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

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Basic information

Entry
Database: PDB / ID: 7emd
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-GLY-ASP-PHE-PHE-HIS-ASP-MET-VAL
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 / 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: 1.7 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 20, 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: TYR-GLY-ASP-PHE-PHE-HIS-ASP-MET-VAL


Theoretical massNumber of molelcules
Total (without water)44,6653
Polymers44,6653
Non-polymers00
Water9,602533
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-12 kcal/mol
Surface area18850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.320, 110.810, 45.989
Angle α, β, γ (deg.)90.000, 102.221, 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-GLY-ASP-PHE-PHE-HIS-ASP-MET-VAL


Mass: 1131.237 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.: 533 / 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: 2.3 Å3/Da / Density % sol: 46.61 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: no

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.03836 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 19, 2016
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03836 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 43514 / % possible obs: 98 % / Redundancy: 6.9 % / Biso Wilson estimate: 12.31 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 5.71
Reflection shellResolution: 1.7→2.28 Å / Rmerge(I) obs: 0.319 / Num. unique obs: 43514

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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: 1.7→44.95 Å / SU ML: 0.2236 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 28.1154 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2603 2054 4.97 %
Rwork0.2079 39257 -
obs0.2106 41311 93.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.91 Å2
Refinement stepCycle: LAST / Resolution: 1.7→44.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3126 0 0 533 3659
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00663217
X-RAY DIFFRACTIONf_angle_d0.86994370
X-RAY DIFFRACTIONf_chiral_restr0.049440
X-RAY DIFFRACTIONf_plane_restr0.0054578
X-RAY DIFFRACTIONf_dihedral_angle_d11.25031908
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.3141060.24542030X-RAY DIFFRACTION72.58
1.74-1.780.34161140.25352185X-RAY DIFFRACTION77.25
1.78-1.830.29721210.25342301X-RAY DIFFRACTION82.86
1.83-1.880.32951250.25432516X-RAY DIFFRACTION88.98
1.88-1.950.32441210.2622629X-RAY DIFFRACTION93.13
1.95-2.020.25511380.24582739X-RAY DIFFRACTION97.86
2.02-2.10.28551350.23792775X-RAY DIFFRACTION98.11
2.1-2.190.27441440.23222786X-RAY DIFFRACTION98.49
2.19-2.310.31761600.23562701X-RAY DIFFRACTION97.05
2.31-2.450.26971520.22122750X-RAY DIFFRACTION98.74
2.45-2.640.2571350.22142777X-RAY DIFFRACTION99.01
2.64-2.910.29741570.20992763X-RAY DIFFRACTION98.52
2.91-3.330.25631330.18852754X-RAY DIFFRACTION97.5
3.33-4.190.22341780.1562778X-RAY DIFFRACTION98.83
4.19-44.950.17791350.1652773X-RAY DIFFRACTION96.84

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