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- PDB-7emb: Mooring Stone-Like Arg114 Pulls Diverse Bulged Peptides: First In... -

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Basic information

Entry
Database: PDB / ID: 7emb
TitleMooring Stone-Like Arg114 Pulls Diverse Bulged Peptides: First Insight into African Swine Fever Virus-Derived T Cell Epitopes Presented by Swine Major Histocompatibility Complex Class I
Components
  • ALA-ALA-ALA-ILE-GLU-GLU-GLU-ASP-ILE
  • Beta-2-microglobulin
  • Leucocyte antigen
KeywordsIMMUNE SYSTEM / MHC I
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 / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex ...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 / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / phagocytic vesicle membrane / MHC class II protein complex binding / late endosome membrane / immune response / lysosomal membrane / extracellular region
Similarity search - Function
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 / : ...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
Leucocyte antigen / Beta-2-microglobulin
Similarity search - Component
Biological speciesSus scrofa (pig)
uncultured virus (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsYue, C. / Xiang, W. / Huang, X. / Sun, Y. / Xiao, J. / Liu, K. / Sun, Z. / Qiao, P. / Li, H. / Gan, J. ...Yue, C. / Xiang, W. / Huang, X. / Sun, Y. / Xiao, J. / Liu, K. / Sun, Z. / Qiao, P. / Li, H. / Gan, J. / Ba, L. / Chai, Y. / Qi, J. / Liu, P. / Qi, P. / Zhao, Y. / Li, Y. / Qiu, H.J. / Gao, G.F. / Gao, G. / Liu, W.J.
CitationJournal: J.Virol. / Year: 2022
Title: Mooring Stone-Like Arg 114 Pulls Diverse Bulged Peptides: First Insight into African Swine Fever Virus-Derived T Cell Epitopes Presented by Swine Major Histocompatibility Complex Class I.
Authors: Yue, C. / Xiang, W. / Huang, X. / Sun, Y. / Xiao, J. / Liu, K. / Sun, Z. / Qiao, P. / Li, H. / Gan, J. / Ba, L. / Chai, Y. / Qi, J. / Liu, P. / Qi, P. / Zhao, Y. / Li, Y. / Qiu, H.J. / Gao, ...Authors: Yue, C. / Xiang, W. / Huang, X. / Sun, Y. / Xiao, J. / Liu, K. / Sun, Z. / Qiao, P. / Li, H. / Gan, J. / Ba, L. / Chai, Y. / Qi, J. / Liu, P. / Qi, P. / Zhao, Y. / Li, Y. / Qiu, H.J. / Gao, G.F. / Gao, G. / Liu, W.J.
History
DepositionApr 13, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _struct.title
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leucocyte antigen
B: Beta-2-microglobulin
C: ALA-ALA-ALA-ILE-GLU-GLU-GLU-ASP-ILE


Theoretical massNumber of molelcules
Total (without water)44,4933
Polymers44,4933
Non-polymers00
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-15 kcal/mol
Surface area18970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.745, 111.407, 46.042
Angle α, β, γ (deg.)90.000, 102.295, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Leucocyte antigen / MHC class I antigen


Mass: 31825.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: sla-, SLA-1 / Production host: Escherichia coli (E. coli) / References: UniProt: O19075
#2: Protein Beta-2-microglobulin / Lactollin


Mass: 11708.207 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 ALA-ALA-ALA-ILE-GLU-GLU-GLU-ASP-ILE


Mass: 959.994 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) uncultured virus (environmental samples)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.35 Å3/Da / Density % sol: 47.68 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Ammonium acetate,0.1 M BIS-TRIS pH 5.5,17% w/v Polyethylene glycol 10,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.97→55.7 Å / Num. obs: 29130 / % possible obs: 99.7 % / Redundancy: 6.4 % / Biso Wilson estimate: 33.51 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 8.1
Reflection shellResolution: 1.97→2.07 Å / Rmerge(I) obs: 0.414 / Num. unique obs: 29130

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Processing

Software
NameVersionClassification
HKL-20001.13_2998data scaling
PHASERphasing
Cootmodel building
PHENIX1.13_2998refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QQ3

3qq3


Resolution: 1.97→25.09 Å / SU ML: 0.2634 / Cross valid method: NONE / σ(F): 1.43 / Phase error: 35.1239 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2832 1474 5.09 %
Rwork0.2176 27474 -
obs0.2208 28948 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.95 Å2
Refinement stepCycle: LAST / Resolution: 1.97→25.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3117 0 0 97 3214
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00733204
X-RAY DIFFRACTIONf_angle_d0.84984353
X-RAY DIFFRACTIONf_chiral_restr0.0509442
X-RAY DIFFRACTIONf_plane_restr0.0065577
X-RAY DIFFRACTIONf_dihedral_angle_d10.53351911
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.030.38011370.33722477X-RAY DIFFRACTION98.83
2.03-2.10.36871460.30722495X-RAY DIFFRACTION98.88
2.1-2.190.31241230.2812507X-RAY DIFFRACTION99.73
2.19-2.290.37221440.2782461X-RAY DIFFRACTION98.86
2.29-2.410.34061500.25942484X-RAY DIFFRACTION99.51
2.41-2.560.3611250.25672492X-RAY DIFFRACTION99.54
2.56-2.750.33541260.24892510X-RAY DIFFRACTION99.47
2.75-3.030.30281330.25242500X-RAY DIFFRACTION99.36
3.03-3.470.30471360.22772514X-RAY DIFFRACTION99.1
3.47-4.370.25641300.18072486X-RAY DIFFRACTION99.2
4.37-25.090.19361240.16332548X-RAY DIFFRACTION98.93

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