4K3H

Immunoglobulin lambda variable domain L5(L89S) fluorogen activationg protein in complex with malachite green

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

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Literature

Malachite Green Mediates Homodimerization of Antibody VL Domains to Form a Fluorescent Ternary Complex with Singular Symmetric Interfaces.

Szent-Gyorgyi, C., Stanfield, R.L., Andreko, S., Dempsey, A., Ahmed, M., Capek, S., Waggoner, A.S., Wilson, I.A., Bruchez, M.P.

(2013) J Mol Biol 425: 4595-4613

  • DOI: 10.1016/j.jmb.2013.08.014
  • Primary Citation of Related Structures:  
    4K3G, 4K3H

  • PubMed Abstract: 

    • We report that a symmetric small-molecule ligand mediates the assembly of antibody light chain variable domains (VLs) into a correspondent symmetric ternary complex with novel interfaces. The L5* fluorogen activating protein is a VL domain that binds malachite green (MG) dye to activate intense fluorescence ...

    We report that a symmetric small-molecule ligand mediates the assembly of antibody light chain variable domains (VLs) into a correspondent symmetric ternary complex with novel interfaces. The L5* fluorogen activating protein is a VL domain that binds malachite green (MG) dye to activate intense fluorescence. Crystallography of liganded L5* reveals a 2:1 protein:ligand complex with inclusive C2 symmetry, where MG is almost entirely encapsulated between an antiparallel arrangement of the two VL domains. Unliganded L5* VL domains crystallize as a similar antiparallel VL/VL homodimer. The complementarity-determining regions are spatially oriented to form novel VL/VL and VL/ligand interfaces that tightly constrain a propeller conformer of MG. Binding equilibrium analysis suggests highly cooperative assembly to form a very stable VL/MG/VL complex, such that MG behaves as a strong chemical inducer of dimerization. Fusion of two VL domains into a single protein tightens MG binding over 1000-fold to low picomolar affinity without altering the large binding enthalpy, suggesting that bonding interactions with ligand and restriction of domain movements make independent contributions to binding. Fluorescence activation of a symmetrical fluorogen provides a selection mechanism for the isolation and directed evolution of ternary complexes where unnatural symmetric binding interfaces are favored over canonical antibody interfaces. As exemplified by L5*, these self-reporting complexes may be useful as modulators of protein association or as high-affinity protein tags and capture reagents.

    Organizational Affiliation: 

    Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, PA 15213, USA. Electronic address: css@andrew.cmu.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Immunoglobulin lambda variable domain L5(L89S)
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H
118Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1OM
Query on 1OM
Download Ideal Coordinates CCD File 
I [auth A],
O [auth D],
R [auth E],
W [auth G]		4-{bis[4-(dimethylamino)phenyl]methyl}phenol
C23 H26 N2 O
ZTXGOUSDKAXJJB-UHFFFAOYSA-N		 Ligand Interaction
MAN
Query on MAN
Download Ideal Coordinates CCD File 
AA [auth H],
Q [auth D],
U [auth E]		alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth C],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth C],
P [auth D],
S [auth E],
T [auth E],
V [auth F],
X [auth G],
Y [auth H],
Z [auth H]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
1OM Binding MOAD:  4K3H Kd: 0.09 (nM) from 1 assay(s)
PDBBind:  4K3H Kd: 140 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.11α = 90
b = 94.11β = 90
c = 175.8γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-09
    Type: Initial release
  • Version 1.1: 2013-11-13
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary