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- PDB-6kwk: Crystal structure of pSLA-1*0401 complex with FMDV-derived epitop... -

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Basic information

Entry
Database: PDB / ID: 6kwk
TitleCrystal structure of pSLA-1*0401 complex with FMDV-derived epitope MTAHITVPY
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 / L-peptidase / symbiont-mediated perturbation of host chromatin organization / Neutrophil degranulation / 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 / L-peptidase / symbiont-mediated perturbation of host chromatin organization / Neutrophil degranulation / antigen processing and presentation of peptide antigen via MHC class I / ribonucleoside triphosphate phosphatase activity / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex / picornain 3C / MHC class II protein complex / T=pseudo3 icosahedral viral capsid / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / host cell cytoplasmic vesicle membrane / positive regulation of T cell activation / phagocytic vesicle membrane / MHC class II protein complex binding / late endosome membrane / regulation of translation / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / viral protein processing / RNA helicase activity / host cell endoplasmic reticulum membrane / immune response / symbiont-mediated activation of host autophagy / lysosomal membrane / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / extracellular region / ATP binding / membrane
Similarity search - Function
Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Aphthovirus leader protease (L(pro)) domain profile. / Foot-and-mouth disease virus VP1 coat / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / MHC class I, alpha chain, C-terminal / MHC_I C-terminus ...Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Aphthovirus leader protease (L(pro)) domain profile. / Foot-and-mouth disease virus VP1 coat / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / Picornavirus coat protein / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Papain-like cysteine peptidase superfamily / Beta-2-Microglobulin / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / : / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / MHC classes I/II-like antigen recognition protein / Picornavirus/Calicivirus coat protein / : / Viral coat protein subunit / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Immunoglobulin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
MHC class I antigen / Genome polyprotein / Beta-2-microglobulin
Similarity search - Component
Biological speciesSus scrofa (pig)
Foot-and-mouth disease virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWei, X.H. / Wang, S. / Zhang, N.Z. / Xia, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31201887 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
Revision 1.3Nov 13, 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)44,2943
Polymers44,2943
Non-polymers00
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-22 kcal/mol
Surface area18640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.671, 77.146, 62.317
Angle α, β, γ (deg.)90.00, 119.42, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein MHC class I antigen


Mass: 31681.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F6N4U7
#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: 1033.220 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Foot-and-mouth disease virus / References: UniProt: P03311*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.1 Å3/Da / Density % sol: 41.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.05 M Calcium Chloride dihydrate, 0.1 M Bis-Tris pH 6.5, 30% v/v Polyethylene Glycol Monomethyl ether 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2→28.59 Å / Num. obs: 23996 / % possible obs: 96.8 % / Redundancy: 6 % / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 26.535
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 12.486 / Num. unique obs: 23996 / Rsym value: 0.157 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX(1.14_3247: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QQ3

3qq3


Resolution: 2.5→28.577 Å / SU ML: 0.33 / Cross valid method: NONE / σ(F): 1.39 / Phase error: 29.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.288 584 4.88 %
Rwork0.2379 --
obs0.2404 11972 93.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→28.577 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3122 0 0 207 3329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053213
X-RAY DIFFRACTIONf_angle_d0.8094369
X-RAY DIFFRACTIONf_dihedral_angle_d21.081199
X-RAY DIFFRACTIONf_chiral_restr0.051445
X-RAY DIFFRACTIONf_plane_restr0.004577
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.75150.33661600.2813003X-RAY DIFFRACTION100
2.7515-3.14920.32731490.25173012X-RAY DIFFRACTION100
3.1492-3.9660.28151290.22362929X-RAY DIFFRACTION96
3.966-28.5770.25161460.22412444X-RAY DIFFRACTION80

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