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- PDB-6kwo: Crystal structure of pSLA-1*1301 complex with mutant epitope ESDTVGWSW -

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Basic information

Entry
Database: PDB / ID: 6kwo
TitleCrystal structure of pSLA-1*1301 complex with mutant epitope ESDTVGWSW
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • MHC class I antigen
  • peptide
KeywordsSTRUCTURAL PROTEIN / MHC class I structure / A single-amino acid mutation / Peptide motifs / Random peptide library
Function / homology
Function and homology information


ER-Phagosome pathway / Endosomal/Vacuolar pathway / DAP12 interactions / DAP12 signaling / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Neutrophil degranulation / antigen processing and presentation of peptide antigen via MHC class I / exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity ...ER-Phagosome pathway / Endosomal/Vacuolar pathway / DAP12 interactions / DAP12 signaling / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Neutrophil degranulation / antigen processing and presentation of peptide antigen via MHC class I / exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / antigen processing and presentation / viral budding from plasma membrane / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / carbohydrate metabolic process / immune response / lysosomal membrane / host cell plasma membrane / virion membrane / extracellular region / membrane / metal ion binding
Similarity search - Function
Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Sialidase superfamily / 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 / Beta-2-Microglobulin / MHC class I-like antigen recognition-like ...Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Sialidase superfamily / 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 / 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
Similarity search - Domain/homology
MHC class I antigen / Beta-2-microglobulin / Neuraminidase
Similarity search - Component
Biological speciesSus scrofa (pig)
Neuraminidase deficient flu strains (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.803 Å
AuthorsWei, X.H. / Wang, S. / Zhang, N.Z. / Xia, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31201887 China
CitationJournal: Front Immunol / Year: 2021
Title: Peptidomes and Structures Illustrate Two Distinguishing Mechanisms of Alternating the Peptide Plasticity Caused by Swine MHC Class I Micropolymorphism.
Authors: Wei, X. / Wang, S. / Li, Z. / Li, Z. / Qu, Z. / Wang, S. / Zou, B. / Liang, R. / Xia, C. / Zhang, N.
History
DepositionSep 7, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: MHC class I antigen
B: Beta-2-microglobulin
C: peptide


Theoretical massNumber of molelcules
Total (without water)43,9493
Polymers43,9493
Non-polymers00
Water6,053336
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-17 kcal/mol
Surface area18660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)218.570, 45.780, 45.450
Angle α, β, γ (deg.)90.00, 99.28, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-107-

HOH

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Components

#1: Protein MHC class I antigen


Mass: 31549.912 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: SLA-1 / Production host: Escherichia coli (E. coli) / References: UniProt: B1PJU7
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin / Lactollin


Mass: 11332.788 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: Q07717
#3: Protein/peptide peptide /


Mass: 1066.078 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Neuraminidase deficient flu strains (virus)
References: UniProt: Q9Q0U7*PLUS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 336 / Source method: isolated from a natural source / Formula: H2O

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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: 2.55 Å3/Da / Density % sol: 51.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.15 M Potassium Bromide, 30% w/v Polyethylene Glycol Monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97931 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.8→53.928 Å / Num. obs: 38597 / % possible obs: 93.8 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 9.9
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.734 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 38597

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Processing

Software
NameVersionClassification
HKL-3000(1.14_3247: ???)data reduction
HKL-3000data scaling
PHENIXphasing
PHENIX(1.14_3247: ???)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3qq3

3qq3


Resolution: 1.803→53.928 Å / SU ML: 0.22 / Cross valid method: NONE / σ(F): 1.39 / Phase error: 24.67
RfactorNum. reflection% reflection
Rfree0.2231 1878 4.87 %
Rwork0.204 --
obs0.2049 38589 93.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.803→53.928 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3075 0 0 336 3411
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043164
X-RAY DIFFRACTIONf_angle_d0.7654299
X-RAY DIFFRACTIONf_dihedral_angle_d24.7891178
X-RAY DIFFRACTIONf_chiral_restr0.047437
X-RAY DIFFRACTIONf_plane_restr0.005566
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8034-1.85210.32161410.25982852X-RAY DIFFRACTION95
1.8521-1.90660.25881830.24272823X-RAY DIFFRACTION95
1.9066-1.96820.29491870.23372778X-RAY DIFFRACTION95
1.9682-2.03850.24741690.22822789X-RAY DIFFRACTION94
2.0385-2.12010.28941230.21442849X-RAY DIFFRACTION95
2.1201-2.21660.23161220.21122829X-RAY DIFFRACTION93
2.2166-2.33350.25551360.21512766X-RAY DIFFRACTION92
2.3335-2.47970.28571070.22172710X-RAY DIFFRACTION88
2.4797-2.67110.21011250.22872719X-RAY DIFFRACTION89
2.6711-2.93990.24431400.22362919X-RAY DIFFRACTION97
2.9399-3.36530.25741650.21072880X-RAY DIFFRACTION96
3.3653-4.23970.1831390.18042889X-RAY DIFFRACTION94
4.2397-53.910.17941410.1812908X-RAY DIFFRACTION93

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