8RMO

Crystal structure of anti-FLAG M2 Fab fragment bound to FLAG-tag peptide epitope

PDB DOI: https://doi.org/10.2210/pdb8RMO/pdb

Classification: IMMUNE SYSTEM
Organism(s): synthetic construct, Mus musculus
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2024-01-08 Released: 2024-04-03
Deposition Author(s): Beugelink, J.W., Janssen, B.J.C., Pronker, M.F.
Funding Organization(s): Netherlands Organisation for Scientific Research (NWO)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.16 Å
R-Value Free: 0.185
R-Value Work: 0.158

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structural basis for recognition of the FLAG-tag by anti-FLAG M2.

Wouter Beugelink, J., Sweep, E., Janssen, B.J.C., Snijder, J., Pronker, M.F.

(2024) J Mol Biol : 168649-168649

PubMed: 38852931 Search on PubMed
DOI: https://doi.org/10.1016/j.jmb.2024.168649
Primary Citation of Related Structures:
8RMO

PubMed Abstract:
The FLAG-tag/anti-FLAG system is a widely used biochemical tool for protein detection and purification. Anti-FLAG M2 is the most popular antibody against the FLAG-tag, due to its ease of use, versatility, and availability in pure form or as bead conjugate. M2 binds N-terminal, C-terminal and internal FLAG-tags and binding is calcium-independent, but the molecular basis for the FLAG-tag specificity and recognition remains unresolved. Here we present an atomic resolution (1.17 Å) structure of the FLAG peptide in complex with the Fab of anti-FLAG M2, revealing key binding determinants. Five of the eight FLAG peptide residues form direct interactions with paratope residues. The FLAG peptide adopts a 3 ₁₀ helix conformation in complex with the Fab. These structural insights allowed us to rationally introduce point mutations on both the peptide and antibody side. We tested these by surface plasmon resonance, leading us to propose a shorter yet equally binding version of the FLAG-tag for the M2 antibody.

Organizational Affiliation

Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands.

Macromolecule Content

Total Structure Weight: 50.02 kDa
Atom Count: 4,020
Modelled Residue Count: 423
Deposited Residue Count: 455
Unique protein chains: 3

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FLAG-tag	A [auth F]	8	synthetic construct	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
anti-FLAG M2 heavy chain	B [auth H]	228	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
anti-FLAG M2 light chain	C [auth L]	219	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth H] SDF format, chain E [auth H] SDF format, chain F [auth H] MOL2 format, chain D [auth H] MOL2 format, chain E [auth H] MOL2 format, chain F [auth H]	D [auth H], E [auth H], F [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth H] Focus chain E [auth H] Focus chain F [auth H] Interactions & Density Focus chain D [auth H] Focus chain E [auth H] Focus chain F [auth H]