7LGT

HLA-B*07:02 in complex with 229E-derived coronavirus nucleocapsid peptide N75-83


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

CD8 + T cells specific for an immunodominant SARS-CoV-2 nucleocapsid epitope cross-react with selective seasonal coronaviruses.

Lineburg, K.E.Grant, E.J.Swaminathan, S.Chatzileontiadou, D.S.M.Szeto, C.Sloane, H.Panikkar, A.Raju, J.Crooks, P.Rehan, S.Nguyen, A.T.Lekieffre, L.Neller, M.A.Tong, Z.W.M.Jayasinghe, D.Chew, K.Y.Lobos, C.A.Halim, H.Burrows, J.M.Riboldi-Tunnicliffe, A.Chen, W.D'Orsogna, L.Khanna, R.Short, K.R.Smith, C.Gras, S.

(2021) Immunity 54: 1055

  • DOI: https://doi.org/10.1016/j.immuni.2021.04.006
  • Primary Citation of Related Structures:  
    7LGD, 7LGT

  • PubMed Abstract: 

    Efforts are being made worldwide to understand the immune response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for the coronavirus disease 2019 (COVID-19) pandemic, including the impact of T cell immunity and cross-recognition with seasonal coronaviruses. Screening of SARS-CoV-2 peptide pools revealed that the nucleocapsid (N) protein induced an immunodominant response in HLA-B7 + COVID-19-recovered individuals that was also detectable in unexposed donors. A single N-encoded epitope that was highly conserved across circulating coronaviruses drove this immunodominant response. In vitro peptide stimulation and crystal structure analyses revealed T cell-mediated cross-reactivity toward circulating OC43 and HKU-1 betacoronaviruses but not 229E or NL63 alphacoronaviruses because of different peptide conformations. T cell receptor (TCR) sequencing indicated that cross-reactivity was driven by private TCR repertoires with a bias for TRBV27 and a long CDR3β loop. Our findings demonstrate the basis of selective T cell cross-reactivity for an immunodominant SARS-CoV-2 epitope and its homologs from seasonal coronaviruses, suggesting long-lasting protective immunity.


  • Organizational Affiliation

    QIMR Berghofer Centre for Immunotherapy and Vaccine Development and Translational and Human Immunology Laboratory, Department of Immunology, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, B alpha chain
A, C
278Homo sapiensMutation(s): 0 
Gene Names: HLA-BHLAB
UniProt & NIH Common Fund Data Resources
Find proteins for P01889 (Homo sapiens)
Explore P01889 
Go to UniProtKB:  P01889
PHAROS:  P01889
GTEx:  ENSG00000234745 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01889
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin
B, D
100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
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
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoprotein peptide N75-83
E, F
9Human coronavirus 229EMutation(s): 0 
UniProt
Find proteins for P15130 (Human coronavirus 229E)
Explore P15130 
Go to UniProtKB:  P15130
Entity Groups  
UniProt GroupP15130
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BR
Query on BR

Download Ideal Coordinates CCD File 
AA [auth B]BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
ZN
Query on ZN

Download Ideal Coordinates CCD File 
DA [auth C]
EA [auth C]
FA [auth C]
G [auth A]
H [auth A]
DA [auth C],
EA [auth C],
FA [auth C],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
OA [auth D],
W [auth B],
X [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
BA [auth B]
CA [auth B]
KA [auth C]
LA [auth C]
MA [auth C]
BA [auth B],
CA [auth B],
KA [auth C],
LA [auth C],
MA [auth C],
NA [auth C],
PA [auth F],
QA [auth F],
S [auth A],
T [auth A],
U [auth A],
V [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
JA [auth C]
M [auth A]
N [auth A]
O [auth A]
P [auth A]
JA [auth C],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
Y [auth B],
Z [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
GA [auth C],
HA [auth C],
IA [auth C],
L [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.144α = 77.15
b = 62.854β = 77
c = 63.01γ = 77.86
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia--
Australian Research Council (ARC)Australia--

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-21
    Type: Initial release
  • Version 1.1: 2021-05-19
    Changes: Database references
  • Version 1.2: 2021-05-26
    Changes: Database references
  • Version 1.3: 2021-08-11
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.4: 2023-10-18
    Changes: Data collection, Refinement description