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- PDB-8cmh: Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV... -

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Basic information

Entry
Database: PDB / ID: 8cmh
TitleHuman Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Omicron (BA.1) Spike peptide S486-505
Components
  • HLA class II histocompatibility antigen, DR alpha chain
  • Human leukocyte antigen DR beta chain allotype DR1 (DRB1*0101)
  • Spike protein S2'
KeywordsIMMUNE SYSTEM / HLA-II / HLA-DR / HLA-DR1 / human leukocyte antigen / major histocompatibility complex / major histocompatibility complex class 2 / SARS-CoV-2 / coronavirus / COVID-19 / Spike / omicron / BA.1 / viral variant / immune escape
Function / homology
Function and homology information


myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / transport vesicle membrane ...myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / transport vesicle membrane / polysaccharide binding / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Generation of second messenger molecules / immunological synapse / PD-1 signaling / T cell receptor binding / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / cognition / peptide antigen assembly with MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / MHC class II protein complex / peptide antigen binding / endocytic vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / Interferon gamma signaling / positive regulation of immune response / positive regulation of T cell activation / Downstream TCR signaling / MHC class II protein complex binding / late endosome membrane / early endosome membrane / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / adaptive immune response / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / lysosome / receptor ligand activity / host cell surface receptor binding / immune response / lysosomal membrane / fusion of virus membrane with host plasma membrane / Golgi membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / cell surface / extracellular exosome / membrane / identical protein binding / plasma membrane
Similarity search - Function
MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / 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 ...MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / 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 / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, 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, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
2-AMINO-ETHANETHIOL / HLA class II histocompatibility antigen, DR alpha chain / Spike glycoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsMacLachlan, B.J. / Mason, G.H. / Sourfield, D.O. / Godkin, A.J. / Rizkallah, P.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other government United Kingdom
CitationJournal: Cell Rep / Year: 2023
Title: Structural definition of HLA class II-presented SARS-CoV-2 epitopes reveals a mechanism to escape pre-existing CD4 + T cell immunity.
Authors: Chen, Y. / Mason, G.H. / Scourfield, D.O. / Greenshields-Watson, A. / Haigh, T.A. / Sewell, A.K. / Long, H.M. / Gallimore, A.M. / Rizkallah, P. / MacLachlan, B.J. / Godkin, A.
History
DepositionFeb 19, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 3, 2024Group: Data collection / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / struct_conn / struct_conn_type
Item: _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class II histocompatibility antigen, DR alpha chain
B: Human leukocyte antigen DR beta chain allotype DR1 (DRB1*0101)
C: Spike protein S2'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,22435
Polymers46,1893
Non-polymers2,03532
Water5,855325
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13830 Å2
ΔGint26 kcal/mol
Surface area18510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.034, 120.186, 40.879
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein HLA class II histocompatibility antigen, DR alpha chain / MHC class II antigen DRA


Mass: 21287.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01903
#2: Protein Human leukocyte antigen DR beta chain allotype DR1 (DRB1*0101)


Mass: 22487.186 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Spike protein S2' / SARS-Cov-2 Omicron (BA.1) Spike epitope S486-505


Mass: 2414.719 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC2

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Non-polymers , 4 types, 357 molecules

#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-DHL / 2-AMINO-ETHANETHIOL / 2,3-DESHYDROLANTHIONINE / Cysteamine


Type: L-peptide linking / Mass: 77.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H7NS
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 2.42 Å3/Da / Density % sol: 49.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M Sodium cacodylate pH 6.0, 25 % PEG4000, 0.2 M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.64→50.16 Å / Num. obs: 55347 / % possible obs: 98.92 % / Redundancy: 13.6 % / Biso Wilson estimate: 19.44 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.341 / Rpim(I) all: 0.0949 / Rrim(I) all: 0.354 / Net I/σ(I): 6.2
Reflection shellResolution: 1.64→1.7 Å / Redundancy: 14.1 % / Rmerge(I) obs: 3.678 / Mean I/σ(I) obs: 0.59 / Num. unique obs: 5416 / CC1/2: 0.34 / CC star: 0.712 / Rpim(I) all: 1.005 / Rrim(I) all: 3.815 / % possible all: 97.87

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
DIALSdata scaling
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→50.15 Å / SU ML: 0.2157 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.8655
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2082 2731 4.94 %
Rwork0.1824 52606 -
obs0.1836 55337 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.8 Å2
Refinement stepCycle: LAST / Resolution: 1.64→50.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3189 0 129 325 3643
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00523428
X-RAY DIFFRACTIONf_angle_d0.80124612
X-RAY DIFFRACTIONf_chiral_restr0.057484
X-RAY DIFFRACTIONf_plane_restr0.0057598
X-RAY DIFFRACTIONf_dihedral_angle_d6.7922479
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.670.33541390.33622570X-RAY DIFFRACTION99.12
1.67-1.70.35381440.31282551X-RAY DIFFRACTION96.39
1.7-1.730.32881040.29682605X-RAY DIFFRACTION99.19
1.73-1.770.29041210.27862581X-RAY DIFFRACTION97.58
1.77-1.80.2891450.25692562X-RAY DIFFRACTION98.47
1.8-1.850.24511340.23352601X-RAY DIFFRACTION98.28
1.85-1.890.24421420.23112550X-RAY DIFFRACTION98.61
1.89-1.940.24851300.22062608X-RAY DIFFRACTION97.93
1.94-20.24931310.21952615X-RAY DIFFRACTION99.71
2-2.070.25011370.19392589X-RAY DIFFRACTION98.13
2.07-2.140.21531290.18132642X-RAY DIFFRACTION99.57
2.14-2.230.22371490.16882589X-RAY DIFFRACTION99.1
2.23-2.330.20731490.17472600X-RAY DIFFRACTION98.88
2.33-2.450.21951370.17692651X-RAY DIFFRACTION99.22
2.45-2.60.20711310.17162659X-RAY DIFFRACTION99.43
2.6-2.80.1931390.17662632X-RAY DIFFRACTION99.57
2.8-3.090.18731430.16512679X-RAY DIFFRACTION99.72
3.09-3.530.17851410.15662704X-RAY DIFFRACTION99.65
3.53-4.450.14551340.14112735X-RAY DIFFRACTION99.86
4.45-50.150.20111520.16392883X-RAY DIFFRACTION99.8
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)
15.268824678683.19707896075-2.90256008364.00473130958-0.8604639182552.031031110010.00633708982435-0.0809346781367-0.1997438139080.0606461139777-0.03479123586-0.201493278683-0.04681485062860.154152100244-0.02588453901320.0989505751654-0.00766490898143-0.0235454705450.1159451769180.004516497167890.073899416614423.102957672214.66530754213.91659277969
23.627449761811.30221877483-0.138467934664.445010199210.1718746731654.2967023250.01496240277260.1403929395170.287049509964-0.1258015529870.006976877760360.139461979996-0.258356427167-0.0909092680788-0.02378094940680.09717810091790.00105833543476-0.00503305603990.1071993303920.008090864010520.098814379294922.219229693625.5419265659-2.44768365196
30.6460564827490.710363058217-0.4857815071321.52041058988-0.7246817899891.60908288997-0.09267698082580.0803259977057-0.0959143266005-0.1472735857070.0441733195869-0.02025926642260.172309792608-0.08286171255370.05857528605770.09420416930390.00654567101448-0.003777953113680.1226586141340.00106229784220.1451548285414.88143329014.198554076014.94829600632
41.595890584890.6217377617150.03077376342785.732565980691.403738467071.416706233150.0111464118323-0.03777066375030.29669172195-0.026228793255-0.03300036874290.00532523309002-0.211078809704-0.01037052286510.02550008438940.130329296578-0.00351596583108-0.003510249185820.1118902313060.000775533030190.12023357650215.232640141431.567515591418.2338828092
52.07137259283-3.25614548512-0.6169588929946.946453938750.9794757057331.545488786370.0675729642362-0.02704726763130.0848101319174-0.0938260868165-0.0528710469605-0.0700379021163-0.04959553930350.0521500529063-0.01718173647730.125917609704-0.0331056941138-0.01208806906330.1566177878390.005457893337350.13656193900319.802529611823.244742220313.11948424
61.575466964531.145296311480.87576679840.8270145082120.6636429062851.912204043440.125761932604-0.1841302284410.4320448058890.297135936893-0.2138082189740.616226008372-0.258102065892-0.1221725020440.1100929542820.1810805689230.003827772434770.0496453718030.153393813565-0.06532499755290.27833732095110.227675443135.210847719323.43496013
72.896993515032.200652186120.682537476796.618386018543.092932776253.527770618160.124684587882-0.2559545846290.2063151939030.735056268519-0.1878907089850.213536149980.132860019095-0.04540421363390.0608966074970.152329900460.00827334279956-0.01595177733820.167815773728-0.01098921954980.10455897834612.292991000726.186194240725.9784381585
81.917418990510.254663941611-0.6926922495141.65475162945-0.5545682236491.37288564694-0.143372496291-0.0499022665108-0.368032400424-0.194389320114-0.0826194055417-0.3273251305690.2372303866310.245349260770.2166084028270.1514380431880.01243231425250.02303148202420.1604234586820.00357429263540.17711499291229.58620668316.023622143782.1219371964
91.440732677480.9136923983490.6230459572332.0741420741.242154873782.573958279380.0260284931483-0.1127290537070.01189912498550.1415113046670.0101347397307-0.01326969010750.0598992762881-0.0285985785507-0.04019813550860.09971609307710.00500703224405-0.004512925524860.114015009721-0.001869349423040.1033297988237.29723910738.656102891224.1856516867
104.621105204552.60477597771-0.4237881258227.03293618451-1.97674574274.65519027525-0.4480407544460.347512917268-0.555240032921-1.128375875780.4394769142120.5504146887310.639801796711-0.196839905818-0.04631543816740.249784056452-0.05079503738540.04583496061560.220922266852-0.03734523321920.29918155130625.52547779879.89533530789-7.91000615423
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 26 )AA3 - 261 - 24
22chain 'A' and (resid 27 through 55 )AA27 - 5525 - 53
33chain 'A' and (resid 56 through 87 )AA56 - 8754 - 85
44chain 'A' and (resid 88 through 133 )AA88 - 13386 - 131
55chain 'A' and (resid 134 through 154 )AA134 - 154132 - 152
66chain 'A' and (resid 155 through 166 )AA155 - 166153 - 164
77chain 'A' and (resid 167 through 182 )AA167 - 182165 - 180
88chain 'B' and (resid -2 through 89 )BB-2 - 892 - 93
99chain 'B' and (resid 90 through 190 )BB90 - 19094 - 194
1010chain 'C' and (resid 1 through 14 )CC1 - 141 - 14

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