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- PDB-8v50: Crystal structure of a HLA-B*35:01-NP6 with D1 TCR -

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Basic information

Entry
Database: PDB / ID: 8v50
TitleCrystal structure of a HLA-B*35:01-NP6 with D1 TCR
Components
  • Beta-2-microglobulin
  • D1 TCR alpha chain
  • D1 TCR beta chain
  • HLA-B35
  • NP6 epitope H1N1
KeywordsIMMUNE SYSTEM / HLA B*3501 / NP418 epitope / T cell immunity / glycoprotein / host-virus interaction / immune response
Function / homology
Function and homology information


: / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...: / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway / 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 / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / lysosomal membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / 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. ...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
HLA-B35 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6500177696 Å
AuthorsLittler, D.R. / Rossjohn, J. / Gras, S.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: Sci Immunol / Year: 2025
Title: Molecular determinants of cross-strain influenza A virus recognition by alpha beta T cell receptors.
Authors: Quinones-Parra, S.M. / Gras, S. / Nguyen, T.H.O. / Farenc, C. / Szeto, C. / Rowntree, L.C. / Chaurasia, P. / Sant, S. / Boon, A.C.M. / Jayasinghe, D. / Rimmelzwaan, G.F. / Petersen, J. / ...Authors: Quinones-Parra, S.M. / Gras, S. / Nguyen, T.H.O. / Farenc, C. / Szeto, C. / Rowntree, L.C. / Chaurasia, P. / Sant, S. / Boon, A.C.M. / Jayasinghe, D. / Rimmelzwaan, G.F. / Petersen, J. / Doherty, P.C. / Uldrich, A.P. / Littler, D.R. / Rossjohn, J. / Kedzierska, K.
History
DepositionNov 30, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA-B35
B: Beta-2-microglobulin
C: NP6 epitope H1N1
D: D1 TCR alpha chain
E: D1 TCR beta chain
F: HLA-B35
G: Beta-2-microglobulin
H: NP6 epitope H1N1
I: D1 TCR alpha chain
J: D1 TCR beta chain
K: HLA-B35
L: Beta-2-microglobulin
M: NP6 epitope H1N1
N: D1 TCR alpha chain
O: D1 TCR beta chain
P: HLA-B35
Q: Beta-2-microglobulin
R: NP6 epitope H1N1
S: D1 TCR alpha chain
T: D1 TCR beta chain


Theoretical massNumber of molelcules
Total (without water)374,85520
Polymers374,85520
Non-polymers00
Water16,862936
1
A: HLA-B35
B: Beta-2-microglobulin
C: NP6 epitope H1N1
D: D1 TCR alpha chain
E: D1 TCR beta chain


Theoretical massNumber of molelcules
Total (without water)93,7145
Polymers93,7145
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: HLA-B35
G: Beta-2-microglobulin
H: NP6 epitope H1N1
I: D1 TCR alpha chain
J: D1 TCR beta chain


Theoretical massNumber of molelcules
Total (without water)93,7145
Polymers93,7145
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
K: HLA-B35
L: Beta-2-microglobulin
M: NP6 epitope H1N1
N: D1 TCR alpha chain
O: D1 TCR beta chain


Theoretical massNumber of molelcules
Total (without water)93,7145
Polymers93,7145
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
P: HLA-B35
Q: Beta-2-microglobulin
R: NP6 epitope H1N1
S: D1 TCR alpha chain
T: D1 TCR beta chain


Theoretical massNumber of molelcules
Total (without water)93,7145
Polymers93,7145
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.580, 192.162, 252.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 4 types, 16 molecules AFKPBGLQDINSEJOT

#1: Protein
HLA-B35


Mass: 31786.080 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B-3501 / Variant: B35:01 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O19626
#2: Protein
Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 4 / Mutation: artificial starting M
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
#4: Protein
D1 TCR alpha chain


Mass: 21807.949 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAV1*01 / Production host: Escherichia coli BL21(DE3) (bacteria)
#5: Protein
D1 TCR beta chain


Mass: 27202.172 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRBV7-8*01 / Production host: Escherichia coli BL21(DE3) (bacteria)

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Protein/peptide / Non-polymers , 2 types, 940 molecules CHMR

#3: Protein/peptide
NP6 epitope H1N1


Mass: 1038.238 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Influenza A virus
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 936 / Source method: isolated from a natural source / Formula: H2O

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Details

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

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→38.6 Å / Num. obs: 112003 / % possible obs: 100 % / Redundancy: 2 % / Biso Wilson estimate: 35.0247001832 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.05 / Net I/σ(I): 10
Reflection shellResolution: 2.65→2.75 Å / Rmerge(I) obs: 0.27 / Num. unique obs: 11071 / CC1/2: 0.87

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6500177696→38.5888715441 Å / SU ML: 0.344092161088 / Cross valid method: FREE R-VALUE / σ(F): 1.96521975925 / Phase error: 28.1860259253
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.265204803721 5586 4.99584127069 %random selection
Rwork0.217710401785 106227 --
obs0.220052221113 111813 99.8196670089 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.5522749746 Å2
Refinement stepCycle: LAST / Resolution: 2.6500177696→38.5888715441 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26347 0 0 936 27283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010280043950627231
X-RAY DIFFRACTIONf_angle_d1.5326029164837047
X-RAY DIFFRACTIONf_chiral_restr0.06567494030653860
X-RAY DIFFRACTIONf_plane_restr0.006086583821534911
X-RAY DIFFRACTIONf_dihedral_angle_d23.524818880410060
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65002-2.68010.3139428235831880.2828210396383508X-RAY DIFFRACTION99.7570850202
2.6801-2.71160.2869859835471870.2693815437813519X-RAY DIFFRACTION99.9730240086
2.7116-2.74470.3466583034371800.2628282627683487X-RAY DIFFRACTION99.9454892341
2.7447-2.77940.3180643119531820.2567063573953497X-RAY DIFFRACTION100
2.7794-2.8160.2869981929441830.2561724680083535X-RAY DIFFRACTION99.9462365591
2.816-2.85460.3166263411491830.2527868896913447X-RAY DIFFRACTION99.8899284535
2.8546-2.89530.3112317857411640.2563947795593557X-RAY DIFFRACTION99.9731327243
2.8953-2.93850.3389824524511940.2553129131583491X-RAY DIFFRACTION99.9728703201
2.9385-2.98440.3001553230211980.2479324324723474X-RAY DIFFRACTION100
2.9844-3.03330.3364621833631860.2416796300813536X-RAY DIFFRACTION99.7855227882
3.0333-3.08560.3284796322411720.2317279689763507X-RAY DIFFRACTION99.8100922409
3.0856-3.14170.2965297377552140.2305802770963529X-RAY DIFFRACTION99.8665955176
3.1417-3.20210.3054272868641970.2352298944883469X-RAY DIFFRACTION99.8366013072
3.2021-3.26740.3284336897621830.2351733126893534X-RAY DIFFRACTION99.7584541063
3.2674-3.33850.3408791716311840.2336851751123474X-RAY DIFFRACTION99.6730245232
3.3385-3.41610.3205927395741910.2261346880163568X-RAY DIFFRACTION99.8141263941
3.4161-3.50140.2543849090241800.211227843663486X-RAY DIFFRACTION99.8910081744
3.5014-3.5960.2378596306481930.2126570769663523X-RAY DIFFRACTION99.8924731183
3.596-3.70180.2684764490432020.2034373887073506X-RAY DIFFRACTION99.8115746972
3.7018-3.82120.2770975125452090.2041037027283501X-RAY DIFFRACTION99.919202801
3.8212-3.95760.2479543113942100.2033473524883543X-RAY DIFFRACTION99.8403830806
3.9576-4.11590.2144448002731640.198814843743549X-RAY DIFFRACTION99.8923863331
4.1159-4.3030.2282940536761620.1944754828553579X-RAY DIFFRACTION99.9198717949
4.303-4.52950.224187603271600.1828826535053578X-RAY DIFFRACTION99.8397435897
4.5295-4.81280.2096755375421990.1760009000733585X-RAY DIFFRACTION99.9471737982
4.8128-5.18360.2014493259812010.183058885313558X-RAY DIFFRACTION99.8937018336
5.1836-5.70380.2129122873511900.2037557392713578X-RAY DIFFRACTION99.9734677633
5.7038-6.52570.2427484633721790.2204325117463656X-RAY DIFFRACTION99.8437906795
6.5257-8.20860.2638590870891660.2272900222643680X-RAY DIFFRACTION99.9220576773
8.2086-38.580.2419790970541850.2164322662593773X-RAY DIFFRACTION98.1646825397
Refinement TLS params.Method: refined / Origin x: 0.131043271211 Å / Origin y: -24.0147400299 Å / Origin z: 62.6799073232 Å
111213212223313233
T0.24601621795 Å20.00972909517853 Å20.00849622292609 Å2-0.202702547303 Å20.00419535909049 Å2--0.282525643304 Å2
L0.0295648261035 °20.00423992667803 °2-0.00619997741101 °2-0.0144688500844 °2-0.00864960959314 °2--0.168518961177 °2
S-0.0159889425972 Å °0.00377989537987 Å °0.00737369631202 Å °-0.000628377294286 Å °-0.00701137914665 Å °0.0109462162216 Å °0.0245992248529 Å °-0.0205753970109 Å °0.0163873348042 Å °
Refinement TLS groupSelection details: all

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