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

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Basic information

Entry
Database: PDB / ID: 7ema
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
  • Beta-2-microglobulin
  • Leucocyte antigen
  • TYR-SER-SER-ASP-VAL-THR-THR-LEU-VAL
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: 1.8 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 1.2Jun 7, 2023Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 30, 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: Leucocyte antigen
B: Beta-2-microglobulin
C: TYR-SER-SER-ASP-VAL-THR-THR-LEU-VAL


Theoretical massNumber of molelcules
Total (without water)44,5173
Polymers44,5173
Non-polymers00
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-16 kcal/mol
Surface area18490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.391, 107.350, 46.105
Angle α, β, γ (deg.)90.000, 101.715, 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 TYR-SER-SER-ASP-VAL-THR-THR-LEU-VAL


Mass: 984.059 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.: 278 / 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: 2.25 Å3/Da / Density % sol: 45.41 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES pH 7.5, 30% w/v Polyethylene glycol 1,000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.03997 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Dec 24, 2019
RadiationMonochromator: 1.03997 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03997 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 36183 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 16.17 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 5.35
Reflection shellResolution: 1.8→1.87 Å / Rmerge(I) obs: 0.529 / Num. unique obs: 36183

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASERphasing
Cootmodel building
PHENIX1.13_2998refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QQ3

3qq3


Resolution: 1.8→26.82 Å / SU ML: 0.2218 / Cross valid method: NONE / σ(F): 1.41 / Phase error: 21.7708 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2238 1836 5.08 %
Rwork0.1835 34280 -
obs0.1855 36116 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.64 Å2
Refinement stepCycle: LAST / Resolution: 1.8→26.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3119 0 0 278 3397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00623207
X-RAY DIFFRACTIONf_angle_d0.83614359
X-RAY DIFFRACTIONf_chiral_restr0.0525445
X-RAY DIFFRACTIONf_plane_restr0.0055575
X-RAY DIFFRACTIONf_dihedral_angle_d10.42361909
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.28211250.23372507X-RAY DIFFRACTION95.43
1.85-1.910.24681560.23412650X-RAY DIFFRACTION99.89
1.91-1.970.27561460.2112627X-RAY DIFFRACTION99.93
1.97-2.040.26121490.20772607X-RAY DIFFRACTION99.82
2.04-2.120.24861740.2042642X-RAY DIFFRACTION99.89
2.12-2.220.27671470.19982639X-RAY DIFFRACTION99.96
2.22-2.330.26661220.20442662X-RAY DIFFRACTION99.86
2.33-2.480.24291120.19042640X-RAY DIFFRACTION99.6
2.48-2.670.24081450.19812646X-RAY DIFFRACTION99.96
2.67-2.940.21731410.18792662X-RAY DIFFRACTION100
2.94-3.360.1991260.17652659X-RAY DIFFRACTION99.79
3.36-4.230.18691450.14992674X-RAY DIFFRACTION99.93
4.23-26.820.18611480.15632665X-RAY DIFFRACTION99.36

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