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- PDB-4prh: Crystal structure of TK3 TCR-HLA-B*35:08-HPVG-D5 complex -

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Basic information

Entry
Database: PDB / ID: 4prh
TitleCrystal structure of TK3 TCR-HLA-B*35:08-HPVG-D5 complex
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • Epstein-Barr nuclear antigen 1Epstein–Barr virus nuclear antigen 1
  • MHC class I antigen
  • TK3 TCR alpha chain
  • TK3 TCR beta chain
KeywordsIMMUNE SYSTEM / human leukocyte antigen class I / Epstein-Barr virus / viral escape / T cell receptor / viral immunity
Function / homology
Function and homology information


symbiont-mediated suppression of host antigen processing and presentation / viral latency / : / alpha-beta T cell receptor complex / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / regulation of DNA replication / alpha-beta T cell activation / Generation of second messenger molecules ...symbiont-mediated suppression of host antigen processing and presentation / viral latency / : / alpha-beta T cell receptor complex / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / regulation of DNA replication / alpha-beta T cell activation / Generation of second messenger molecules / PD-1 signaling / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / 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 / 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 binding / lumenal side of endoplasmic reticulum membrane / 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 / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / 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 / recycling endosome membrane / specific granule lumen / 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 / sensory perception of smell / positive regulation of T cell activation / Downstream TCR signaling / 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 differentiation in thymus / T cell receptor signaling pathway / ER-Phagosome pathway / iron ion transport / early endosome membrane / protein refolding / antibacterial humoral response / endonuclease activity / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / blood microparticle / learning or memory / immune response / Amyloid fiber formation / DNA-binding transcription factor activity / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / signaling receptor binding / focal adhesion / host cell nucleus / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / positive regulation of DNA-templated transcription / Golgi apparatus / endoplasmic reticulum
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 / 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 ...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 / 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
HLA-B*3507 / T cell receptor alpha chain constant / T cell receptor beta constant 1 / Beta-2-microglobulin / Epstein-Barr nuclear antigen 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Human herpesvirus 4 (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsYu Chih, L. / Rossjohn, J. / Gras, S.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: A Molecular Basis for the Interplay between T Cells, Viral Mutants, and Human Leukocyte Antigen Micropolymorphism.
Authors: Liu, Y.C. / Chen, Z. / Neller, M.A. / Miles, J.J. / Purcell, A.W. / McCluskey, J. / Burrows, S.R. / Rossjohn, J. / Gras, S.
History
DepositionMar 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2Jul 2, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: MHC class I antigen
B: Beta-2-microglobulin
C: Epstein-Barr nuclear antigen 1
D: TK3 TCR alpha chain
E: TK3 TCR beta chain


Theoretical massNumber of molelcules
Total (without water)95,3435
Polymers95,3435
Non-polymers00
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10420 Å2
ΔGint-52 kcal/mol
Surface area37680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.835, 62.081, 98.334
Angle α, β, γ (deg.)92.70, 101.92, 108.21
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 MHC class I antigen


Mass: 31600.889 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C5MK56
#2: Protein Beta-2-microglobulin / 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: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61769
#4: Protein TK3 TCR alpha chain


Mass: 23099.428 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01848*PLUS
#5: Protein TK3 TCR beta chain


Mass: 27450.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01850*PLUS

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Protein/peptide / Non-polymers , 2 types, 67 molecules C

#3: Protein/peptide Epstein-Barr nuclear antigen 1 / Epstein–Barr virus nuclear antigen 1 / EBNA-1 / EBV nuclear antigen 1


Mass: 1313.348 Da / Num. of mol.: 1 / Fragment: unp residues 407-417 / Source method: obtained synthetically / Source: (synth.) Human herpesvirus 4 (Epstein-Barr virus) / References: UniProt: Q3KSS4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

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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: 2.66 Å3/Da / Density % sol: 53.73 %
Crystal growTemperature: 298 K / pH: 5.6
Details: 18% PEG 3350, 0.2M LiSO4 and 0.1M Na-Citrate pH 5.6, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.984
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 32833 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 60.34 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 11.79
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 3.27 / % possible all: 98.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.14data extraction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FYY

2fyy


Resolution: 2.5→35.68 Å / Cor.coef. Fo:Fc: 0.9251 / Cor.coef. Fo:Fc free: 0.8946 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2526 1635 4.98 %RANDOM
Rwork0.2122 ---
obs0.2142 32831 97 %-
all-33844 --
Displacement parametersBiso mean: 59.64 Å2
Baniso -1Baniso -2Baniso -3
1--3.0611 Å20.8384 Å2-1.4106 Å2
2--9.5265 Å2-1.8904 Å2
3----6.4654 Å2
Refine analyzeLuzzati coordinate error obs: 0.426 Å
Refinement stepCycle: LAST / Resolution: 2.5→35.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6271 0 0 66 6337
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0096438HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.178734HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2205SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes184HARMONIC2
X-RAY DIFFRACTIONt_gen_planes929HARMONIC5
X-RAY DIFFRACTIONt_it6438HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact
LS refinement shellResolution: 2.5→2.58 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.3038 156 5.04 %
Rwork0.2695 2938 -
all0.2713 3094 -
obs--97 %
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)
10.82710.2173-1.21081.88691.62130.43930.1549-0.2401-0.06670.1444-0.16410.2641-0.13790.14290.00910.20440.1736-0.0997-0.1194-0.0427-0.1406-16.930229.08753.6106
20.39290.91861.6093.96691.8151.41060.1195-0.1402-0.0528-0.0406-0.1189-0.1111-0.16190.3135-0.00070.1544-0.07840.03420.097-0.0604-0.2689-9.098548.08678.9761
30.3359-0.19370.34982.230.53192.20540.0329-0.0592-0.04320.05710.010.14320.2734-0.1209-0.0429-0.1340.0332-0.0064-0.14160.04040.0073-16.057-16.8857-24.1112
40.36140.3180.55691.92071.11342.2738-0.05440.07680.018-0.23390.0780.0595-0.22560.0006-0.0236-0.04730.018-0.0345-0.11660.0464-0.0688-8.6922-5.3409-37.6648
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A2 - 275
2X-RAY DIFFRACTION2{ B|* }B3 - 99
3X-RAY DIFFRACTION3{ D|* }D1 - 218
4X-RAY DIFFRACTION4{ E|* }E2 - 254

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