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- PDB-3dxa: Crystal Structure of the DM1 TCR in complex with HLA-B*4405 and d... -

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Basic information

Entry
Database: PDB / ID: 3dxa
TitleCrystal Structure of the DM1 TCR in complex with HLA-B*4405 and decamer EBV antigen
Components
  • Beta-2-microglobulin
  • DM1 T cell receptor alpha chain
  • DM1 T cell receptor beta chain
  • EBV decapeptide epitope
  • HLA class I histocompatibility complex HLA-B*4402
KeywordsIMMUNE SYSTEM / MHC / Glycoprotein / Glycation / Host-virus interaction / Immune response / Membrane / MHC I / Transmembrane / Pyrrolidone carboxylic acid / Disease mutation
Function / homology
Function and homology information


host cell nuclear matrix / viral latency / alpha-beta T cell receptor complex / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint ...host cell nuclear matrix / viral latency / alpha-beta T cell receptor complex / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / alpha-beta T cell activation / Generation of second messenger molecules / TAP binding / protection from natural killer cell mediated cytotoxicity / PD-1 signaling / detection of bacterium / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / response to bacterium / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / 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 / MHC class I protein complex / defense response / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / sensory perception of smell / Downstream TCR signaling / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / ER-Phagosome pathway / iron ion transport / early endosome membrane / protein-folding chaperone binding / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / innate immune response / focal adhesion / signaling receptor binding / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface
Similarity search - Function
Epstein-Barr virus nuclear antigen 3/4/6 / Epstein-Barr virus nuclear antigen 3 (EBNA-3) / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 ...Epstein-Barr virus nuclear antigen 3/4/6 / Epstein-Barr virus nuclear antigen 3 (EBNA-3) / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
T cell receptor alpha chain constant / HLA class I histocompatibility antigen, B alpha chain / Epstein-Barr nuclear antigen 6 / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.5 Å
AuthorsArchbold, J.K. / Macdonald, W.A. / Gras, S. / Rossjohn, J.
CitationJournal: J.Exp.Med. / Year: 2009
Title: Natural micropolymorphism in human leukocyte antigens provides a basis for genetic control of antigen recognition.
Authors: Archbold, J.K. / Macdonald, W.A. / Gras, S. / Ely, L.K. / Miles, J.J. / Bell, M.J. / Brennan, R.M. / Beddoe, T. / Wilce, M.C. / Clements, C.S. / Purcell, A.W. / McCluskey, J. / Burrows, S.R. / Rossjohn, J.
History
DepositionJul 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class I histocompatibility complex HLA-B*4402
B: Beta-2-microglobulin
C: EBV decapeptide epitope
D: DM1 T cell receptor alpha chain
E: DM1 T cell receptor beta chain
F: HLA class I histocompatibility complex HLA-B*4402
G: Beta-2-microglobulin
H: EBV decapeptide epitope
I: DM1 T cell receptor alpha chain
J: DM1 T cell receptor beta chain
K: HLA class I histocompatibility complex HLA-B*4402
L: Beta-2-microglobulin
M: EBV decapeptide epitope
N: DM1 T cell receptor alpha chain
O: DM1 T cell receptor beta chain


Theoretical massNumber of molelcules
Total (without water)286,36215
Polymers286,36215
Non-polymers00
Water00
1
A: HLA class I histocompatibility complex HLA-B*4402
B: Beta-2-microglobulin
C: EBV decapeptide epitope
D: DM1 T cell receptor alpha chain
E: DM1 T cell receptor beta chain


Theoretical massNumber of molelcules
Total (without water)95,4545
Polymers95,4545
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: HLA class I histocompatibility complex HLA-B*4402
G: Beta-2-microglobulin
H: EBV decapeptide epitope
I: DM1 T cell receptor alpha chain
J: DM1 T cell receptor beta chain


Theoretical massNumber of molelcules
Total (without water)95,4545
Polymers95,4545
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
K: HLA class I histocompatibility complex HLA-B*4402
L: Beta-2-microglobulin
M: EBV decapeptide epitope
N: DM1 T cell receptor alpha chain
O: DM1 T cell receptor beta chain


Theoretical massNumber of molelcules
Total (without water)95,4545
Polymers95,4545
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.954, 121.954, 695.914
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11K
21A
31F
12G
22B
32L
13I
23D
33N
14O
24E
34J
15A
25K
35F
16I
26D
36N
17J
27E
37O
18I
28D
38N
19H
29C
39M

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLNKK1 - 1801 - 180
21GLYGLNAA1 - 1801 - 180
31GLYGLNFF1 - 1801 - 180
12ILEMETGG1 - 991 - 99
22ILEMETBB1 - 991 - 99
32ILEMETLL1 - 991 - 99
13ALAGLYII2 - 1081 - 91
23ALAGLYDD2 - 1081 - 91
33ALAGLYNN2 - 1081 - 91
14GLYGLYOO3 - 1192 - 106
24GLYGLYEE3 - 1192 - 106
34GLYGLYJJ3 - 1192 - 106
15ARGPROAA181 - 276181 - 276
25ARGPROKK181 - 276181 - 276
35ARGPROFF181 - 276181 - 276
16GLYGLYII109 - 11892 - 101
26GLYGLYDD109 - 11892 - 101
36GLYGLYNN109 - 11892 - 101
17PROTHRJJ120 - 245107 - 232
27PROTHREE120 - 245107 - 232
37PROTHROO120 - 245107 - 232
18THRASNII119 - 199102 - 182
28THRASNDD119 - 199102 - 182
38THRASNNN119 - 199102 - 182
19GLUPHEHH1 - 101 - 10
29GLUPHECC1 - 101 - 10
39GLUPHEMM1 - 101 - 10

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9

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Components

#1: Protein HLA class I histocompatibility complex HLA-B*4402 / HLA class I histocompatibility antigen / B-44 alpha chain / MHC class I antigen B*44 / Bw-44


Mass: 32028.348 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P30481, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11748.160 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61769
#3: Protein/peptide EBV decapeptide epitope


Mass: 1282.421 Da / Num. of mol.: 3 / Fragment: residues 281-290 / Source method: obtained synthetically
Details: sequence occurs in Human herpesvirus 4, gene EBNA6, BERF3-BERF4
References: UniProt: P03204
#4: Protein DM1 T cell receptor alpha chain


Mass: 22255.746 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01848*PLUS
#5: Protein DM1 T cell receptor beta chain


Mass: 28139.178 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)

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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: 2.61 Å3/Da / Density % sol: 52.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: Bicine, Lithium Sulfate, PEG 3350, pH 9.0, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 25, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→100 Å / Num. obs: 40244 / Observed criterion σ(I): 0

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→100 Å / Cor.coef. Fo:Fc: 0.803 / Cor.coef. Fo:Fc free: 0.748 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 130.072 / SU ML: 0.846 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.873 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33 1970 5 %RANDOM
Rwork0.286 ---
all0.289 36429 --
obs0.289 39229 97.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 66.41 Å2 / Biso mean: 63.928 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20.1 Å20 Å2
2--0.21 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 3.5→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20168 0 0 0 20168
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02120718
X-RAY DIFFRACTIONr_bond_other_d0.0040.0214229
X-RAY DIFFRACTIONr_angle_refined_deg1.3481.93628160
X-RAY DIFFRACTIONr_angle_other_deg0.983.00334308
X-RAY DIFFRACTIONr_dihedral_angle_1_deg20.74652471
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.27423.761101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.244153376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.03415171
X-RAY DIFFRACTIONr_chiral_restr0.1080.22950
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0223280
X-RAY DIFFRACTIONr_gen_planes_other0.0030.024426
X-RAY DIFFRACTIONr_nbd_refined0.1950.24291
X-RAY DIFFRACTIONr_nbd_other0.1850.215091
X-RAY DIFFRACTIONr_nbtor_refined0.180.29410
X-RAY DIFFRACTIONr_nbtor_other0.0830.211416
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2395
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0110.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2490.267
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2510.2120
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2360.27
X-RAY DIFFRACTIONr_mcbond_it0.0781.515863
X-RAY DIFFRACTIONr_mcbond_other0.0281.54948
X-RAY DIFFRACTIONr_mcangle_it0.113220137
X-RAY DIFFRACTIONr_scbond_it0.16239928
X-RAY DIFFRACTIONr_scangle_it0.2364.58022
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11K2534TIGHT POSITIONAL0.030.05
12A2534TIGHT POSITIONAL0.030.05
13F2534TIGHT POSITIONAL0.020.05
11K2534TIGHT THERMAL0.020.5
12A2534TIGHT THERMAL0.020.5
13F2534TIGHT THERMAL0.020.5
21G1414TIGHT POSITIONAL0.020.05
22B1414TIGHT POSITIONAL0.030.05
23L1414TIGHT POSITIONAL0.020.05
21G1414TIGHT THERMAL0.020.5
22B1414TIGHT THERMAL0.020.5
23L1414TIGHT THERMAL0.020.5
31I1404TIGHT POSITIONAL0.030.05
32D1404TIGHT POSITIONAL0.060.05
33N1404TIGHT POSITIONAL0.050.05
31I1404TIGHT THERMAL0.020.5
32D1404TIGHT THERMAL0.030.5
33N1404TIGHT THERMAL0.020.5
41O1683TIGHT POSITIONAL0.030.05
42E1683TIGHT POSITIONAL0.020.05
43J1683TIGHT POSITIONAL0.020.05
41O1683TIGHT THERMAL0.030.5
42E1683TIGHT THERMAL0.030.5
43J1683TIGHT THERMAL0.030.5
51A1336TIGHT POSITIONAL0.050.05
52K1336TIGHT POSITIONAL0.030.05
53F1336TIGHT POSITIONAL0.030.05
51A1336TIGHT THERMAL0.020.5
52K1336TIGHT THERMAL0.020.5
53F1336TIGHT THERMAL0.020.5
61I131TIGHT POSITIONAL0.030.05
62D131TIGHT POSITIONAL0.050.05
63N131TIGHT POSITIONAL0.030.05
61I131TIGHT THERMAL0.020.5
62D131TIGHT THERMAL0.020.5
63N131TIGHT THERMAL0.010.5
71J1713TIGHT POSITIONAL0.020.05
72E1713TIGHT POSITIONAL0.040.05
73O1713TIGHT POSITIONAL0.020.05
71J1713TIGHT THERMAL0.020.5
72E1713TIGHT THERMAL0.020.5
73O1713TIGHT THERMAL0.020.5
81I1066TIGHT POSITIONAL0.030.05
82D1066TIGHT POSITIONAL0.050.05
83N1066TIGHT POSITIONAL0.050.05
81I1066TIGHT THERMAL0.020.5
82D1066TIGHT THERMAL0.020.5
83N1066TIGHT THERMAL0.020.5
91H153TIGHT POSITIONAL0.130.05
92C153TIGHT POSITIONAL0.080.05
93M153TIGHT POSITIONAL0.130.05
91H153TIGHT THERMAL0.030.5
92C153TIGHT THERMAL0.020.5
93M153TIGHT THERMAL0.020.5
LS refinement shellResolution: 3.5→3.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 129 -
Rwork0.336 2778 -
all-2907 -
obs--99.49 %
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)
11.46640.0701-0.85274.23992.47943.93450.0370.2873-0.3158-0.5609-0.1856-0.09340.2676-0.69070.1486-0.2719-0.0595-0.0603-0.1236-0.2011-0.1192-34.748514.5218-23.4117
21.15210.07880.17982.6461.58312.0980.0864-0.07720.00690.04240.0492-0.5008-0.17440.1219-0.1356-0.4015-0.05130.0224-0.3837-0.2065-0.2229-20.006951.028320.3747
31.2862-0.1751-0.66761.46812.47094.941-0.2316-0.0999-0.13650.4016-0.01520.26990.3301-0.00850.2468-0.0617-0.00020.0036-0.5416-0.261-0.1001-37.217367.91281.7491
41.47950.36690.98291.59731.33485.01380.1156-0.13450.07260.04-0.3130.22930.0448-1.17680.1974-0.4216-0.0836-0.044-0.1247-0.2644-0.2084-55.482941.449332.9489
51.49370.37170.80834.07182.28263.79340.20050.6559-0.2315-0.9259-0.0376-0.58570.23150.5753-0.1629-0.06380.06430.0524-0.0627-0.06930.1396-44.101965.1621-26.9043
62.6222-1.1277-1.64112.67450.06354.32690.2851-1.00310.00380.9382-0.01550.061-0.2270.3339-0.2695-0.0412-0.3515-0.1321-0.0246-0.0941-0.1371-57.325194.119422.5083
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 2761 - 276
2X-RAY DIFFRACTION1BB1 - 991 - 99
3X-RAY DIFFRACTION1CC1 - 101 - 10
4X-RAY DIFFRACTION2DD3 - 1952 - 178
5X-RAY DIFFRACTION2EE3 - 2452 - 232
6X-RAY DIFFRACTION3FF1 - 2761 - 276
7X-RAY DIFFRACTION3GG1 - 991 - 99
8X-RAY DIFFRACTION3HH1 - 101 - 10
9X-RAY DIFFRACTION4II3 - 1952 - 178
10X-RAY DIFFRACTION4JJ3 - 2452 - 232
11X-RAY DIFFRACTION5KK1 - 2761 - 276
12X-RAY DIFFRACTION5LL1 - 991 - 99
13X-RAY DIFFRACTION5MM1 - 101 - 10
14X-RAY DIFFRACTION6NN3 - 1952 - 178
15X-RAY DIFFRACTION6OO3 - 2452 - 232

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