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

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Basic information

Entry
Database: PDB / ID: 8cmb
TitleHuman Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 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
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 / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / polysaccharide binding / Generation of second messenger molecules / immunological synapse / Co-inhibition by PD-1 / T cell receptor binding / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / peptide antigen binding / positive regulation of T cell mediated cytotoxicity / cognition / Interferon gamma signaling / MHC class II protein complex binding / endocytic vesicle membrane / late endosome membrane / Downstream TCR signaling / early endosome membrane / symbiont-mediated disruption of host tissue / 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 / adaptive immune response / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / lysosome / 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 / Golgi membrane / lysosomal membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / 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 / cell surface / extracellular exosome / identical protein binding / membrane / 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 ...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 / 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
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: 1.84 Å
AuthorsMacLachlan, B.J. / Mason, G.H. / 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)46,77514
Polymers46,0773
Non-polymers69811
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9940 Å2
ΔGint-21 kcal/mol
Surface area18410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.290, 136.120, 41.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab

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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 Spike epitope S486-505


Mass: 2302.519 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 , 3 types, 207 molecules

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


Mass: 62.068 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: C2H6O2
#5: Chemical ChemComp-DHL / 2-AMINO-ETHANETHIOL / 2,3-DESHYDROLANTHIONINE


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


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.72 Å3/Da / Density % sol: 54.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M MES pH 6.0, 20 % PEG1500

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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: Oct 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.84→42.43 Å / Num. obs: 84216 / % possible obs: 100 % / Redundancy: 13 % / Biso Wilson estimate: 36.33 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.126 / Rrim(I) all: 0.137 / Net I/σ(I): 7.71
Reflection shellResolution: 1.84→1.9 Å / Redundancy: 13.9 % / Rmerge(I) obs: 3.046 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4359 / CC1/2: 0.368 / CC star: 0.734 / Rpim(I) all: 0.842 / Rrim(I) all: 3.162 / % possible all: 99.98

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→41.18 Å / SU ML: 0.2937 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.2549
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2312 2182 4.9 %
Rwork0.1931 42341 -
obs0.195 44523 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.93 Å2
Refinement stepCycle: LAST / Resolution: 1.84→41.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3183 0 44 196 3423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01553339
X-RAY DIFFRACTIONf_angle_d1.36544525
X-RAY DIFFRACTIONf_chiral_restr0.0822476
X-RAY DIFFRACTIONf_plane_restr0.012594
X-RAY DIFFRACTIONf_dihedral_angle_d7.6413448
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.880.45631350.39722602X-RAY DIFFRACTION99.96
1.88-1.920.38521390.33942579X-RAY DIFFRACTION99.96
1.92-1.970.35391530.29962618X-RAY DIFFRACTION100
1.97-2.030.32511490.25892571X-RAY DIFFRACTION100
2.03-2.080.29091210.2382623X-RAY DIFFRACTION100
2.08-2.150.27071340.24142633X-RAY DIFFRACTION100
2.15-2.230.29581280.23642602X-RAY DIFFRACTION99.89
2.23-2.320.30221290.22212618X-RAY DIFFRACTION100
2.32-2.420.25431330.20832651X-RAY DIFFRACTION99.96
2.42-2.550.24221390.20082629X-RAY DIFFRACTION100
2.55-2.710.28061280.20772649X-RAY DIFFRACTION99.96
2.71-2.920.22041240.21252652X-RAY DIFFRACTION100
2.92-3.210.23091380.20262669X-RAY DIFFRACTION100
3.22-3.680.20791440.18972675X-RAY DIFFRACTION100
3.68-4.630.17641340.14972721X-RAY DIFFRACTION100
4.63-41.180.20721540.15382849X-RAY DIFFRACTION99.87
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)
18.642420157234.30638353363-2.572910832875.26017307283-1.298313358851.97785842311-0.3517169417320.00929063480205-0.231845184531-0.1535099289270.113949427232-0.1090929118160.1020828664940.1044585567180.2154860589410.2745178329640.00162548899864-0.001134782764920.268672689827-0.01125385590560.18689547778814.724208834319.50993887723.49193792846
24.697201966231.8104367410.1104905618493.594822179920.9344716832653.924983140120.05630981639760.1528380624280.204741484786-0.215465379179-0.1029877169140.114647724961-0.0593411627967-0.02789529761860.04458192173930.2624835118-0.00273404016523-0.01017494118750.2789336902190.02006023936370.25928263494313.177809931130.1116496776-2.78973304948
31.464592172690.61540456245-1.248368702951.61709200079-0.6071960515062.39855412664-0.2895425004490.135897974477-0.399713092422-0.1667702883430.0890116278461-0.005923384462650.408580702855-0.2249420613430.2000258763810.261371234713-0.02805635339970.04097388740970.271194391116-0.0122790159240.3409098182097.458383880678.119631340674.62847720925
43.722147738481.60867583697-0.2390827920244.50362946164-0.4144433722643.075904350140.00346996822367-0.258117036010.665157887042-0.7894213976-0.05921227639950.125620820406-0.419832213070.1820164004620.059595369620.413082150329-0.04437025328960.04285740779080.397452391973-0.09336514394210.42359627513211.146562530842.518204997221.0984005442
52.119149802621.87340837544-1.035143545543.996919747250.8596621979951.900291410110.09297803790610.01679575117190.414631374394-0.262141984215-0.05631816408060.389524566095-0.23087128827-0.167572381647-0.03666429547050.3037696588230.0242622643345-0.03303923937760.307748751921-0.01222633017130.3071406486353.577471581532.193175636916.6162561501
61.88105408363-0.921607985679-0.2095084782686.766892065560.4383114769162.182364943710.128811764594-0.006449418170120.136324884979-0.161337142907-0.171919174347-0.0550542730150.005182044248980.1465033462530.04028610828840.294793572219-0.0331014209629-0.006468647134810.3373129612060.0006349233907180.26973100804711.285030100527.310478540713.0204546464
72.868205618231.3444590452-0.1966864122178.871244214181.865260348212.861104129620.238879635043-0.4753875435940.4428988546350.813723858452-0.2301789788130.378969865517-0.207447873563-0.09218380519090.03403194072130.320349597929-0.02098813196710.05491468922130.387047434806-0.09432428618560.3436326354022.3685954441733.918147642724.8109407733
82.989401017640.353027634055-1.012729972742.24632044597-0.5406955069581.47523161926-0.297814222753-0.0455691360116-0.635425373356-0.220748256532-0.0548421294441-0.3898878077580.2441677961920.2005528034150.3604277069420.2865582787150.002390712461650.05237819810290.299739549775-0.005728635633560.33764204123221.707744518211.40942079662.13694683453
91.940116645580.7197505614980.5366243366991.798462776620.5818704663062.529998925340.0750488922822-0.1846954515910.1080118353120.190754230323-0.00710543103494-0.093938011923-0.140558883695-0.017293436261-0.05179809510750.306973247652-0.028111068865-8.40279837733E-50.31620805758-0.01082089833840.28091911792127.724283126343.866036113124.1907358823
105.448792189912.71437480028-2.200457080954.19919143828-4.989350844886.73118350019-0.7841928969180.658616350601-0.821700947718-1.704190833631.026221338120.8892491488050.886048944782-0.473991193121-0.318349565010.442342868676-0.04601777037510.03820205579030.435611828209-0.04124902060680.51703877548317.691946402615.2385907084-8.00873741984
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 101 )AA88 - 10186 - 99
55chain 'A' and (resid 102 through 134 )AA102 - 134100 - 132
66chain 'A' and (resid 135 through 154 )AA135 - 154133 - 152
77chain 'A' and (resid 155 through 182 )AA155 - 182153 - 180
88chain 'B' and (resid -3 through 89 )BB-3 - 891 - 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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