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- PDB-6jq2: Crystal Structure of H2-Kb in complex with a DPAGT1 self-peptide -

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Basic information

Entry
Database: PDB / ID: 6jq2
TitleCrystal Structure of H2-Kb in complex with a DPAGT1 self-peptide
Components
  • Beta-2-microglobulin
  • DPATG1 antigen SIIVFNLV
  • H-2 class I histocompatibility antigen, K-B alpha chain
KeywordsIMMUNE SYSTEM / MHC complex / antigen / H-2 / Kb
Function / homology
Function and homology information


: / Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein / UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase / UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase activity / UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity / dolichol-linked oligosaccharide biosynthetic process / UDP-N-acetylglucosamine metabolic process / natural killer cell lectin-like receptor binding / TAP2 binding / TAP1 binding ...: / Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein / UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase / UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase activity / UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity / dolichol-linked oligosaccharide biosynthetic process / UDP-N-acetylglucosamine metabolic process / natural killer cell lectin-like receptor binding / TAP2 binding / TAP1 binding / MHC class Ib protein complex / cis-Golgi network membrane / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP complex binding / inner ear development / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / glycosyltransferase activity / regulation of membrane depolarization / CD8 receptor binding / endoplasmic reticulum exit site / TAP binding / 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 / lumenal side of endoplasmic reticulum membrane / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / regulation of iron ion transport / cellular response to iron(III) ion / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / response to molecule of bacterial origin / regulation of erythrocyte differentiation / 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 / multicellular organismal-level iron ion homeostasis / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / negative regulation of epithelial cell proliferation / cellular response to nicotine / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / phagocytic vesicle membrane / positive regulation of T cell activation / T cell differentiation in thymus / sensory perception of smell / positive regulation of cellular senescence / MHC class II protein complex binding / negative regulation of neuron projection development / late endosome membrane / antimicrobial humoral immune response mediated by antimicrobial peptide / cellular response to lipopolysaccharide / protein refolding / antibacterial humoral response / protein-folding chaperone binding / early endosome membrane / amyloid fibril formation / defense response to Gram-negative bacterium / protein homotetramerization / intracellular iron ion homeostasis / early endosome / 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 / Golgi apparatus / structural molecule activity / cell surface / endoplasmic reticulum / protein homodimerization activity
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: 2.4 Å
AuthorsBai, 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 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _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 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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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, K-B alpha chain
P: DPATG1 antigen SIIVFNLV
B: Beta-2-microglobulin


Theoretical massNumber of molelcules
Total (without water)44,2133
Polymers44,2133
Non-polymers00
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-15 kcal/mol
Surface area19190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.240, 69.420, 70.440
Angle α, β, γ (deg.)90.00, 103.79, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 31648.322 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P01901
#2: Protein/peptide DPATG1 antigen SIIVFNLV


Mass: 904.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P42867*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 (E. coli) / References: UniProt: P01887
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.87 Å3/Da / Density % sol: 57.16 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 4% v/v Tacsimate (pH 573 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: 2.4→57.76 Å / Num. obs: 19013 / % possible obs: 96 % / Redundancy: 2 % / Rmerge(I) obs: 0.02281 / Net I/σ(I): 14.38
Reflection shellResolution: 2.4→2.486 Å / Redundancy: 2 % / Rmerge(I) obs: 0.1159 / Num. unique obs: 1886 / % possible all: 96

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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: 2.4→57.76 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2747 1899 10 %
Rwork0.2206 --
obs0.2261 18982 95.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→57.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2999 0 0 105 3104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093084
X-RAY DIFFRACTIONf_angle_d1.0594187
X-RAY DIFFRACTIONf_dihedral_angle_d18.7771823
X-RAY DIFFRACTIONf_chiral_restr0.059436
X-RAY DIFFRACTIONf_plane_restr0.006540
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4002-2.46020.38681350.29261208X-RAY DIFFRACTION95
2.4602-2.52670.36261370.26751231X-RAY DIFFRACTION98
2.5267-2.60110.37741390.26491258X-RAY DIFFRACTION98
2.6011-2.6850.38241360.26181224X-RAY DIFFRACTION98
2.685-2.7810.34751390.26021244X-RAY DIFFRACTION98
2.781-2.89240.3171400.25291253X-RAY DIFFRACTION98
2.8924-3.0240.32691350.25411227X-RAY DIFFRACTION97
3.024-3.18340.33021350.24361213X-RAY DIFFRACTION96
3.1834-3.38290.28321260.23121136X-RAY DIFFRACTION90
3.3829-3.64410.30161260.22541135X-RAY DIFFRACTION90
3.6441-4.01070.2491390.20191253X-RAY DIFFRACTION98
4.0107-4.5910.22081380.18041242X-RAY DIFFRACTION98
4.591-5.78370.20911360.18641219X-RAY DIFFRACTION94
5.7837-68.43710.22451380.20881240X-RAY DIFFRACTION94

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