9HY4 | pdb_00009hy4

Solubly expressed miniaturized SMART H2-Db


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.281 (Depositor), 0.281 (DCC) 
  • R-Value Work: 
    0.225 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 
    0.228 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9HY4

This is version 1.1 of the entry. See complete history

Literature

Design of solubly expressed miniaturized SMART MHCs.

White, W.L.Bai, H.Kim, C.J.Jude, K.M.Sun, R.Guerrero, L.Han, X.Chen, X.Chaudhuri, A.Bonzanini, J.E.Sun, Y.Onwuka, A.E.Wang, N.Wang, C.Nygren, P.A.Li, X.Goreshnik, I.Allen, A.Levine, P.M.Kueh, H.Y.Jewett, M.C.Sgourakis, N.G.Achour, A.Garcia, K.C.Baker, D.

(2026) Proc Natl Acad Sci U S A 123: e2505932123-e2505932123

  • DOI: https://doi.org/10.1073/pnas.2505932123
  • Primary Citation Related Structures: 
    9HY4, 9NDS

  • PubMed Abstract: 

    The precise recognition of specific peptide-major histocompatibility complex (pMHC) complexes by T cell receptors (TCRs) plays a key role in infectious disease, cancer, and autoimmunity. A critical step in many immunobiological studies is the identification of T cells expressing TCRs specific to a given pMHC antigen. However, the intrinsic instability of empty class-I MHCs limits their soluble expression in Escherichia coli and makes it very difficult to characterize even a small fraction of possible pMHC/TCR interactions. To overcome this limitation, we designed small proteins which buttress the peptide binding groove of class I MHCs, replacing β2-microglobulin (β2m) and the heavy chain α3 domain, and enable soluble and partially soluble expression in E. coli of H-2D b and A*02:01, respectively. We demonstrate that these soluble, monomeric, antigen-receptive, truncated (SMART) MHCs retain both peptide- and TCR-binding specificity and that peptide-bound structures of both allomorphs are similar to their full-length, native counterparts. With extension to the majority of HLA alleles, SMART MHCs should be broadly useful for probing the T cell repertoire in approaches ranging from yeast display to T cell staining.


  • Organizational Affiliation
    • Department of Bioengineering, University of Washington, Seattle, WA 98195.

Macromolecule Content 

  • Total Structure Weight: 60.22 kDa 
  • Atom Count: 4,076 
  • Modeled Residue Count: 480 
  • Deposited Residue Count: 528 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
H-2 class I histocompatibility antigen, D-B alpha chain
A, C
255Mus musculusMutation(s): 0 
Gene Names: H2-D1
UniProt
Find proteins for P01899 (Mus musculus)
Explore P01899 
Go to UniProtKB:  P01899
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01899
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
LYS-ALA-VAL-TYR-ASN-PHE-ALA-THR-MET
B, D
9Mammarenavirus choriomeningitidisMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.281 (Depositor), 0.281 (DCC) 
  • R-Value Work:  0.225 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 0.228 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.954α = 90
b = 93.237β = 94.08
c = 75.856γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata processing
autoPROCdata reduction
Aimlessdata scaling
PHENIXphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-31
    Type: Initial release
  • Version 1.1: 2026-01-14
    Changes: Database references