3ULA

Crystal structure of the TV3 mutant F63W-MD-2-Eritoran complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.341 
  • R-Value Work: 0.306 

wwPDB Validation   3D Report Full Report



Literature

Structure-Based Rational Design of a Toll-like Receptor 4 (TLR4) Decoy Receptor with High Binding Affinity for a Target Protein.

Han, J., Kim, H.J., Lee, S.C., Hong, S., Park, K., Jeon, Y.H., Kim, D., Cheong, H.K., Kim, H.S.

(2012) PLoS One 7: e30929-e30929

  • DOI: 10.1371/journal.pone.0030929
  • Primary Citation of Related Structures:  
    3ULA, 3UL7, 3UL8, 3UL9

  • PubMed Abstract: 

    • Repeat proteins are increasingly attracting much attention as alternative scaffolds to immunoglobulin antibodies due to their unique structural features. Nonetheless, engineering interaction interface and understanding molecular basis for affinity matura ...

    Repeat proteins are increasingly attracting much attention as alternative scaffolds to immunoglobulin antibodies due to their unique structural features. Nonetheless, engineering interaction interface and understanding molecular basis for affinity maturation of repeat proteins still remain a challenge. Here, we present a structure-based rational design of a repeat protein with high binding affinity for a target protein. As a model repeat protein, a Toll-like receptor4 (TLR4) decoy receptor composed of leucine-rich repeat (LRR) modules was used, and its interaction interface was rationally engineered to increase the binding affinity for myeloid differentiation protein 2 (MD2). Based on the complex crystal structure of the decoy receptor with MD2, we first designed single amino acid substitutions in the decoy receptor, and obtained three variants showing a binding affinity (K(D)) one-order of magnitude higher than the wild-type decoy receptor. The interacting modes and contributions of individual residues were elucidated by analyzing the crystal structures of the single variants. To further increase the binding affinity, single positive mutations were combined, and two double mutants were shown to have about 3000- and 565-fold higher binding affinities than the wild-type decoy receptor. Molecular dynamics simulations and energetic analysis indicate that an additive effect by two mutations occurring at nearby modules was the major contributor to the remarkable increase in the binding affinities.

    Organizational Affiliation: 

    Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Yuseong-gu, Daejeon, Korea.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Toll-like receptor 4, Variable lymphocyte receptor B A, C279Homo sapiens, Eptatretus burgeri
This entity is chimeric		Mutation(s): 1 
Gene Names: TLR4, VLRB
EC: 3.2.2.6
Find proteins for O00206 (Homo sapiens)
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Go to UniProtKB:  O00206
NIH Common Fund Data Resources
PHAROS:  O00206
GTEx:  ENSG00000136869
Find proteins for Q4G1L2 (Eptatretus burgeri)
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Go to UniProtKB:  Q4G1L2
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Lymphocyte antigen 96 B, D142Homo sapiensMutation(s): 0 
Gene Names: LY96, ESOP1, MD2
Find proteins for Q9Y6Y9 (Homo sapiens)
Explore Q9Y6Y9 
Go to UniProtKB:  Q9Y6Y9
NIH Common Fund Data Resources
PHAROS:  Q9Y6Y9
GTEx:  ENSG00000154589
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, F
3 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
E55
Query on E55
Download Ideal Coordinates CCD File 
A, C
3-O-DECYL-2-DEOXY-6-O-{2-DEOXY-3-O-[(3R)-3-METHOXYDECYL]-6-O-METHYL-2-[(11Z)-OCTADEC-11-ENOYLAMINO]-4-O-PHOSPHONO-BETA-D-GLUCOPYRANOSYL}-2-[(3-OXOTETRADECANOYL)AMINO]-1-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE
C66 H126 N2 O19 P2
BPSMYQFMCXXNPC-MFCPCZTFSA-N		 Ligand Interaction
NAG
Query on NAG
Download Ideal Coordinates CCD File 
A, C
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
E55IC50:  1.5   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.341 
  • R-Value Work: 0.306 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.21α = 90
b = 126.935β = 90
c = 129.506γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-04-04
    Type: Initial release
  • Version 1.1: 2013-10-09
    Changes: Derived calculations
  • Version 1.2: 2017-08-23
    Changes: Advisory, Refinement description, Source and taxonomy
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary