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- PDB-8rh6: Crystal structure of HLA-A*11:01 in complex with SVLNDILSRL, an 1... -

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Basic information

Entry
Database: PDB / ID: 8rh6
TitleCrystal structure of HLA-A*11:01 in complex with SVLNDILSRL, an 10-mer epitope from SARS-CoV-2 Spike (S975-984)
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen
  • Spike protein S2'
KeywordsIMMUNE SYSTEM / human leukocyte antigen / major histocompatibility complex / HLA-A11 / HLA-A*11:01 / SARS-CoV-2 / Spike
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...antigen processing and presentation of peptide antigen via MHC class I / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / 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 / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / symbiont-mediated disruption of host tissue / protein homotetramerization / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / amyloid fibril formation / Induction of Cell-Cell Fusion / structural constituent of virion / intracellular iron ion homeostasis / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / learning or memory / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / immune response / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / fusion of virus membrane with host plasma membrane / external side of plasma membrane / focal adhesion / fusion of virus membrane with host endosome membrane / viral envelope / Neutrophil degranulation / symbiont entry into host cell / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome
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 / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Spike glycoprotein / Beta-2-microglobulin / HLA class I histocompatibility antigen A alpha chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.32 Å
AuthorsAhn, Y.M. / Maddumage, J.C. / Szeto, C. / Gras, S.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Curr Res Struct Biol / Year: 2024
Title: The impact of SARS-CoV-2 spike mutation on peptide presentation is HLA allomorph-specific.
Authors: Ahn, Y.M. / Maddumage, J.C. / Grant, E.J. / Chatzileontiadou, D.S.M. / Perera, W.W.J.G. / Baker, B.M. / Szeto, C. / Gras, S.
History
DepositionDec 15, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen
B: Beta-2-microglobulin
C: HLA class I histocompatibility antigen
D: Beta-2-microglobulin
E: HLA class I histocompatibility antigen
F: Beta-2-microglobulin
I: Spike protein S2'
H: Spike protein S2'
G: Spike protein S2'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,15411
Polymers161,9869
Non-polymers1682
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.850, 84.850, 311.296
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 10 or resid 12...
d_2ens_1(chain "C" and (resid 1 through 10 or resid 12...
d_3ens_1(chain "E" and (resid 1 through 10 or resid 12...
d_1ens_2(chain "B" and (resid 1 through 19 or resid 21...
d_2ens_2(chain "D" and (resid 1 through 19 or resid 21...
d_3ens_2(chain "F" and (resid 1 through 19 or resid 21...
d_1ens_3chain "G"
d_2ens_3chain "H"
d_3ens_3chain "I"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1GLYGLYTHRTHRAA1 - 1025 - 34
d_12ens_1VALVALPROPROAA12 - 4736 - 71
d_13ens_1ALAALATHRTHRAA49 - 6473 - 88
d_14ens_1ASNASNVALVALAA66 - 6790 - 91
d_15ens_1ALAALAGLNGLNAA69 - 8793 - 111
d_16ens_1GLUGLUTRPTRPAA89 - 133113 - 157
d_17ens_1ALAALATHRTHRAA135 - 271159 - 295
d_18ens_1ARGARGGLUGLUAA273 - 275297 - 299
d_21ens_1GLYGLYTHRTHRCC1 - 1025 - 34
d_22ens_1VALVALPROPROCC12 - 4736 - 71
d_23ens_1ALAALATHRTHRCC49 - 6473 - 88
d_24ens_1ASNASNVALVALCC66 - 6790 - 91
d_25ens_1ALAALAGLNGLNCC69 - 8793 - 111
d_26ens_1GLUGLUTRPTRPCC89 - 133113 - 157
d_27ens_1ALAALATHRTHRCC135 - 271159 - 295
d_28ens_1ARGARGGLUGLUCC273 - 275297 - 299
d_31ens_1GLYGLYTHRTHREE1 - 1025 - 34
d_32ens_1VALVALPROPROEE12 - 4736 - 71
d_33ens_1ALAALATHRTHREE49 - 6473 - 88
d_34ens_1ASNASNVALVALEE66 - 6790 - 91
d_35ens_1ALAALAGLNGLNEE69 - 8793 - 111
d_36ens_1GLUGLUTRPTRPEE89 - 133113 - 157
d_37ens_1ALAALATHRTHREE135 - 271159 - 295
d_38ens_1ARGARGGLUGLUEE273 - 275297 - 299
d_11ens_2ILEILELYSLYSBB1 - 192 - 20
d_12ens_2ASNASNTYRTYRBB21 - 2622 - 27
d_13ens_2SERSERGLUGLUBB28 - 4429 - 45
d_14ens_2ILEILELEULEUBB46 - 8747 - 88
d_15ens_2GLNGLNASPASPBB89 - 9890 - 99
d_21ens_2ILEILELYSLYSDD1 - 192 - 20
d_22ens_2ASNASNTYRTYRDD21 - 2622 - 27
d_23ens_2SERSERGLUGLUDD28 - 4429 - 45
d_24ens_2ILEILELEULEUDD46 - 8747 - 88
d_25ens_2GLNGLNASPASPDD89 - 9890 - 99
d_31ens_2ILEILELYSLYSFF1 - 192 - 20
d_32ens_2ASNASNTYRTYRFF21 - 2622 - 27
d_33ens_2SERSERGLUGLUFF28 - 4429 - 45
d_34ens_2ILEILELEULEUFF46 - 8747 - 88
d_35ens_2GLNGLNASPASPFF89 - 9890 - 99
d_11ens_3SERSERLEULEUGI1 - 101 - 10
d_21ens_3SERSERLEULEUHH1 - 101 - 10
d_31ens_3SERSERLEULEUIG1 - 101 - 10

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.514796180022, 0.857218761158, -0.012684185153), (-0.857196997288, -0.51442746241, 0.0240352607266), (0.0140783832432, 0.0232461058341, 0.999630640631)-41.566369923, 83.5219849647, -1.27373864975
2given(-0.493478889161, -0.869078102636, 0.0343778630815), (0.869445479939, -0.491857104698, 0.0462725185416), (-0.0233054364173, 0.0527241887148, 0.998337125703)51.5837699281, 78.7204313625, -0.435766686203
3given(-0.520690164884, 0.852669097191, -0.0428621381776), (-0.853405250044, -0.518408436295, 0.0543338971144), (0.0241087409705, 0.0648698995962, 0.997602458264)-41.6833511361, 84.5443192675, -2.97260205105
4given(-0.50569362948, -0.861992781623, 0.0352476599573), (0.862482818504, -0.504192475967, 0.0437416845054), (-0.0199334113538, 0.0525203923028, 0.998420886953)51.663202676, 79.1167350689, -0.220113492461
5given(-0.522566184003, 0.852598462027, -0.000667746792884), (-0.852476155129, -0.522477620833, 0.0173649262961), (0.0144564266976, 0.00964356148866, 0.999848995323)-41.1228130071, 83.9162327131, -0.806469647594
6given(-0.487949541936, -0.872484117287, 0.0260136427103), (0.872660192557, -0.486958291782, 0.0365487399372), (-0.0192206360848, 0.0405350113674, 0.998993233211)51.2416807257, 78.3330831768, -0.0688390813959

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Components

#1: Protein HLA class I histocompatibility antigen / HLA class I histocompatibility antigen A alpha chain / MHC class I antigen / MHC class I protein / ...HLA class I histocompatibility antigen A alpha chain / MHC class I antigen / MHC class I protein / MHC class I protein (HLA-A)


Mass: 40985.727 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLA, HLA-A11
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q5S3G3
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 3 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P61769
#3: Protein/peptide Spike protein S2'


Mass: 1130.317 Da / Num. of mol.: 3 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25% PEG3350, 0.2M NaCl and 0.1M Tris HCl pH8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953732 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953732 Å / Relative weight: 1
ReflectionResolution: 3.32→47.5 Å / Num. obs: 20087 / % possible obs: 99.6 % / Redundancy: 4.1 % / Biso Wilson estimate: 71.74 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.215 / Rpim(I) all: 0.119 / Rrim(I) all: 0.248 / Net I/σ(I): 5.9
Reflection shellResolution: 3.32→3.59 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.877 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4051 / CC1/2: 0.553 / Rpim(I) all: 0.495 / Rrim(I) all: 1.014 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5127refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.32→47.5 Å / SU ML: 0.4841 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.7599
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2514 971 4.85 %
Rwork0.2212 19051 -
obs0.2228 20022 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.67 Å2
Refinement stepCycle: LAST / Resolution: 3.32→47.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9451 0 11 0 9462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00139790
X-RAY DIFFRACTIONf_angle_d0.408713290
X-RAY DIFFRACTIONf_chiral_restr0.03831360
X-RAY DIFFRACTIONf_plane_restr0.00331758
X-RAY DIFFRACTIONf_dihedral_angle_d10.51053666
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.975667299124
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS1.11629562993
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS0.606910923532
ens_2d_3BBX-RAY DIFFRACTIONTorsion NCS0.635191542964
ens_3d_2IGX-RAY DIFFRACTIONTorsion NCS0.863192707405
ens_3d_3IGX-RAY DIFFRACTIONTorsion NCS0.383903450021
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.32-3.50.36671360.31072652X-RAY DIFFRACTION99.22
3.5-3.710.31851380.26462682X-RAY DIFFRACTION99.75
3.71-40.2921300.24182686X-RAY DIFFRACTION99.68
4-4.40.22911400.22452681X-RAY DIFFRACTION99.93
4.4-5.040.23251390.19122719X-RAY DIFFRACTION99.72
5.04-6.350.25281350.21812753X-RAY DIFFRACTION99.86
6.35-47.50.20561530.18392878X-RAY DIFFRACTION98.41
Refinement TLS params.Method: refined / Origin x: 3.10984833855 Å / Origin y: 53.4704841872 Å / Origin z: -26.6287429168 Å
111213212223313233
T0.508473681385 Å20.0837943814809 Å20.0101177459772 Å2-0.559839692521 Å2-0.0315978623605 Å2--0.567908591425 Å2
L0.100737210408 °20.196268691195 °2-0.0535107314662 °2-0.175260388509 °2-0.0145781818665 °2--0.0823593667051 °2
S-0.0304723797588 Å °0.0250816505367 Å °0.0130896695624 Å °-0.0576622861001 Å °0.0235367893118 Å °-0.0188826120203 Å °0.0108484216048 Å °0.0124946841357 Å °0.0115945155291 Å °
Refinement TLS groupSelection details: all

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