4Y1A | pdb_00004y1a

immune complex


Experimental Data Snapshot

  • Method:&nbspX-RAY DIFFRACTION
  • Resolution:&nbsp4.00 Å
  • R-Value Free:&nbsp
    0.283 (Depositor), 0.285 (DCC)&nbsp
  • R-Value Work:&nbsp
    0.225 (Depositor), 0.231 (DCC)&nbsp
  • R-Value Observed:&nbsp
    0.227&nbsp(Depositor)&nbsp

wwPDB Validation&nbsp &nbsp3D Report&nbspFull Report


This is version 2.1 of the entry. See complete&nbsphistory.&nbsp


Literature

T cell receptor reversed polarity recognition of a self-antigen major histocompatibility complex.

Beringer, D.X.,&nbspKleijwegt, F.S.,&nbspWiede, F.,&nbspvan der Slik, A.R.,&nbspLoh, K.L.,&nbspPetersen, J.,&nbspDudek, N.L.,&nbspDuinkerken, G.,&nbspLaban, S.,&nbspJoosten, A.,&nbspVivian, J.P.,&nbspChen, Z.,&nbspUldrich, A.P.,&nbspGodfrey, D.I.,&nbspMcCluskey, J.,&nbspPrice, D.A.,&nbspRadford, K.J.,&nbspPurcell, A.W.,&nbspNikolic, T.,&nbspReid, H.H.,&nbspTiganis, T.,&nbspRoep, B.O.,&nbspRossjohn, J.

(2015) Nat Immunol&nbsp16: 1153-1161

  • DOI:&nbsphttps://doi.org/10.1038/ni.3271
  • Primary Citation of Related Structures: &nbsp
    4Y19, 4Y1A

  • PubMed Abstract:&nbsp

    Central to adaptive immunity is the interaction between the αβ T cell receptor (TCR) and peptide presented by the major histocompatibility complex (MHC) molecule. Presumably reflecting TCR-MHC bias and T cell signaling constraints, the TCR universally adopts a canonical polarity atop the MHC. We report the structures of two TCRs, derived from human induced T regulatory (iT(reg)) cells, complexed to an MHC class II molecule presenting a proinsulin-derived peptide. The ternary complexes revealed a 180° polarity reversal compared to all other TCR-peptide-MHC complex structures. Namely, the iT(reg) TCR α-chain and β-chain are overlaid with the α-chain and β-chain of MHC class II, respectively. Nevertheless, this TCR interaction elicited a peptide-reactive, MHC-restricted T cell signal. Thus TCRs are not 'hardwired' to interact with MHC molecules in a stereotypic manner to elicit a T cell signal, a finding that fundamentally challenges our understanding of TCR recognition.


  • Organizational Affiliation:&nbsp

    Infection and Immunity Program and The Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DR alpha chain181Homo sapiensMutation(s): 0&nbsp
Gene Names:&nbspHLA-DRA,&nbspHLA-DRA1
UniProt & NIH Common Fund Data Resources
Find proteins for&nbspP01903&nbsp(Homo sapiens)
Explore&nbspP01903&nbsp
Go to UniProtKB: &nbspP01903
PHAROS: &nbspP01903
GTEx: &nbspENSG00000204287&nbsp
Entity Groups &nbsp
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01903
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P01903-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DRB1-4 beta chain200Homo sapiensMutation(s): 0&nbsp
Gene Names:&nbspHLA-DRB1
UniProt & NIH Common Fund Data Resources
Find proteins for&nbspP01911&nbsp(Homo sapiens)
Explore&nbspP01911&nbsp
Go to UniProtKB: &nbspP01911
PHAROS: &nbspP01911
GTEx: &nbspENSG00000196126&nbsp
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01911
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Insulin16Homo sapiensMutation(s): 0&nbsp
UniProt & NIH Common Fund Data Resources
Find proteins for&nbspP01308&nbsp(Homo sapiens)
Explore&nbspP01308&nbsp
Go to UniProtKB: &nbspP01308
PHAROS: &nbspP01308
GTEx: &nbspENSG00000254647&nbsp
Entity Groups &nbsp
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01308
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
FS17_alpha210Homo sapiensMutation(s): 0&nbsp
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
FS17_beta243Homo sapiensMutation(s): 0&nbsp
Entity Groups &nbsp
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Oligosaccharides

Help

Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F
2N-Glycosylation
Glycosylation Resources
GlyTouCan: &nbspG42666HT
GlyCosmos: &nbspG42666HT
GlyGen: &nbspG42666HT
Experimental Data & Validation

Experimental Data

  • Method:&nbspX-RAY DIFFRACTION
  • Resolution:&nbsp4.00 Å
  • R-Value Free:&nbsp 0.283 (Depositor), 0.285 (DCC)&nbsp
  • R-Value Work:&nbsp 0.225 (Depositor), 0.231 (DCC)&nbsp
  • R-Value Observed:&nbsp0.227&nbsp(Depositor)&nbsp
Space Group:&nbspI 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.908α = 90
b = 153.93β = 90
c = 164.311γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
iMOSFLMdata reduction

Structure Validation

View&nbspFull Validation Report



Entry History&nbsp& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)Australia--

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-23
    Type: Initial release
  • Version 1.1: 2015-10-21
    Changes: Data collection, Database references
  • Version 1.2: 2015-11-04
    Changes: Database references
  • Version 1.3: 2017-09-27
    Changes: Author supporting evidence, Data collection, Derived calculations
  • Version 1.4: 2018-01-17
    Changes: Author supporting evidence
  • Version 1.5: 2020-01-01
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-10-30
    Changes: Data collection, Database references, Structure summary