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- PDB-8pjf: Human Leukocyte Antigen class II allotype DR1 presenting P11T->R ... -

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Basic information

Entry
Database: PDB / ID: 8pjf
TitleHuman Leukocyte Antigen class II allotype DR1 presenting P11T->R modified influenza A virus haemagglutinin (HA)306-318 PKYVKQNTLKLAR
Components
  • (HLA class II histocompatibility antigen, ...) x 2
  • Hemagglutinin HA2 chain
KeywordsIMMUNE SYSTEM / HLA-II / HLA-DR / HLA-DR1 / human leukocyte antigen / major histocompatibility complex / major histocompatibility complex class 2 / influenza A virus / flu / haemagglutinin / HA / infection / vaccine
Function / homology
Function and homology information


regulation of interleukin-4 production / regulation of interleukin-10 production / 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 / positive regulation of T cell mediated immune response to tumor cell / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation ...regulation of interleukin-4 production / regulation of interleukin-10 production / 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 / positive regulation of T cell mediated immune response to tumor cell / 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 / CD4 receptor binding / positive regulation of monocyte differentiation / positive regulation of kinase activity / inflammatory response to antigenic stimulus / intermediate filament / T-helper 1 type immune response / polysaccharide binding / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of insulin secretion involved in cellular response to glucose stimulus / macrophage differentiation / humoral immune response / negative regulation of type II interferon production / Generation of second messenger molecules / immunological synapse / epidermis development / PD-1 signaling / trans-Golgi network membrane / T cell receptor binding / detection of bacterium / negative regulation of T cell proliferation / negative regulation of inflammatory response to antigenic stimulus / MHC class II antigen presentation / viral budding from plasma membrane / cognition / lumenal side of endoplasmic reticulum membrane / protein tetramerization / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / Interferon gamma signaling / endocytic vesicle membrane / positive regulation of T cell activation / Downstream TCR signaling / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / early endosome membrane / clathrin-dependent endocytosis of virus by host cell / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / lysosome / positive regulation of viral entry into host cell / host cell surface receptor binding / immune response / positive regulation of protein phosphorylation / lysosomal membrane / Golgi membrane / external side of plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / positive regulation of DNA-templated transcription / cell surface / signal transduction / extracellular space / extracellular exosome / identical protein binding / membrane / plasma membrane
Similarity search - Function
MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta 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 / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin ...MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta 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 / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / 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
HLA class II histocompatibility antigen, DR alpha chain / HLA class II histocompatibility antigen, DRB1 beta chain / Hemagglutinin
Similarity search - Component
Biological speciesHomo sapiens (human)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsMacLachlan, B.J. / Wall, A. / Greenshields-Watson, A.L. / Cole, D.K. / Rizkallah, P.J. / Godkin, A.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust209213/Z/17/Z United Kingdom
CitationJournal: Cell Rep / Year: 2024
Title: A targeted single mutation in influenza A virus universal epitope transforms immunogenicity and protective immunity via CD4 + T cell activation.
Authors: Hulin-Curtis, S. / Geary, J.K. / MacLachlan, B.J. / Altmann, D.M. / Baillon, L. / Cole, D.K. / Greenshields-Watson, A. / Hesketh, S.J. / Humphreys, I.R. / Jones, I.M. / Lauder, S.N. / Mason, ...Authors: Hulin-Curtis, S. / Geary, J.K. / MacLachlan, B.J. / Altmann, D.M. / Baillon, L. / Cole, D.K. / Greenshields-Watson, A. / Hesketh, S.J. / Humphreys, I.R. / Jones, I.M. / Lauder, S.N. / Mason, G.H. / Smart, K. / Scourfield, D.O. / Scott, J. / Sukhova, K. / Stanton, R.J. / Wall, A. / Rizkallah, P.J. / Barclay, W.S. / Gallimore, A. / Godkin, A.
History
DepositionJun 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release

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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: HLA class II histocompatibility antigen, DRB1 beta chain
C: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,18225
Polymers45,6133
Non-polymers1,56922
Water5,513306
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.350, 134.430, 40.250
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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HLA class II histocompatibility antigen, ... , 2 types, 2 molecules AB

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


Mass: 21562.426 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 HLA class II histocompatibility antigen, DRB1 beta chain / Human leukocyte antigen DRB1 / HLA-DRB1


Mass: 22487.186 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01911

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Hemagglutinin HA2 chain


Mass: 1562.896 Da / Num. of mol.: 1 / Mutation: T318R / Source method: obtained synthetically / Source: (synth.) Influenza A virus / References: UniProt: P03435

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Non-polymers , 3 types, 328 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.84 Å3/Da / Density % sol: 56.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M MES pH 7.0, 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: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.48→54.14 Å / Num. obs: 83579 / % possible obs: 99.69 % / Redundancy: 7.1 % / Biso Wilson estimate: 20.19 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.0797 / Rpim(I) all: 0.0324 / Rrim(I) all: 0.0861 / Net I/σ(I): 12.79
Reflection shellResolution: 1.48→1.53 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.627 / Mean I/σ(I) obs: 1.49 / Num. unique obs: 8248 / CC1/2: 0.527 / CC star: 0.831 / Rpim(I) all: 0.653 / Rrim(I) all: 1.755 / % possible all: 99.92

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
xia2data reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→54.14 Å / SU ML: 0.168 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.1655
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.192 4216 5.06 %
Rwork0.1671 79166 -
obs0.1684 83382 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.34 Å2
Refinement stepCycle: LAST / Resolution: 1.48→54.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3157 0 94 306 3557
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01423431
X-RAY DIFFRACTIONf_angle_d1.40074656
X-RAY DIFFRACTIONf_chiral_restr0.122491
X-RAY DIFFRACTIONf_plane_restr0.0146600
X-RAY DIFFRACTIONf_dihedral_angle_d7.5845473
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.50.35071380.30292623X-RAY DIFFRACTION99.86
1.5-1.510.32281340.2862586X-RAY DIFFRACTION100
1.51-1.530.27021290.27142638X-RAY DIFFRACTION99.89
1.53-1.550.33391160.25932622X-RAY DIFFRACTION99.85
1.55-1.570.29111370.24652570X-RAY DIFFRACTION99.85
1.57-1.590.25891410.2282651X-RAY DIFFRACTION99.89
1.59-1.620.24141240.22592623X-RAY DIFFRACTION99.78
1.62-1.640.26031320.21422607X-RAY DIFFRACTION99.67
1.64-1.670.25241500.21412623X-RAY DIFFRACTION99.93
1.67-1.690.22431480.2052599X-RAY DIFFRACTION99.75
1.69-1.720.23871260.20552620X-RAY DIFFRACTION99.64
1.72-1.750.23571280.20212631X-RAY DIFFRACTION99.71
1.75-1.790.24131510.19172578X-RAY DIFFRACTION99.96
1.79-1.830.21141610.17962649X-RAY DIFFRACTION99.96
1.83-1.860.21341300.16792595X-RAY DIFFRACTION100
1.86-1.910.20591490.172655X-RAY DIFFRACTION100
1.91-1.960.19421350.16862615X-RAY DIFFRACTION100
1.96-2.010.19571410.16212662X-RAY DIFFRACTION99.96
2.01-2.070.17331570.16412579X-RAY DIFFRACTION99.96
2.07-2.130.19661400.1672654X-RAY DIFFRACTION99.82
2.13-2.210.20611450.16862628X-RAY DIFFRACTION99.82
2.21-2.30.18711600.1592625X-RAY DIFFRACTION99.93
2.3-2.40.20131190.16542682X-RAY DIFFRACTION99.82
2.4-2.530.1971640.16472639X-RAY DIFFRACTION99.89
2.53-2.690.15991340.16572680X-RAY DIFFRACTION99.86
2.69-2.90.17991470.16762643X-RAY DIFFRACTION99.43
2.9-3.190.18711610.1592636X-RAY DIFFRACTION99.11
3.19-3.650.19191350.1542713X-RAY DIFFRACTION99.27
3.65-4.60.14431410.13512699X-RAY DIFFRACTION98.58
4.6-54.140.17491430.15532841X-RAY DIFFRACTION97.87
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)
10.21131938992-0.00893367907047-0.7553657658633.362618799390.2412482127842.62231212205-0.181069392386-0.136641196124-0.09416089084950.06163147631980.08926990400970.03985024044720.0609021335779-0.1479908589940.06640444964070.1226075399930.0040859118864-0.009842963176410.140358594389-0.005482837256880.10902155588530.311655416119.124380199817.2240010346
26.97811780565-2.116541122591.147403453354.3134425969-1.598336966034.4824080985-0.00744825226678-0.2932296194320.1053209322650.322855661510.188681529409-0.346367099511-0.08985758782690.305127221519-0.1413269489850.157108696510.0227464501304-0.04185934108080.177756235238-0.04135049646140.14523108579832.184267407129.473788550124.3710855052
31.55362219967-0.793388537613-0.963684369092.561459291980.008089721139942.27053009749-0.406064002504-0.168344956495-0.4900152763780.2450437760530.0382870079255-0.03816350075240.4271245129410.05304821261920.3050814088170.1772239216040.01787549091630.0529845563040.1624133891570.02882026533650.29385303687938.40397873748.0182775950916.1134307657
44.360696141150.251440946344-0.6562313763393.51465654699-1.420540857434.958711826370.1690779257160.3396894151290.6085289437250.119717605495-0.1410788357280.389441133049-0.476400354734-0.0710490810553-0.0608399040210.1466678089040.0149430188384-0.02237744156960.2133932887930.06170749538290.24473972941533.807681537341.39852595870.523567819007
51.647305737620.311681154426-0.5946054544895.59539744158-0.9960189251881.728557974850.005776278384620.04448083853890.16479973983-0.00321172779388-0.0634311874099-0.057451155218-0.126542025495-0.01309946874120.04918100958680.1046021443580.00118599498924-0.02182623250370.149886690207-0.007866763265030.12320945938.260250574230.2951555546.52212362514
62.73390484088-1.17857976644-0.2619478417136.98411356589-1.337870781352.904235145630.05913475469840.3967618600210.371551055282-0.4556960723060.0284842815844-0.225410045378-0.266593837759-0.0835242162466-0.02454889398820.1755109129240.01150712910060.03153061403830.2514133886560.06298061972790.19461763478843.202742899333.9947565244-2.6979768345
71.440959058940.0324759967844-0.4286045435611.747580141750.2257295181960.913918013551-0.3010757764340.00909821380581-0.4568610419950.251997787217-0.01495522130280.2811455767660.272603921856-0.1897379354030.2801421853840.220449977775-0.01525479607310.1011013878480.207292545683-0.02043189672590.28931472004923.477322814110.438550219719.0842335445
81.65085306552-0.6807290703831.084790283221.82292713401-0.6010141740812.867545827870.0547799519060.1633631826410.0791711407742-0.168317811243-0.0007477137026530.0454835823985-0.07171669104850.0981810712003-0.04638342419750.1367739258060.00125364620845-0.002063152502320.1547423680410.0004681098041510.1434528876817.494821783443.4976096026-2.09621642435
95.62962770789-4.3958768547-2.995334903724.025427905563.800333930315.18725837267-0.712751080893-0.354074019357-0.5504424706531.078129127240.463695722397-0.1051511738650.6700153452950.235859662820.2078590990330.3005487493170.04876123368710.1009595732120.2548835461580.05190012640620.2642129224328.855032042612.140449853827.3261618184
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 26 )AA2 - 261 - 25
22chain 'A' and (resid 27 through 55 )AA27 - 5526 - 54
33chain 'A' and (resid 56 through 87 )AA56 - 8755 - 86
44chain 'A' and (resid 88 through 101 )AA88 - 10187 - 100
55chain 'A' and (resid 102 through 154 )AA102 - 154101 - 153
66chain 'A' and (resid 155 through 181 )AA155 - 181154 - 180
77chain 'B' and (resid 0 through 89 )BB0 - 891 - 90
88chain 'B' and (resid 90 through 190 )BB90 - 19091 - 191
99chain 'C' and (resid 1 through 13 )CC1 - 131 - 13

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