6SSA

Human Leukocyte Antigen Class I A02 Carrying LLWNGPMQV

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report


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


Literature

Identification of a superagonist variant of the immunodominant Yellow fever virus epitope NS4b214-222by combinatorial peptide library screening.

Bovay, A., Zoete, V., Rizkallah, P.J., Beck, K., Delbreil, P., Speiser, D.E., Cole, D.K., Fuertes Marraco, S.A.

(2020) Mol Immunol 125: 43-50

  • DOI: 10.1016/j.molimm.2020.06.025
  • Primary Citation of Related Structures:  
    6SS7, 6SS8, 6SS9, 6SSA

  • PubMed Abstract: 

    • The CD8 T cell response to the HLA-A2-restricted epitope LLWNGPMAV (LLW) of the non-structural protein 4b of Yellow Fever Virus (YFV) is remarkably immunodominant, highly prevalent and powerful in YFV-vaccinated humans. Here we used a combinatorial peptide library screening in the context of an A2/LLW-specific CD8 T cell clone to identify a superagonist that features a methionine to isoleucine substitution at position 7 ...

    The CD8 T cell response to the HLA-A2-restricted epitope LLWNGPMAV (LLW) of the non-structural protein 4b of Yellow Fever Virus (YFV) is remarkably immunodominant, highly prevalent and powerful in YFV-vaccinated humans. Here we used a combinatorial peptide library screening in the context of an A2/LLW-specific CD8 T cell clone to identify a superagonist that features a methionine to isoleucine substitution at position 7. Based on in silico modeling, the functional enhancement of this LLW-7I mutation was associated with alterations in the structural dynamics of the peptide in the major histocompatibility complex (pMHC) binding with the T cell receptor (TCR). While the TCR off-rate of LLW-7I pMHC is comparable to the wild type peptide, the rigidity of the 7I peptide seems to confer less entropy loss upon TCR binding. This LLW-7I superagonist is an example of improved functionality in human CD8 T cells associated with optimized ligand rigidity for TCR binding and not with changes in TCR:pMHC off-rate kinetics.

    Organizational Affiliation: 

    Department of Oncology, Lausanne University Hospital (CHUV), Lausanne, Switzerland. Electronic address: silvia.fuertes@chuv.ch.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, A-2 alpha chainA, D, G, J276Homo sapiensMutation(s): 0 
Gene Names: HLA-A, HLAA
UniProt & NIH Common Fund Data Resources
Find proteins for P04439 (Homo sapiens)
Explore P04439 
Go to UniProtKB:  P04439
PHAROS:  P04439
GTEx:  ENSG00000206503 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04439
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinB, E, H, K100Homo sapiensMutation(s): 0 
Gene Names: B2M, CDABP0092, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61769
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
LEU-LEU-TRP-ASN-GLY-PRO-MET-GLN-VALC, F, I, L9Yellow fever virusMutation(s): 0 
EC: 3.4.21.91 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt), 2.1.1.56 (UniProt), 2.1.1.57 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for P03314 (Yellow fever virus (strain 17D vaccine))
Explore P03314 
Go to UniProtKB:  P03314
Entity Groups  
UniProt GroupP03314
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG
Download Ideal Coordinates CCD File 
BA [auth J],
O [auth B],
P [auth B],
R [auth D],
V [auth G]		DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
AA [auth J],
EA [auth K],
FA [auth K],
GA [auth K],
N [auth B],
AA [auth J],
EA [auth K],
FA [auth K],
GA [auth K],
N [auth B],
Q [auth D],
S [auth E],
U [auth G],
W [auth H],
X [auth H],
Y [auth H],
Z [auth J]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
DA [auth K],
M [auth B],
T [auth G]		1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
CA [auth K]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 
  • Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.908α = 90
b = 49.071β = 92.48
c = 169.011γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland310030B_179570

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-15
    Type: Initial release
  • Version 1.1: 2020-07-22
    Changes: Database references