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- PDB-7p3e: MHC I A02 Allele presenting YLQLRTFLL -

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Basic information

Entry
Database: PDB / ID: 7p3e
TitleMHC I A02 Allele presenting YLQLRTFLL
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • MHC class I antigen
  • TYR-LEU-GLN-LEU-ARG-THR-PHE-LEU-LEU
KeywordsIMMUNE SYSTEM / Viral epitope / Escape mutant / S protein epitope / P272L variant / MHC presentation
Function / homology
Function and homology information


antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway ...antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / positive regulation of T cell mediated cytotoxicity / MHC class II protein complex / cellular response to nicotine / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / ER-Phagosome pathway / iron ion transport / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / signaling receptor binding / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
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 ...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
IODIDE ION / DI(HYDROXYETHYL)ETHER / MHC class I antigen / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome-related coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsRizkallah, P.J. / Sewell, A.K. / Wall, A. / Fuller, A.
CitationJournal: Cell / Year: 2022
Title: Emergence of immune escape at dominant SARS-CoV-2 killer T cell epitope.
Authors: Dolton, G. / Rius, C. / Hasan, M.S. / Wall, A. / Szomolay, B. / Behiry, E. / Whalley, T. / Southgate, J. / Fuller, A. / Morin, T. / Topley, K. / Tan, L.R. / Goulder, P.J.R. / Spiller, O.B. / ...Authors: Dolton, G. / Rius, C. / Hasan, M.S. / Wall, A. / Szomolay, B. / Behiry, E. / Whalley, T. / Southgate, J. / Fuller, A. / Morin, T. / Topley, K. / Tan, L.R. / Goulder, P.J.R. / Spiller, O.B. / Rizkallah, P.J. / Jones, L.C. / Connor, T.R. / Sewell, A.K.
History
DepositionJul 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Aug 17, 2022Group: Database references / Category: citation / citation_author
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.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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: TYR-LEU-GLN-LEU-ARG-THR-PHE-LEU-LEU
D: MHC class I antigen
E: Beta-2-microglobulin
F: TYR-LEU-GLN-LEU-ARG-THR-PHE-LEU-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,25432
Polymers89,9966
Non-polymers3,25826
Water2,360131
1
A: MHC class I antigen
B: Beta-2-microglobulin
C: TYR-LEU-GLN-LEU-ARG-THR-PHE-LEU-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,62716
Polymers44,9983
Non-polymers1,62913
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6660 Å2
ΔGint-22 kcal/mol
Surface area18520 Å2
MethodPISA
2
D: MHC class I antigen
E: Beta-2-microglobulin
F: TYR-LEU-GLN-LEU-ARG-THR-PHE-LEU-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,62716
Polymers44,9983
Non-polymers1,62913
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7060 Å2
ΔGint-22 kcal/mol
Surface area18880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.802, 85.802, 217.564
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number153
Space group name H-MP3212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYPROPROAA1 - 2761 - 276
21GLYGLYPROPRODD1 - 2761 - 276
12METMETMETMETBB0 - 991 - 100
22METMETMETMETEE0 - 991 - 100

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ADBE

#1: Protein MHC class I antigen


Mass: 31951.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5B8RNS7
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769

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Protein/peptide , 1 types, 2 molecules CF

#3: Protein/peptide TYR-LEU-GLN-LEU-ARG-THR-PHE-LEU-LEU


Mass: 1167.420 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: SARS-Cov 2 epitope
Source: (synth.) Severe acute respiratory syndrome-related coronavirus

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Non-polymers , 3 types, 157 molecules

#4: Chemical...
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: I
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.57 Å3/Da / Density % sol: 52.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M sodium iodide, 0.1 M Bis Tris propane pH 7.5, and 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91808 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91808 Å / Relative weight: 1
ReflectionResolution: 2→74.31 Å / Num. obs: 62446 / % possible obs: 99.7 % / Redundancy: 11.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.027 / Rrim(I) all: 0.09 / Net I/σ(I): 15.1 / Num. measured all: 720769 / Scaling rejects: 770
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.0511.81.0945225544150.7790.3341.1452.396.3
8.93-74.3111.40.03489727870.9980.0110.03646.1100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.91 Å74.27 Å
Translation3.91 Å74.27 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.7data scaling
PHASER2.8.3phasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I4W

4i4w


Resolution: 2→74.31 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.94 / SU B: 10.769 / SU ML: 0.147 / SU R Cruickshank DPI: 0.1932 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.193 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2479 3051 4.9 %RANDOM
Rwork0.2141 ---
obs0.2158 59258 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 138.75 Å2 / Biso mean: 46.994 Å2 / Biso min: 26.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å2-0.25 Å2-0 Å2
2---0.49 Å20 Å2
3---1.59 Å2
Refinement stepCycle: final / Resolution: 2→74.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6348 0 38 131 6517
Biso mean--57.5 42.71 -
Num. residues----770
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0136556
X-RAY DIFFRACTIONr_bond_other_d0.0020.0175842
X-RAY DIFFRACTIONr_angle_refined_deg1.4641.6578893
X-RAY DIFFRACTIONr_angle_other_deg1.2511.58413445
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9325766
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.13321.241411
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.169151068
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9491558
X-RAY DIFFRACTIONr_chiral_restr0.0670.2801
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.027492
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021656
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A85510.12
12D85510.12
21B29100.14
22E29100.14
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 226 -
Rwork0.291 4327 -
all-4553 -
obs--99.61 %
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)
11.98290.4512-0.64583.7728-0.57171.2869-0.09930.4415-0.4046-0.15170.1384-0.23510.1489-0.0395-0.03910.021-0.02890.00650.2957-0.11760.21512.391629.19616.3951
25.232-1.34130.80422.0375-0.05382.9196-0.0876-0.1257-0.22350.06270.15760.0691-0.1503-0.4726-0.070.0815-0.0586-0.00590.19810.00410.1901-22.12622.673723.5208
33.7911.1689-1.62133.0592-1.29754.94290.1373-0.11-0.25990.3969-0.02210.2264-0.0975-0.1928-0.11520.0679-0.019-0.00740.0920.01240.1607-5.293329.609337.2593
42.6632-0.0529-0.53153.0751-1.23022.20230.01150.14010.2071-0.0979-0.07760.1449-0.154-0.08870.06610.17460.0792-0.10430.0436-0.02970.200523.693621.363761.069
54.5088-3.10260.15416.32931.95371.8661-0.12920.0186-0.07760.4130.13160.23510.40130.2348-0.00240.2280.06020.03450.0770.02470.153232.472-13.436863.8875
63.86261.1904-1.26795.5774-0.61942.9653-0.24490.7538-0.7176-0.76170.02110.55180.5243-0.69620.22370.3951-0.0038-0.13970.3196-0.23450.418.5502-2.772148.9898
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 180
2X-RAY DIFFRACTION1C1 - 10
3X-RAY DIFFRACTION2A181 - 276
4X-RAY DIFFRACTION3B0 - 99
5X-RAY DIFFRACTION4D1 - 180
6X-RAY DIFFRACTION4F1 - 10
7X-RAY DIFFRACTION5D181 - 276
8X-RAY DIFFRACTION6E0 - 99

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