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

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Entry
Database: PDB / ID: 7emc
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-THR-GLU-ILE-ARG-GLU-LEU-LEU-VAL
  • Beta-2-microglobulin
  • Leucocyte antigen
KeywordsIMMUNE SYSTEM / MHC class 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 / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent ...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 / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / 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 / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / 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 / MHC class II protein complex binding / late endosome membrane / immune response / external side of plasma membrane / lysosomal membrane / signaling receptor binding / extracellular space / 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: 1.9 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 13, 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-THR-GLU-ILE-ARG-GLU-LEU-LEU-VAL
D: Leucocyte antigen
E: Beta-2-microglobulin
F: ALA-THR-GLU-ILE-ARG-GLU-LEU-LEU-VAL
G: Leucocyte antigen
H: Beta-2-microglobulin
I: ALA-THR-GLU-ILE-ARG-GLU-LEU-LEU-VAL


Theoretical massNumber of molelcules
Total (without water)133,7339
Polymers133,7339
Non-polymers00
Water25,5091416
1
A: Leucocyte antigen
B: Beta-2-microglobulin
C: ALA-THR-GLU-ILE-ARG-GLU-LEU-LEU-VAL


Theoretical massNumber of molelcules
Total (without water)44,5783
Polymers44,5783
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-13 kcal/mol
Surface area18850 Å2
MethodPISA
2
D: Leucocyte antigen
E: Beta-2-microglobulin
F: ALA-THR-GLU-ILE-ARG-GLU-LEU-LEU-VAL


Theoretical massNumber of molelcules
Total (without water)44,5783
Polymers44,5783
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-11 kcal/mol
Surface area19020 Å2
MethodPISA
3
G: Leucocyte antigen
H: Beta-2-microglobulin
I: ALA-THR-GLU-ILE-ARG-GLU-LEU-LEU-VAL


Theoretical massNumber of molelcules
Total (without water)44,5783
Polymers44,5783
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-12 kcal/mol
Surface area18840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.534, 110.632, 136.228
Angle α, β, γ (deg.)90.000, 95.422, 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.: 3
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.: 3
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-THR-GLU-ILE-ARG-GLU-LEU-LEU-VAL


Mass: 1044.222 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) uncultured virus (environmental samples)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1416 / 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: 2.33 Å3/Da / Density % sol: 47.21 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M BIS-TRIS pH6.5,16%w/v polyethylene glycol 10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 95001 / % possible obs: 98.3 % / Redundancy: 6.8 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 8.92
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.219 / Num. unique obs: 95001

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Processing

Software
NameVersionClassification
XDS1.13_2998data scaling
PHASERphasing
Cootmodel building
PHENIX1.13_2998refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QQ3

3qq3


Resolution: 1.9→45.21 Å / SU ML: 0.1832 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 25.7025 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.226 4738 5 %
Rwork0.1802 90067 -
obs0.1825 94805 98.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.86 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9372 0 0 1416 10788
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00689637
X-RAY DIFFRACTIONf_angle_d0.835613096
X-RAY DIFFRACTIONf_chiral_restr0.05141336
X-RAY DIFFRACTIONf_plane_restr0.0051732
X-RAY DIFFRACTIONf_dihedral_angle_d13.09926294
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.29571310.22862860X-RAY DIFFRACTION94.23
1.92-1.940.26641360.20432977X-RAY DIFFRACTION97.01
1.94-1.970.24761420.18292988X-RAY DIFFRACTION96.99
1.97-1.990.23261650.17112976X-RAY DIFFRACTION97.21
1.99-2.020.23841500.1742961X-RAY DIFFRACTION97.46
2.02-2.040.22111620.18142935X-RAY DIFFRACTION97.39
2.04-2.070.23221690.17893031X-RAY DIFFRACTION97.44
2.07-2.10.26441560.18482936X-RAY DIFFRACTION97.45
2.1-2.140.25821490.1832978X-RAY DIFFRACTION97.48
2.14-2.170.25081530.18013014X-RAY DIFFRACTION97.96
2.17-2.210.22251560.17822967X-RAY DIFFRACTION97.65
2.21-2.250.20481700.18012969X-RAY DIFFRACTION97.82
2.25-2.290.23881600.17913008X-RAY DIFFRACTION97.96
2.29-2.340.22791610.18662974X-RAY DIFFRACTION98
2.34-2.390.22761560.18533015X-RAY DIFFRACTION98.11
2.39-2.450.25161620.18533062X-RAY DIFFRACTION98.41
2.45-2.510.23791420.18542975X-RAY DIFFRACTION98.55
2.51-2.580.22911720.18843019X-RAY DIFFRACTION98.67
2.58-2.650.24661600.1993005X-RAY DIFFRACTION98.81
2.65-2.740.24511910.18793020X-RAY DIFFRACTION98.71
2.74-2.830.22091610.19163000X-RAY DIFFRACTION98.94
2.83-2.950.22681700.18193069X-RAY DIFFRACTION98.99
2.95-3.080.2221840.18362958X-RAY DIFFRACTION98.99
3.08-3.240.23671650.18583062X-RAY DIFFRACTION99.17
3.24-3.450.23241530.17313069X-RAY DIFFRACTION98.96
3.45-3.710.19521570.16783013X-RAY DIFFRACTION99.03
3.71-4.090.19461590.16843066X-RAY DIFFRACTION98.93
4.09-4.680.18771450.15463038X-RAY DIFFRACTION98.73
4.68-5.890.21771480.16693104X-RAY DIFFRACTION98.97
5.89-45.210.22511530.20053018X-RAY DIFFRACTION96.41

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