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- PDB-6r2l: NYBR1-A2-SLSKILDTV -

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Basic information

Entry
Database: PDB / ID: 6r2l
TitleNYBR1-A2-SLSKILDTV
Components
  • (T cell receptor ...T-cell receptor) x 2
  • Beta-2-microglobulinBeta-2 microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • SER-LEU-SER-LYS-ILE-LEU-ASP-THR-VAL
KeywordsIMMUNE SYSTEM / NYBR1 / TCR / HLA-A*0201 / A2 / HLA-A2 / MHC-I / cancer / NY-BR-1 / breast cancer / high affinity TCR / immunotherapy / T-cell / 3D Structure
Function / homology
Function and homology information


T cell receptor complex / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation ...T cell receptor complex / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / endoplasmic reticulum exit site / beta-2-microglobulin binding / 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 / detection of bacterium / T cell receptor binding / 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 / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / negative regulation of epithelial cell proliferation / Interferon gamma signaling / positive regulation of T cell activation / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / positive regulation of type II interferon production / sensory perception of smell / E3 ubiquitin ligases ubiquitinate target proteins / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / positive regulation of protein binding / ER-Phagosome pathway / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / adaptive immune response / learning or memory / cell surface receptor signaling pathway / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity
Similarity search - Function
CCDC144C-like, coiled-coil domain / CCDC144C protein coiled-coil region / Domain of unknown function DUF3447 / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / Ankyrin repeat / 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 ...CCDC144C-like, coiled-coil domain / CCDC144C protein coiled-coil region / Domain of unknown function DUF3447 / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / Ankyrin repeat / 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 / Immunoglobulin V-Type / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / Beta-2-Microglobulin / ankyrin repeats / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Ankyrin repeat / Immunoglobulin V-set domain / Ankyrin repeat-containing domain superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin / 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
DI(HYDROXYETHYL)ETHER / T cell receptor alpha variable 22 / T cell receptor beta variable 11-2 / Human nkt tcr alpha chain / Human nkt tcr beta chain / HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin / Ankyrin repeat domain-containing protein 30A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRizkallah, P.J. / Cole, D.K. / Sami, M.
CitationJournal: To Be Published
Title: NYBR1-A2-SLSKILDTV
Authors: Rizkallah, P.J. / Cole, D.K. / Sami, M.
History
DepositionMar 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release

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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, A-2 alpha chain
B: Beta-2-microglobulin
C: SER-LEU-SER-LYS-ILE-LEU-ASP-THR-VAL
D: T cell receptor alpha variable 22,Human nkt tcr alpha chain
E: T cell receptor beta variable 11-2,Human nkt tcr beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,89020
Polymers94,3775
Non-polymers1,51315
Water6,846380
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14630 Å2
ΔGint-157 kcal/mol
Surface area39160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.210, 99.330, 111.440
Angle α, β, γ (deg.)90.00, 90.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein HLA class I histocompatibility antigen, A-2 alpha chain / MHC class I antigen A*2


Mass: 31951.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Production host: Escherichia coli (E. coli) / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


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 / Production host: Escherichia coli (E. coli) / References: UniProt: P61769

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide SER-LEU-SER-LYS-ILE-LEU-ASP-THR-VAL


Mass: 976.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9BXX3*PLUS

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T cell receptor ... , 2 types, 2 molecules DE

#4: Protein T cell receptor alpha variable 22,Human nkt tcr alpha chain / Human nkt tcr beta chain


Mass: 21676.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAV22, B2M, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B4J277, UniProt: K7N5M3
#5: Protein T cell receptor beta variable 11-2,Human nkt tcr beta chain


Mass: 27893.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRBV11-2, TCRBV21S3A2N2T, B2M, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: A0A584, UniProt: K7N5M4

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Non-polymers , 6 types, 395 molecules

#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#10: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 380 / 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: 3.06 Å3/Da / Density % sol: 59.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2 M NaCl, 0.1 M MES, 20% PEG 6000, pH 6.0 . Condition B07 from Molecular Dimensions PACT premier HT-96/FX-96, MD1-36

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 2.3→52.21 Å / Num. obs: 50452 / % possible obs: 99.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 25.9 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.207 / Rrim(I) all: 0.24 / Net I/σ(I): 9.7
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.089 / Num. unique obs: 3747 / CC1/2: 0.522 / Rrim(I) all: 1.278 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
xia2data reduction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→52.21 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.909 / SU B: 18.957 / SU ML: 0.221 / Cross valid method: THROUGHOUT / ESU R: 0.305 / ESU R Free: 0.239 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26498 2435 4.8 %RANDOM
Rwork0.21432 ---
obs0.21677 47996 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.008 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20.96 Å2
2--0.3 Å20 Å2
3----0.57 Å2
Refinement stepCycle: 1 / Resolution: 2.3→52.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6654 0 88 380 7122
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0136951
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176056
X-RAY DIFFRACTIONr_angle_refined_deg1.8531.6499452
X-RAY DIFFRACTIONr_angle_other_deg1.2521.58114097
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8625829
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.72522.393397
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.375151108
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5611546
X-RAY DIFFRACTIONr_chiral_restr0.0850.2867
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027813
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021529
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6751.3933319
X-RAY DIFFRACTIONr_mcbond_other0.6751.3923318
X-RAY DIFFRACTIONr_mcangle_it1.2082.0824147
X-RAY DIFFRACTIONr_mcangle_other1.2082.0834148
X-RAY DIFFRACTIONr_scbond_it0.9151.6133632
X-RAY DIFFRACTIONr_scbond_other0.7851.5293601
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.2752.2425258
X-RAY DIFFRACTIONr_long_range_B_refined7.35315.9637091
X-RAY DIFFRACTIONr_long_range_B_other7.11415.6597044
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 198 -
Rwork0.312 3542 -
obs--99.73 %
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)
13.4624-0.04760.09931.70250.28031.40240.05160.00070.2183-0.13340.0285-0.0256-0.050.0051-0.08010.151-0.0137-0.16090.00140.01340.221217.637863.716437.351
23.56032.72430.09657.6393-0.48082.6947-0.02310.65130.6279-0.59220.15920.585-0.5570.0069-0.13610.3925-0.0262-0.16940.29690.09330.359316.670399.909840.7728
31.3218-0.9343-0.68626.23933.34323.42680.0076-0.10310.06370.08110.1187-0.24660.02520.3312-0.12640.1358-0.0312-0.17720.09690.0130.245928.874184.135452.3741
42.73490.44232.0582.38821.10363.9595-0.06660.131-0.0053-0.2726-0.1460.25150.096-0.43750.21260.1634-0.0377-0.16040.1341-0.04460.2362-2.425747.458820.0138
53.67430.81-0.71657.7298-1.79274.4881-0.1288-0.0692-0.12490.07480.12020.84410.0137-0.50690.00860.4124-0.0369-0.20840.5376-0.1680.4243-21.459423.33463.9177
63.14592.93530.12155.38450.01621.1431-0.0626-0.1315-0.30530.1922-0.0357-0.18080.4613-0.14540.09830.3514-0.0232-0.09640.069-0.03060.2434.915832.504935.4292
70.57240.03411.36991.26650.03967.41840.04470.0395-0.13370.0493-0.15680.25350.3484-0.14660.11210.3381-0.0768-0.15350.3009-0.09620.3615-9.521915.498513.1316
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 180
2X-RAY DIFFRACTION1C1 - 9
3X-RAY DIFFRACTION2A181 - 276
4X-RAY DIFFRACTION3B0 - 99
5X-RAY DIFFRACTION4D1 - 113
6X-RAY DIFFRACTION5D114 - 194
7X-RAY DIFFRACTION6E3 - 112
8X-RAY DIFFRACTION7E113 - 249

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