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- PDB-6a6h: Crystal Structure of Swine Major Histocompatibility Complex Class... -

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Basic information

Entry
Database: PDB / ID: 6a6h
TitleCrystal Structure of Swine Major Histocompatibility Complex Class I SLA-2*040202 For 2.3 Angstrom
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • MET-THR-ALA-HIS-ILE-VAL-VAL-PRO-TYR
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / MHC / Immunology / Immune system- transferase complex
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 / IRES-dependent viral translational initiation / modulation by virus of host chromatin organization / Neutrophil degranulation ...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 / IRES-dependent viral translational initiation / modulation by virus of host chromatin organization / Neutrophil degranulation / antigen processing and presentation of peptide antigen via MHC class I / antigen processing and presentation / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle 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 / positive regulation of immune response / positive regulation of T cell activation / nucleoside-triphosphate phosphatase / regulation of translation / protein complex oligomerization / MHC class II protein complex binding / late endosome membrane / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / membrane => GO:0016020 / viral protein processing / immune response / induction by virus of host autophagy / RNA-directed RNA polymerase / lysosomal membrane / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / extracellular region / ATP binding / membrane
Similarity search - Function
Aphthovirus leader protease (L(pro)) domain profile. / Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / 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 ...Aphthovirus leader protease (L(pro)) domain profile. / Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / 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 / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / 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 class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Papain-like cysteine peptidase superfamily / Picornavirus/Calicivirus coat protein / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Viral coat protein subunit / 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 / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Genome polyprotein / Beta-2-microglobulin / MHC class I antigen
Similarity search - Component
Biological speciesSus scrofa (pig)
Foot-and-mouth disease virus - type A
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsNing, S. / Wang, Z.B.
CitationJournal: Res. Vet. Sci. / Year: 2019
Title: Crystallization of SLA-2*04:02:02 complexed with a CTL epitope derived from FMDV.
Authors: Ning, S. / Wang, Z.B. / Qi, P. / Xiao, J. / Wang, X.J.
History
DepositionJun 28, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs
Revision 1.2Jan 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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 1.3Nov 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

Downloads & links

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: MET-THR-ALA-HIS-ILE-VAL-VAL-PRO-TYR


Theoretical massNumber of molelcules
Total (without water)44,0113
Polymers44,0113
Non-polymers00
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-17 kcal/mol
Surface area18640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.802, 101.802, 73.455
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein MHC class I antigen


Mass: 31547.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: SLA-B, SLA-2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8MHU4
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin / Lactollin


Mass: 11431.918 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 MET-THR-ALA-HIS-ILE-VAL-VAL-PRO-TYR


Mass: 1031.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Foot-and-mouth disease virus - type A / References: UniProt: P49303*PLUS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.5 Å3/Da / Density % sol: 50.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium acetate pH4.6 25% polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.31→88.16 Å / Num. obs: 19686 / % possible obs: 89.9 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.01538 / Net I/σ(I): 22.96
Reflection shellResolution: 2.31→2.5 Å / Rmerge(I) obs: 0.099 / Num. unique obs: 19686

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H94

5h94


Resolution: 2.31→88.16 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.879 / SU B: 17.316 / SU ML: 0.209 / Cross valid method: THROUGHOUT / ESU R: 0.456 / ESU R Free: 0.298 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27605 896 5.1 %RANDOM
Rwork0.19905 ---
obs0.2029 16579 88.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.541 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å2-0.15 Å20 Å2
2---0.29 Å2-0 Å2
3---0.95 Å2
Refinement stepCycle: 1 / Resolution: 2.31→88.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3095 0 0 132 3227
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193186
X-RAY DIFFRACTIONr_bond_other_d0.0020.022775
X-RAY DIFFRACTIONr_angle_refined_deg2.0331.9324334
X-RAY DIFFRACTIONr_angle_other_deg1.14736456
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.945378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.47923.882170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.6215507
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0961525
X-RAY DIFFRACTIONr_chiral_restr0.120.2441
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213578
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02679
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.121.891521
X-RAY DIFFRACTIONr_mcbond_other1.1111.8871520
X-RAY DIFFRACTIONr_mcangle_it1.9752.8291896
X-RAY DIFFRACTIONr_mcangle_other1.9772.8321897
X-RAY DIFFRACTIONr_scbond_it0.9841.9841665
X-RAY DIFFRACTIONr_scbond_other0.9841.9861666
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7272.9322439
X-RAY DIFFRACTIONr_long_range_B_refined4.9222.1013531
X-RAY DIFFRACTIONr_long_range_B_other4.86121.9293512
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.305→2.365 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 33 -
Rwork0.27 613 -
obs--44.67 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.459-0.6944-1.02550.38730.04931.63580.078-0.12150.062-0.0346-0.1351-0.0605-0.09660.15660.05710.07380.0189-0.04050.15540.02570.0472-32.5236-27.39515.2204
23.77460.78721.90111.6061.70785.40690.32680.46220.0169-0.379-0.1603-0.3676-0.36250.1249-0.16650.20680.13950.14370.12450.09610.1404-27.3007-21.8685-12.2283
39.2245-1.7483-2.46992.5313-1.87273.15250.1464-1.02711.90410.4643-0.0953-0.7756-0.56240.5987-0.05110.2539-0.0376-0.0570.1881-0.15250.4718-35.3003-14.080721.2019
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 275
2X-RAY DIFFRACTION2B4 - 100
3X-RAY DIFFRACTION3C1 - 9

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