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- PDB-3o4l: Genetic and structural basis for selection of a ubiquitous T cell... -

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Basic information

Entry
Database: PDB / ID: 3o4l
TitleGenetic and structural basis for selection of a ubiquitous T cell receptor deployed in Epstein-Barr virus
Components
  • (T-CELL RECEPTOR, ...) x 2
  • BSLF2/BMLF1 protein
  • Beta-2-microglobulin
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / MHC I / Immunoglobulin / Antigen Presentation / Immune Recognition
Function / homology
Function and homology information


symbiont-mediated suppression of host PKR/eIFalpha signaling / alpha-beta T cell receptor complex / protein serine/threonine kinase inhibitor activity / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / Co-inhibition by PD-1 / mRNA transport / : ...symbiont-mediated suppression of host PKR/eIFalpha signaling / alpha-beta T cell receptor complex / protein serine/threonine kinase inhibitor activity / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / Co-inhibition by PD-1 / mRNA transport / : / : / 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 / response to bacterium / 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 / Downstream TCR signaling / T cell receptor signaling pathway / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / host cell cytoplasm / learning or memory / immune response / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / lysosomal membrane / focal adhesion / Neutrophil degranulation / regulation of DNA-templated transcription / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / RNA binding / extracellular exosome / extracellular region / zinc ion binding / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Herpesvirus ICP27-like / Herpesvirus transcriptional regulator family / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / : / 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 ...Herpesvirus ICP27-like / Herpesvirus transcriptional regulator family / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / : / 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
BSLF2/BMLF1 protein / T cell receptor alpha chain constant / T cell receptor beta constant 1 / Beta-2-microglobulin / mRNA export factor ICP27 homolog / MHC class I antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
Human herpesvirus 4 (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.54 Å
AuthorsMiles, J.J. / Bulek, A.M. / Cole, D.K. / Gostick, E. / Schauenburg, J.A. / Dolton, G. / Venturi, V. / Davenport, M.P. / Tan, M.P. / Burrows, S.R. ...Miles, J.J. / Bulek, A.M. / Cole, D.K. / Gostick, E. / Schauenburg, J.A. / Dolton, G. / Venturi, V. / Davenport, M.P. / Tan, M.P. / Burrows, S.R. / Wooldridge, L. / Price, D.A. / Rizkallah, P.J. / Sewell, A.K.
CitationJournal: Plos Pathog. / Year: 2010
Title: Genetic and structural basis for selection of a ubiquitous T cell receptor deployed in Epstein-Barr virus infection.
Authors: Miles, J.J. / Bulek, A.M. / Cole, D.K. / Gostick, E. / Schauenburg, A.J. / Dolton, G. / Venturi, V. / Davenport, M.P. / Tan, M.P. / Burrows, S.R. / Wooldridge, L. / Price, D.A. / Rizkallah, P.J. / Sewell, A.K.
History
DepositionJul 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 12, 2014Group: Refinement description
Revision 1.3Oct 6, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Dec 27, 2023Group: Derived calculations / Category: struct_conn / struct_conn_type
Item: _struct_conn.conn_type_id / _struct_conn.id ..._struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: BSLF2/BMLF1 protein
D: T-CELL RECEPTOR, ALPHA CHAIN
E: T-CELL RECEPTOR, BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,97824
Polymers94,0985
Non-polymers1,88119
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14450 Å2
ΔGint-124 kcal/mol
Surface area38260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.080, 122.500, 82.370
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
DetailsThe contents of the asymmetric unit constitute one complete biological assembly.

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein MHC class I antigen


Mass: 31951.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8WLS4
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11853.319 Da / Num. of mol.: 1 / Mutation: K111C / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61769

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide BSLF2/BMLF1 protein


Mass: 920.191 Da / Num. of mol.: 1 / Fragment: residues 286-294 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 4 (Epstein-Barr virus) / References: UniProt: A7UMS0, UniProt: Q3KSU1*PLUS

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T-CELL RECEPTOR, ... , 2 types, 2 molecules DE

#4: Protein T-CELL RECEPTOR, ALPHA CHAIN


Mass: 21960.381 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01848*PLUS
#5: Protein T-CELL RECEPTOR, BETA CHAIN


Mass: 27412.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01850*PLUS

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Non-polymers , 4 types, 353 molecules

#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.52 Å3/Da / Density % sol: 51.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.16 M Ca Acetate, 0.08 M Na Cacodylate, 12.5% PEG 8000, 20% Glycerol, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 27, 2009
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.54→61.25 Å / Num. all: 31817 / Num. obs: 31817 / % possible obs: 99.1 % / Redundancy: 7.9 % / Rsym value: 0.163 / Net I/σ(I): 12.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.54-2.617.90.8320.91750522220.83295.1
2.61-2.688.20.6831.11855922690.683100
2.68-2.768.20.5971.31816522190.59799.9
2.76-2.848.20.5051.51764921590.50599.9
2.84-2.938.10.4111.81704920930.41199.9
2.93-3.048.10.3262.31644820230.32699.8
3.04-3.158.10.2562.91581019490.256100
3.15-3.288.10.2043.71537718990.204100
3.28-3.438.10.1714.31459318100.17199.9
3.43-3.5980.1465.11399317450.14699.8
3.59-3.796.70.14551007415000.14591.5
3.79-4.027.50.1245.91150215300.12498.7
4.02-4.297.90.0878.51180714980.08799.9
4.29-4.647.80.07210.11084713820.07299.9
4.64-5.087.80.06910.3988512730.069100
5.08-5.687.60.07310894411750.07399.9
5.68-6.567.90.0799.5822910380.079100
6.56-8.037.80.06511.669808910.065100
8.03-11.367.50.03917.554417210.039100
11.36-61.256.70.03516.628204210.03598.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.479 / Cor.coef. Fo:Fc: 0.497 / Cor.coef. Io to Ic: 0.52

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
GDAdata collection
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2P5E

2p5e


Resolution: 2.54→61.25 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.833 / WRfactor Rfree: 0.261 / WRfactor Rwork: 0.1936 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7883 / SU B: 27.238 / SU ML: 0.274 / SU R Cruickshank DPI: 0.2811 / SU Rfree: 0.3704 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.37 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2962 1603 5 %RANDOM
Rwork0.2207 ---
obs0.2245 31773 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 100 Å2 / Biso mean: 27.6561 Å2 / Biso min: 4.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20 Å2
2---0.98 Å20 Å2
3---1.26 Å2
Refinement stepCycle: LAST / Resolution: 2.54→61.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6618 0 113 334 7065
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0216890
X-RAY DIFFRACTIONr_bond_other_d0.0020.024658
X-RAY DIFFRACTIONr_angle_refined_deg1.2331.9449343
X-RAY DIFFRACTIONr_angle_other_deg0.756311281
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.7165820
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.95423.947342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.696151110
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2161545
X-RAY DIFFRACTIONr_chiral_restr0.1120.2980
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217633
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021439
X-RAY DIFFRACTIONr_mcbond_it1.39524116
X-RAY DIFFRACTIONr_mcbond_other1.47821653
X-RAY DIFFRACTIONr_mcangle_it2.44136652
X-RAY DIFFRACTIONr_scbond_it3.09842774
X-RAY DIFFRACTIONr_scangle_it4.7462691
X-RAY DIFFRACTIONr_rigid_bond_restr1.56936795
LS refinement shellResolution: 2.54→2.606 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 112 -
Rwork0.297 2105 -
all-2217 -
obs--100 %
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)
10.2963-0.2580.13840.3143-0.15180.48340.00290.00870.0011-0.00360.00520.0002-0.0075-0.0106-0.00820.0219-0.00430.00310.0051-0.00890.057419.020242.408717.616
20.316-0.2752-0.57283.12580.96761.1172-0.0362-0.00520.0114-0.11420.04450.02140.02950.013-0.00830.01960.0128-0.00510.0225-0.00720.068818.77015.443915.2426
30.6823-0.0833-0.10351.0503-0.23510.9389-0.0328-0.0209-0.0852-0.00550.02570.07880.082-0.0550.00710.01710.00080.00910.0089-0.00430.06534.29920.664224.2631
40.36640.70070.07911.79670.09740.0247-0.01750.0424-0.00130.01450.0088-0.1567-0.01390.01450.00870.03790.00650.0090.02240.02690.075836.969167.737119.9042
51.0964-0.1167-0.87621.35910.20112.07450.0249-0.10420.04670.05510.0065-0.1027-0.0950.1427-0.03140.0151-0.009-0.01010.0328-0.00460.015140.0838101.166826.1606
60.5188-0.2084-0.15191.23510.83711.2805-0.00910.0081-0.01410.1065-0.03140.06460.0504-0.01550.04050.0272-0.00210.00460.0020.00280.052615.202768.902529.9109
70.53430.3292-0.39060.4718-0.4130.83240.0170.01120.0118-0.0088-0.00860.0215-0.00220.0059-0.00840.0260.00890.00290.0054-0.0090.050323.2297.745525.9887
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 181
2X-RAY DIFFRACTION1C1 - 9
3X-RAY DIFFRACTION2A182 - 276
4X-RAY DIFFRACTION3B0 - 99
5X-RAY DIFFRACTION4D1 - 113
6X-RAY DIFFRACTION5D114 - 201
7X-RAY DIFFRACTION6E1 - 113
8X-RAY DIFFRACTION7E114 - 246

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