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- PDB-9hy4: Solubly expressed miniaturized SMART H2-Db -

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Basic information

Entry
Database: PDB / ID: 9hy4
TitleSolubly expressed miniaturized SMART H2-Db
Components
  • H-2 class I histocompatibility antigen, D-B alpha chain
  • LYS-ALA-VAL-TYR-ASN-PHE-ALA-THR-MET
KeywordsIMMUNE SYSTEM / MHC / soluble expression
Function / homology
Function and homology information


antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / lumenal side of endoplasmic reticulum membrane / T cell mediated cytotoxicity / MHC class I protein complex / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / negative regulation of neuron projection development / external side of plasma membrane / plasma membrane
Similarity search - Function
MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
H-2 class I histocompatibility antigen, D-B alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
Mammarenavirus choriomeningitidis
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSun, R. / White, W. / Bai, H. / Baker, D. / Achour, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2026
Title: Design of solubly expressed miniaturized SMART MHCs.
Authors: 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. / ...Authors: 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.
History
DepositionJan 9, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 31, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: LYS-ALA-VAL-TYR-ASN-PHE-ALA-THR-MET
C: H-2 class I histocompatibility antigen, D-B alpha chain
D: LYS-ALA-VAL-TYR-ASN-PHE-ALA-THR-MET


Theoretical massNumber of molelcules
Total (without water)60,2164
Polymers60,2164
Non-polymers00
Water1,60389
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-23 kcal/mol
Surface area23250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.954, 93.237, 75.856
Angle α, β, γ (deg.)90.000, 94.080, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein H-2 class I histocompatibility antigen, D-B alpha chain / H-2D(B)


Mass: 29062.990 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01899
#2: Protein/peptide LYS-ALA-VAL-TYR-ASN-PHE-ALA-THR-MET


Mass: 1045.232 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mammarenavirus choriomeningitidis
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.33 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M sodium acetate trihydrate, 0.1 M TRIS hydrochloride pH 8.5, and 30% w/v polyethylene glycol, PEG 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9655 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 2→53.75 Å / Num. obs: 29279 / % possible obs: 95.2 % / Redundancy: 2 % / Biso Wilson estimate: 21.23 Å2 / CC1/2: 1 / Net I/av σ(I): 9.4 / Net I/σ(I): 8
Reflection shellResolution: 2→2.05 Å / Mean I/σ(I) obs: 4.1 / Num. unique obs: 2209 / CC1/2: 0.9 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata processing
autoPROCdata reduction
Aimlessdata scaling
PHENIX1.20.1_4487phasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→53.75 Å / SU ML: 0.2961 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.9319
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2805 1451 4.97 %
Rwork0.2248 27753 -
obs0.2276 29204 94.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.24 Å2
Refinement stepCycle: LAST / Resolution: 2→53.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3987 0 0 89 4076
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00874076
X-RAY DIFFRACTIONf_angle_d0.97535497
X-RAY DIFFRACTIONf_chiral_restr0.0523542
X-RAY DIFFRACTIONf_plane_restr0.0296728
X-RAY DIFFRACTIONf_dihedral_angle_d22.0764551
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.070.35231520.24362829X-RAY DIFFRACTION96.32
2.07-2.150.31551420.25292808X-RAY DIFFRACTION96.69
2.15-2.250.3321360.23652822X-RAY DIFFRACTION95.36
2.25-2.370.34921420.23912807X-RAY DIFFRACTION95.13
2.37-2.520.35281290.24042716X-RAY DIFFRACTION93.1
2.52-2.710.28071550.2412799X-RAY DIFFRACTION95.44
2.71-2.990.31851530.2462796X-RAY DIFFRACTION95.38
2.99-3.420.26971580.22762756X-RAY DIFFRACTION94.15
3.42-4.310.23951320.20062749X-RAY DIFFRACTION92.79
4.31-53.750.22881520.20282671X-RAY DIFFRACTION89.34

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