6BGA

2B4 I-Ek TCR-MHC complex with affinity-enhancing Velcro peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 

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This is version 2.0 of the entry. See complete history


Literature

Stress-testing the relationship between T cell receptor/peptide-MHC affinity and cross-reactivity using peptide velcro.

Gee, M.H.Sibener, L.V.Birnbaum, M.E.Jude, K.M.Yang, X.Fernandes, R.A.Mendoza, J.L.Glassman, C.R.Garcia, K.C.

(2018) Proc Natl Acad Sci U S A 115: E7369-E7378

  • DOI: 10.1073/pnas.1802746115
  • Primary Citation of Related Structures:  
    6BGA

  • PubMed Abstract: 
  • T cell receptors (TCRs) bind to peptide-major histocompatibility complex (pMHC) with low affinity ( K d ∼ μM), which is generally assumed to facilitate cross-reactive TCR "scanning" of ligands. To understand the relationship between TCR/pMHC affinity and cross-reactivity, we sought to engineer an additional weak interaction, termed "velcro," between the TCR and pMHC to probe the specificities of TCRs at relatively low and high affinities ...

    T cell receptors (TCRs) bind to peptide-major histocompatibility complex (pMHC) with low affinity ( K d ∼ μM), which is generally assumed to facilitate cross-reactive TCR "scanning" of ligands. To understand the relationship between TCR/pMHC affinity and cross-reactivity, we sought to engineer an additional weak interaction, termed "velcro," between the TCR and pMHC to probe the specificities of TCRs at relatively low and high affinities. This additional interaction was generated through an eight-amino acid peptide library covalently linked to the N terminus of the MHC-bound peptide. Velcro was selected through an affinity-based isolation and was subsequently shown to enhance the cognate TCR/pMHC affinity in a peptide-dependent manner by ∼10-fold. This was sufficient to convert a nonstimulatory ultra-low-affinity ligand into a stimulatory ligand. An X-ray crystallographic structure revealed how velcro interacts with the TCR. To probe TCR cross-reactivity, we screened TCRs against yeast-displayed pMHC libraries with and without velcro, and found that the peptide cross-reactivity profiles of low-affinity ( K d > 100 μM) and high-affinity ( K d ∼ μM) TCR/pMHC interactions are remarkably similar. The conservation of recognition of the TCR for pMHC across affinities reveals the nature of low-affinity ligands for which there are important biological functions and has implications for understanding the specificities of affinity-matured TCRs.


    Organizational Affiliation

    Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
H-2 class II histocompatibility antigen, E-K alpha chainA204Mus musculusMutation(s): 0 
UniProt
Find proteins for P04224 (Mus musculus)
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Go to UniProtKB:  P04224
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UniProt GroupP04224
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
2B4 peptide,MHC I-Ek B chainB233Mus musculusMutation(s): 0 
Gene Names: H2-Eb1
UniProt & NIH Common Fund Data Resources
Find proteins for Q31163 (Mus musculus)
Explore Q31163 
Go to UniProtKB:  Q31163
IMPC:  MGI:95901
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UniProt GroupQ31163
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
T cell receptor 2B4 alpha chainC220Mus musculusMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
T cell receptor 2B4 beta chainD255Mus musculusMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Velcro peptideE15synthetic constructMutation(s): 0 
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Oligosaccharides

Help

Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranoseF, G 2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G86851RC
GlyCosmos:  G86851RC
GlyGen:  G86851RC
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
M [auth B]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
J [auth A],
K [auth A],
L [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 
  • Space Group: I 1 2 1
  • Diffraction Data DOI: 10.15785/SBGRID/515 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.107α = 90
b = 58.851β = 91.71
c = 224.619γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI103867
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI045757
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI057229

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-18
    Type: Initial release
  • Version 1.1: 2018-08-01
    Changes: Data collection, Database references
  • Version 1.2: 2018-08-08
    Changes: Data collection, Database references
  • Version 1.3: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.4: 2019-12-11
    Changes: Author supporting evidence, Data collection
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary