FLAG-binding epitope into a known loop region of the protein and creating a complex with Fab fragments from commercially available anti-FLAG M2 monoclonal antibodies is reported. Although well diffracting crystals of the complex have not yet been obtained, during the course of crystallization trials the structure of the anti-FLAG M2 Fab domain was solved to 1.86 A resolution. This structure, which should aid future structure-determination efforts using this approach by facilitating molecular-replacement phasing, reveals that the binding pocket appears to be specific only for the first four amino acids of the traditional FLAG epitope, namely DYKD. Thus, the use of antibody fragments for improving the stability of target proteins can be rapidly applied to the study of membrane-protein structure by placing the short DKYD motif within a predicted peripheral loop of that protein and utilizing commercially available anti-FLAG M2 antibody fragments.

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Organizational Affiliation: 

Structural Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
anti-FLAG M2 Fab light chain	L	216	Mus musculus	Mutation(s): 0
Find proteins for Q65ZC0 (Mus musculus) Explore Q65ZC0  Go to UniProtKB:  Q65ZC0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
anti-FLAG M2 Fab heavy chain	H	215	Mus musculus	Mutation(s): 0
Find proteins for Q5BJZ2 (Rattus norvegicus) Explore Q5BJZ2  Go to UniProtKB:  Q5BJZ2

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.278 
• R-Value Work: 0.235 
• R-Value Observed: 0.237 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.36	α = 90
b = 133.76	β = 90
c = 41.48	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-02-23 
• Released Date: 2006-09-12 
Deposition Author(s): Roosild, T.P.

Revision History 

• Version 1.0: 2006-09-12
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description