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- PDB-6jq3: Crystal Structure of H2-Kb in complex with a DPAGT1 mutant peptide -

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Basic information

Entry
Database: PDB / ID: 6jq3
TitleCrystal Structure of H2-Kb in complex with a DPAGT1 mutant peptide
Components
  • Beta-2-microglobulin
  • DPAGT1 mutant antigen SIIVFNLL
  • H-2 class I histocompatibility antigen, K-B alpha chain
KeywordsIMMUNE SYSTEM / major histocompatibility complex / H2-Kb / antigen / mouse / MHC
Function / homology
Function and homology information


Defective DPAGT1 causes CDG-1j, CMSTA2 / UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase / UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase activity / Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein / UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity / dolichol-linked oligosaccharide biosynthetic process / natural killer cell lectin-like receptor binding / TAP2 binding / TAP1 binding / cis-Golgi network membrane ...Defective DPAGT1 causes CDG-1j, CMSTA2 / UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase / UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase activity / Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein / UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity / dolichol-linked oligosaccharide biosynthetic process / natural killer cell lectin-like receptor binding / TAP2 binding / TAP1 binding / cis-Golgi network membrane / protein N-linked glycosylation / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / DAP12 signaling / cellular response to iron(III) ion / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / MHC class Ib protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / inner ear development / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / glycosyltransferase activity / multicellular organismal-level iron ion homeostasis / regulation of membrane depolarization / CD8 receptor binding / TAP binding / intracellular membrane-bounded organelle / endoplasmic reticulum exit site / T cell differentiation in thymus / MHC class I protein binding / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / beta-2-microglobulin binding / cellular defense response / T cell receptor binding / Neutrophil degranulation / 14-3-3 protein binding / positive regulation of T cell mediated cytotoxicity / negative regulation of neuron projection development / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / peptide antigen assembly with MHC class I protein complex / iron ion transport / HFE-transferrin receptor complex / MHC class I peptide loading complex / transferrin transport / negative regulation of receptor-mediated endocytosis / cellular response to iron ion / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / peptide antigen assembly with MHC class II protein complex / protein refolding / MHC class I protein complex / negative regulation of epithelial cell proliferation / cellular response to nicotine / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / positive regulation of immune response / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / phagocytic vesicle membrane / positive regulation of T cell activation / sensory perception of smell / positive regulation of cellular senescence / MHC class II protein complex binding / late endosome membrane / cellular response to lipopolysaccharide / protein-folding chaperone binding / antimicrobial humoral immune response mediated by antimicrobial peptide / early endosome membrane / antibacterial humoral response / defense response to Gram-negative bacterium / amyloid fibril formation / protein homotetramerization / early endosome / intracellular iron ion homeostasis / learning or memory / defense response to bacterium / defense response to Gram-positive bacterium / immune response / receptor ligand activity / external side of plasma membrane / signaling receptor binding / Golgi membrane / innate immune response / lysosomal membrane / endoplasmic reticulum membrane / structural molecule activity / Golgi apparatus / cell surface
Similarity search - Function
UDP-GlcNAc-dolichyl-phosphate GlcNAc phosphotransferase / : / DPAGT1 insertion domain / Glycosyl transferase, family 4 / Glycosyl transferase family 4 / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains ...UDP-GlcNAc-dolichyl-phosphate GlcNAc phosphotransferase / : / DPAGT1 insertion domain / Glycosyl transferase, family 4 / Glycosyl transferase family 4 / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Beta-2-microglobulin / H-2 class I histocompatibility antigen, K-B alpha chain / UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBai, P. / Zhou, Q. / Wei, P. / Yin, L.
CitationJournal: Oncoimmunology / Year: 2021
Title: Immune-based mutation classification enables neoantigen prioritization and immune feature discovery in cancer immunotherapy.
Authors: Bai, P. / Li, Y. / Zhou, Q. / Xia, J. / Wei, P.C. / Deng, H. / Wu, M. / Chan, S.K. / Kappler, J.W. / Zhou, Y. / Tran, E. / Marrack, P. / Yin, L.
History
DepositionMar 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Feb 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, K-B alpha chain
P: DPAGT1 mutant antigen SIIVFNLL
B: Beta-2-microglobulin


Theoretical massNumber of molelcules
Total (without water)44,2273
Polymers44,2273
Non-polymers00
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-17 kcal/mol
Surface area19290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.630, 67.970, 70.730
Angle α, β, γ (deg.)90.00, 103.86, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11P-104-

HOH

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Components

#1: Protein H-2 class I histocompatibility antigen, K-B alpha chain / major histocompatibility complex chain a


Mass: 31648.322 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-K1, H2-K / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P01901
#2: Protein/peptide DPAGT1 mutant antigen SIIVFNLL


Mass: 918.132 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q9H3H5*PLUS
#3: Protein Beta-2-microglobulin


Mass: 11660.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P01887
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.81 Å3/Da / Density % sol: 56.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 4% v/v Tacsimate (pH 7.0), 12% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.5→68.67 Å / Num. obs: 16646 / % possible obs: 97 % / Redundancy: 2 % / Rmerge(I) obs: 0.02767 / Net I/σ(I): 11.6
Reflection shellResolution: 2.5→2.589 Å / Redundancy: 2 % / Rmerge(I) obs: 0.1982 / Mean I/σ(I) obs: 2.85 / Num. unique obs: 1679 / CC1/2: 0.944 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→68.67 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.74
RfactorNum. reflection% reflection
Rfree0.2964 1663 10 %
Rwork0.2165 --
obs0.2243 16622 96.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→68.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3037 0 0 56 3093
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153123
X-RAY DIFFRACTIONf_angle_d1.5194238
X-RAY DIFFRACTIONf_dihedral_angle_d19.6631850
X-RAY DIFFRACTIONf_chiral_restr0.068441
X-RAY DIFFRACTIONf_plane_restr0.008546
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.57360.37551400.28681263X-RAY DIFFRACTION99
2.5736-2.65660.3371410.2731261X-RAY DIFFRACTION99
2.6566-2.75160.34741390.25451254X-RAY DIFFRACTION98
2.7516-2.86180.35491380.26951241X-RAY DIFFRACTION98
2.8618-2.9920.37821390.27511255X-RAY DIFFRACTION98
2.992-3.14980.37861400.26071254X-RAY DIFFRACTION98
3.1498-3.34710.3271330.24481207X-RAY DIFFRACTION95
3.3471-3.60550.31471300.23251169X-RAY DIFFRACTION91
3.6055-3.96830.31131420.20541276X-RAY DIFFRACTION99
3.9683-4.54240.27871420.18631272X-RAY DIFFRACTION98
4.5424-5.72260.22731380.18321241X-RAY DIFFRACTION96
5.7226-68.69650.23121410.18311266X-RAY DIFFRACTION95

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