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- PDB-6kwn: Crystal structure of pSLA-1*1301(F99Y) complex with S-OIV-derived... -

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Basic information

Entry
Database: PDB / ID: 6kwn
TitleCrystal structure of pSLA-1*1301(F99Y) complex with S-OIV-derived epitope NSDTVGWSW
Components
  • Beta-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 / exo-alpha-sialidase / exo-alpha-sialidase activity / antigen processing and presentation of peptide antigen via MHC class I ...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 / exo-alpha-sialidase / exo-alpha-sialidase activity / antigen processing and presentation of peptide antigen via MHC class I / viral budding from plasma membrane / lumenal side of endoplasmic reticulum membrane / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / phagocytic vesicle membrane / 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 / metal ion binding / membrane
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 / : ...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)
Swine influenza virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)44,2533
Polymers44,2533
Non-polymers00
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-14 kcal/mol
Surface area18880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)218.314, 46.306, 45.024
Angle α, β, γ (deg.)90.000, 90.656, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein MHC class I antigen


Mass: 31622.965 Da / Num. of mol.: 1 / Mutation: F99Y
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 / Lactollin


Mass: 11579.093 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: 1051.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Swine influenza virus / References: UniProt: Q9Q0U7*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.59 Å3/Da / Density % sol: 52.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis-Tris pH 6.5, 20% w/v Polyethylene Glycol Monomethyl ether 5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97931 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.37→50 Å / Num. obs: 17844 / % possible obs: 98.3 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.159 / Rsym value: 0.159 / Net I/σ(I): 8.4
Reflection shellResolution: 2.37→2.41 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 5.7 / Num. unique obs: 17844 / Rsym value: 0.241 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC7.0.077refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3qq3

3qq3


Resolution: 2.4→41.824 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.859 / SU B: 0.005 / SU ML: 0 / Cross valid method: NONE / ESU R: 0.291 / ESU R Free: 0.337
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2822 840 5.394 %
Rwork0.2441 --
all0.246 --
obs-15572 86.922 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.866 Å2
Baniso -1Baniso -2Baniso -3
1--0.146 Å2-0 Å2-0.054 Å2
2--0.089 Å2-0 Å2
3---0.058 Å2
Refinement stepCycle: LAST / Resolution: 2.4→41.824 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3103 0 0 94 3197
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.4620.329380.287792X-RAY DIFFRACTION64.5412
2.462-2.5290.349390.295847X-RAY DIFFRACTION69.0569
2.529-2.6030.338470.299852X-RAY DIFFRACTION71.92
2.603-2.6820.372420.312856X-RAY DIFFRACTION74.8957
2.682-2.770.381420.295869X-RAY DIFFRACTION78.8745
2.77-2.8670.305440.299931X-RAY DIFFRACTION84.4887
2.867-2.9750.291420.291971X-RAY DIFFRACTION93.1923
2.975-3.0960.368470.296986X-RAY DIFFRACTION96.8135
3.096-3.2330.345480.271958X-RAY DIFFRACTION98.7242
3.233-3.390.292450.249896X-RAY DIFFRACTION98.7408
3.39-3.5730.32590.241848X-RAY DIFFRACTION97.1092
3.573-3.7880.257510.227778X-RAY DIFFRACTION94.6347
3.788-4.0480.231560.201743X-RAY DIFFRACTION96.7312
4.048-4.370.24500.199657X-RAY DIFFRACTION93.7666
4.37-4.7830.32380.187619X-RAY DIFFRACTION92.7966
4.783-5.3420.257480.21574X-RAY DIFFRACTION94.6728
5.342-6.1570.221330.23527X-RAY DIFFRACTION97.7312
6.157-7.5120.224370.227464X-RAY DIFFRACTION99.2079
7.512-10.5060.264120.192356X-RAY DIFFRACTION96.8421
10.506-41.8240.23210.3205X-RAY DIFFRACTION93.7759

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