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- PDB-3mv8: Crystal Structure of the TK3-Gln55His TCR in complex with HLA-B*3... -

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Basic information

Entry
Database: PDB / ID: 3mv8
TitleCrystal Structure of the TK3-Gln55His TCR in complex with HLA-B*3501/HPVG
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B-35 alpha chain
  • HPVG peptide from Epstein-Barr nuclear antigen 1
  • alpha chain of the TK3 TCR
  • beta chain of the TK3 TCR
KeywordsIMMUNE SYSTEM / HLA B*3501 / EBV / TCR / TCRpMHC complex / HPVG / TCR polymorphism
Function / homology
Function and homology information


host cell PML body / viral latency / regulation of interleukin-12 production / regulation of dendritic cell differentiation / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / regulation of T cell anergy / regulation of interleukin-6 production / symbiont-mediated disruption of host cell PML body / regulation of DNA replication / TAP binding ...host cell PML body / viral latency / regulation of interleukin-12 production / regulation of dendritic cell differentiation / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / regulation of T cell anergy / regulation of interleukin-6 production / symbiont-mediated disruption of host cell PML body / regulation of DNA replication / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 / enzyme-substrate adaptor activity / detection of bacterium / : / : / secretory granule membrane / 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 / lumenal side of endoplasmic reticulum membrane / 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 / defense response / 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 / Interferon alpha/beta 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 / protein-folding chaperone binding / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / endonuclease activity / symbiont-mediated suppression of host NF-kappaB cascade / protein homotetramerization / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / DNA-binding transcription factor activity / Golgi membrane / external side of plasma membrane / signaling receptor binding / lysosomal membrane / innate immune response / focal adhesion / Neutrophil degranulation / positive regulation of DNA-templated transcription / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity
Similarity search - Function
Epstein Barr virus nuclear antigen-1, DNA-binding / Epstein Barr virus nuclear antigen-1, DNA-binding domain / Epstein Barr virus nuclear antigen-1, DNA-binding domain superfamily / E2/EBNA1, C-terminal / 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-1, DNA-binding / Epstein Barr virus nuclear antigen-1, DNA-binding domain / Epstein Barr virus nuclear antigen-1, DNA-binding domain superfamily / E2/EBNA1, C-terminal / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, B alpha chain / Epstein-Barr nuclear antigen 1 / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 2fyy, 3ffc / molecular replacement / Resolution: 2.1 Å
AuthorsGras, S. / Chen, Z. / Miles, J.J. / Liu, Y.C. / Bell, M.J. / Sullivan, L.C. / Kjer-Nielsen, L. / Brennan, R.M. / Burrows, J.M. / Neller, M.A. ...Gras, S. / Chen, Z. / Miles, J.J. / Liu, Y.C. / Bell, M.J. / Sullivan, L.C. / Kjer-Nielsen, L. / Brennan, R.M. / Burrows, J.M. / Neller, M.A. / Khanna, R. / Purcell, A.W. / Brooks, A.G. / McCluskey, J. / Rossjohn, J. / Burrows, S.R.
CitationJournal: J.Exp.Med. / Year: 2010
Title: Allelic polymorphism in the T cell receptor and its impact on immune responses
Authors: Gras, S. / Chen, Z. / Miles, J.J. / Liu, Y.C. / Bell, M.J. / Sullivan, L.C. / Kjer-Nielsen, L. / Brennan, R.M. / Burrows, J.M. / Neller, M.A. / Khanna, R. / Purcell, A.W. / Brooks, A.G. / ...Authors: Gras, S. / Chen, Z. / Miles, J.J. / Liu, Y.C. / Bell, M.J. / Sullivan, L.C. / Kjer-Nielsen, L. / Brennan, R.M. / Burrows, J.M. / Neller, M.A. / Khanna, R. / Purcell, A.W. / Brooks, A.G. / McCluskey, J. / Rossjohn, J. / Burrows, S.R.
History
DepositionMay 3, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Database references
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, B-35 alpha chain
B: Beta-2-microglobulin
C: HPVG peptide from Epstein-Barr nuclear antigen 1
D: alpha chain of the TK3 TCR
E: beta chain of the TK3 TCR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,7516
Polymers94,6555
Non-polymers961
Water3,621201
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.760, 63.610, 88.140
Angle α, β, γ (deg.)101.12, 97.60, 112.00
Int Tables number1
Space group name H-MP1

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Components

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Protein , 4 types, 4 molecules ABDE

#1: Protein HLA class I histocompatibility antigen, B-35 alpha chain / HLA B*3501 heavy chain / MHC class I antigen B*35


Mass: 31940.246 Da / Num. of mol.: 1 / Fragment: Extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P30685, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61769
#4: Protein alpha chain of the TK3 TCR


Mass: 22185.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#5: Protein beta chain of the TK3 TCR


Mass: 27322.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Q55H mutant / Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide HPVG peptide from Epstein-Barr nuclear antigen 1


Mass: 1327.374 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide / References: UniProt: P03211

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Non-polymers , 2 types, 202 molecules

#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE SEQUENCE DATABASE REFERENCE FOR CHAIN D, E DO NOT CURRENTLY EXIST IN UNP DATABASE. CHAIN D: ...THE SEQUENCE DATABASE REFERENCE FOR CHAIN D, E DO NOT CURRENTLY EXIST IN UNP DATABASE. CHAIN D: TRAV20/TRAJ58 TCR ALPHA CHAIN CHAIN E : TRBV9 WITH THE MUTATION Q55H, TRBJ2-2 TCR BETA CHAIN THE ABOVE CODES ARE FROM IMGT DATABASES.

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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: 2.35 Å3/Da / Density % sol: 47.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 15%PEG 3350, 0.2M LiSO4, 0.1M Na-citrate, pH 5.6, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.979457 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 4, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979457 Å / Relative weight: 1
ReflectionNumber: 194018 / Rmerge(I) obs: 0.097 / D res high: 2.1 Å / Num. obs: 49428 / % possible obs: 98.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
610169799.410.04
56153999.210.043
45352699.110.045
34987598.810.063
2.93181698.410.104
2.82.9208498.310.125
2.72.8244598.110.16
2.62.7273798.110.177
2.52.6323897.910.219
2.42.5383797.910.268
2.32.4449797.510.33
2.22.3530197.510.381
2.12.2637097.310.477
ReflectionResolution: 2.1→100 Å / Num. obs: 49428 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 30.885 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 11.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.1-2.20.477325191637097.3
2.2-2.30.3813.720970530197.5
2.3-2.40.334.417791449797.5
2.4-2.50.2685.215153383797.9
2.5-2.60.2196.412752323897.9
2.6-2.70.1777.810818273798.1
2.7-2.80.168.69617244598.1
2.8-2.90.12510.68161208498.3
2.9-30.10412.57129181698.4
3-40.06318.938458987598.8
4-50.04525.513542352699.1
5-60.04325.55875153999.2
6-100.0427.76727169799.4
100.0332183446698.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.5.0088refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: 2fyy, 3ffc / Resolution: 2.1→84.22 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.887 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 16.111 / SU ML: 0.189 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.303 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.276 2513 5.1 %RANDOM
Rwork0.229 ---
obs0.231 49426 98.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 104.04 Å2 / Biso mean: 30.518 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å2-0.37 Å20.59 Å2
2---1.28 Å20.61 Å2
3---1.6 Å2
Refinement stepCycle: LAST / Resolution: 2.1→84.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6672 0 5 201 6878
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0217063
X-RAY DIFFRACTIONr_angle_refined_deg1.0461.9429628
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9255867
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81123.859368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.468151153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7011556
X-RAY DIFFRACTIONr_chiral_restr0.0730.21003
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215609
X-RAY DIFFRACTIONr_mcbond_it0.2441.54272
X-RAY DIFFRACTIONr_mcangle_it0.46926931
X-RAY DIFFRACTIONr_scbond_it0.65632791
X-RAY DIFFRACTIONr_scangle_it1.094.52697
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 178 -
Rwork0.292 3459 -
all-3637 -
obs--97.35 %
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)
12.9353-0.27631.32663.0801-1.09434.2234-0.07-0.0253-0.0612-0.1857-0.0701-0.28430.30480.04240.14020.09410.01840.03060.0411-0.03040.11910.947827.50552.7562
22.71970.3752-0.72521.5257-0.26081.23850.01420.04730.0729-0.0928-0.015-0.0639-0.0028-0.01690.00080.08560.0069-0.03190.0315-0.0340.07622.391530.99255.8375
31.19090.0434-0.49521.36570.41381.81590.02930.26130.0181-0.36310.0027-0.0346-0.1208-0.1002-0.03210.16410.0018-0.02950.10530.02340.12172.551632.7593-9.8852
45.7661.71411.93124.17540.51546.4624-0.04730.6836-0.0108-0.37210.29070.32460.6396-0.8063-0.24340.2552-0.1309-0.02630.35660.0390.0522-3.398214.38-26.3192
53.84450.5549-5.41821.9781-0.412917.19690.20980.09680.17410.24590.04550.4680.1857-0.9672-0.25520.2096-0.01890.02730.14340.00510.24322.19499.9015-4.8156
63.4219-0.5046-1.94621.41230.78854.2665-0.00310.195-0.1253-0.1775-0.2225-0.27350.17980.35550.22560.20540.08150.08310.16610.02710.211512.542212.017-13.3163
77.1418-1.7836-0.17136.68120.0010.3236-0.1279-1.5452-0.48430.4460.0163-1.03950.39070.65590.11160.63570.71650.17231.56030.29620.414420.3486.4319-8.7131
80.3532-0.94-1.24312.99742.54245.60110.0392-0.02970.0234-0.1266-0.152-0.2301-0.04510.48090.11280.2510.01470.01840.22450.0190.18738.895617.694-6.3527
93.7125-0.262-2.40032.35832.02655.952-0.7866-0.0651-0.77410.11240.15310.15321.86820.55910.63360.76230.17950.2040.16920.03130.380411.65152.2132-12.6883
101.38651.1008-1.20772.0269-3.38546.20210.08220.02880.1411-0.1464-0.0880.02470.3910.30650.00580.11290.0289-0.04390.1969-0.05850.17696.179639.70487.2971
111.17192.7160.495511.87472.41180.49580.188-0.0514-0.09290.2271-0.1076-0.40980.0356-0.023-0.08040.1408-0.0013-0.05170.1276-0.02060.11230.167835.22115.5483
122.4626-1.1867-0.02622.136-1.31471.15770.0362-0.0657-0.1027-0.1214-0.1892-0.10010.02790.21630.15290.1302-0.0428-0.00760.10580.00640.20227.013473.23313.5335
131.17-0.9491-0.01523.95911.26511.3415-0.00620.00240.0228-0.161-0.13940.2631-0.0399-0.05990.14560.0658-0.026-0.0150.03830.00340.15650.341262.608913.0091
140.19690.41180.01013.24931.34781.25960.0383-0.08110.03540.09390.0143-0.0921-0.12710.0472-0.05260.0808-0.003-0.01790.0997-0.00770.11797.613877.610529.3755
152.45513.12760.13753.98590.17580.0134-0.11670.1143-0.3108-0.12570.1302-0.39620.03480.0414-0.01350.41840.10450.0820.3997-0.02430.294816.53289.334428.1818
163.45741.99090.49085.30230.61022.2496-0.07180.2477-0.6768-0.39860.19530.48070.0088-0.3081-0.12350.2466-0.0243-0.05610.14530.00180.32743.283983.700633.0608
172.5671-1.8866-0.17235.6516-3.66934.747-0.0509-0.32890.53190.4617-0.2675-0.7206-0.330.32390.31840.1535-0.0651-0.02720.1239-0.04720.192914.623895.614235.7145
183.98491.25071.63121.8051.13941.81240.0468-0.07510.02810.1627-0.0439-0.08380.1138-0.0319-0.00290.09540.0023-0.02740.0022-0.00240.101114.653450.192527.6869
192.2717-0.78480.47163.8483-0.53241.1138-0.0197-0.1732-0.20850.12610.16620.2452-0.0957-0.055-0.14650.0979-0.01380.02260.06080.00580.099510.445978.549542.1175
209.9013-3.1805-1.98555.6684-0.87694.1868-0.1837-0.6282-0.6880.5720.2166-0.05340.10540.2611-0.03280.1703-0.0361-0.02490.12390.07550.183115.704569.037749.5325
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 46
2X-RAY DIFFRACTION2A47 - 144
3X-RAY DIFFRACTION3A145 - 196
4X-RAY DIFFRACTION4A197 - 276
5X-RAY DIFFRACTION5B0 - 10
6X-RAY DIFFRACTION6B11 - 36
7X-RAY DIFFRACTION7B37 - 52
8X-RAY DIFFRACTION8B53 - 70
9X-RAY DIFFRACTION9B71 - 99
10X-RAY DIFFRACTION10C1 - 7
11X-RAY DIFFRACTION11C8 - 11
12X-RAY DIFFRACTION12D5 - 20
13X-RAY DIFFRACTION13D21 - 92
14X-RAY DIFFRACTION14D93 - 142
15X-RAY DIFFRACTION15D143 - 155
16X-RAY DIFFRACTION16D156 - 175
17X-RAY DIFFRACTION17D176 - 204
18X-RAY DIFFRACTION18E2 - 114
19X-RAY DIFFRACTION19E115 - 204
20X-RAY DIFFRACTION20E205 - 243

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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