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- PDB-1lp9: Xenoreactive complex AHIII 12.2 TCR bound to p1049/HLA-A2.1 -

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Basic information

Entry
Database: PDB / ID: 1lp9
TitleXenoreactive complex AHIII 12.2 TCR bound to p1049/HLA-A2.1
Components
  • (T-cell Receptor ...) x 2
  • Beta-2-microglobulinBeta-2 microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • self-peptide P1049
KeywordsIMMUNE SYSTEM / Immunoregulatory complex / Class I MHC:TCR co-crystal
Function / homology
Function and homology information


Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / EMC complex / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / PD-1 signaling / Generation of second messenger molecules / tail-anchored membrane protein insertion into ER membrane / Downstream TCR signaling / alpha-beta T cell receptor complex / T cell receptor complex ...Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / EMC complex / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / PD-1 signaling / Generation of second messenger molecules / tail-anchored membrane protein insertion into ER membrane / Downstream TCR signaling / alpha-beta T cell receptor complex / T cell receptor complex / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / 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 / early endosome lumen / positive regulation of receptor binding / 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 / response to bacterium / 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 / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / positive regulation of type II interferon production / sensory perception of smell / negative regulation of neuron projection development / E3 ubiquitin ligases ubiquitinate target proteins / tertiary granule lumen / DAP12 signaling / signaling receptor activity / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway / protein refolding / early endosome membrane / carbohydrate binding / 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
Similarity search - Function
ER membrane protein complex subunit 7, beta-sandwich domain / ER membrane protein complex subunit 7 / ER membrane protein complex subunit 7, beta-sandwich domain / Carbohydrate-binding-like fold / 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 ...ER membrane protein complex subunit 7, beta-sandwich domain / ER membrane protein complex subunit 7 / ER membrane protein complex subunit 7, beta-sandwich domain / Carbohydrate-binding-like fold / 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 / Immunoglobulin V-Type / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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, A alpha chain / T-cell receptor beta chain V region C5 / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin / Endoplasmic reticulum membrane protein complex subunit 7
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBuslepp, J. / Wang, H. / Biddison, W.E. / Appella, E. / Collins, E.J.
CitationJournal: Immunity / Year: 2003
Title: A correlation between TCR Valpha docking on MHC and CD8 dependence: implications for T cell selection.
Authors: Buslepp, J. / Wang, H. / Biddison, W.E. / Appella, E. / Collins, E.J.
History
DepositionMay 7, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_sheet.number_strands
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 999SEQUENCE At the time of processing, there is no sequence database reference for chains EL, FM, and CJ.

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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: self-peptide P1049
E: T-cell Receptor alpha chain
F: T-cell Receptor beta chain
H: HLA class I histocompatibility antigen, A-2 alpha chain
I: Beta-2-microglobulin
J: self-peptide P1049
L: T-cell Receptor alpha chain
M: T-cell Receptor beta chain


Theoretical massNumber of molelcules
Total (without water)186,66010
Polymers186,66010
Non-polymers00
Water7,494416
1
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: self-peptide P1049
E: T-cell Receptor alpha chain
F: T-cell Receptor beta chain


Theoretical massNumber of molelcules
Total (without water)93,3305
Polymers93,3305
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11010 Å2
ΔGint-59 kcal/mol
Surface area37850 Å2
MethodPISA
2
H: HLA class I histocompatibility antigen, A-2 alpha chain
I: Beta-2-microglobulin
J: self-peptide P1049
L: T-cell Receptor alpha chain
M: T-cell Receptor beta chain


Theoretical massNumber of molelcules
Total (without water)93,3305
Polymers93,3305
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10950 Å2
ΔGint-60 kcal/mol
Surface area37640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.708, 84.469, 121.336
Angle α, β, γ (deg.)90.00, 92.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules AHBI

#1: Protein HLA class I histocompatibility antigen, A-2 alpha chain / class I MHC / A2.1


Mass: 31854.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A*0201 / Plasmid: pLM1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(pLysE) / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin / HDCMA22P


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Plasmid: pLM1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(pLysE) / References: UniProt: P61769

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T-cell Receptor ... , 2 types, 4 molecules ELFM

#4: Protein T-cell Receptor alpha chain / AHIII12.2 TCR alpha


Mass: 21656.322 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P01849*PLUS
#5: Protein T-cell Receptor beta chain / AHIII 12.2 TCR beta


Mass: 26890.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P04213*PLUS

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Protein/peptide / Non-polymers , 2 types, 418 molecules CJ

#3: Protein/peptide self-peptide P1049


Mass: 1049.263 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: This sequence occurs naturally in humans, but is synthesized chemically for this structure.
References: UniProt: Q9NPA0*PLUS
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 416 / 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: 2.57 Å3/Da / Density % sol: 52.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG3350, 25mM MES , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.1 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
212 %PEG80001reservoir
325 mMHEPES1reservoirpH7.1
41 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.01715 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 12, 2001
Details: Bent Cylinder, 1:1 defocused rhodium-coated electroless nickel-plated bent aluminum cylinder
RadiationMonochromator: Double flat crystal fixed-exit monochromator using Si(111) flats
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.01715 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 122580 / Num. obs: 121366 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Rsym value: 0.074 / Net I/σ(I): 28.5
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 3.5 / % possible all: 99.9
Reflection
*PLUS
Rmerge(I) obs: 0.074
Reflection shell
*PLUS
% possible obs: 99.9 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Class I MHC, PDB ENTRY 1B0G. TCR, PDB ENTRY 2CKB

1b0g

2ckb


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.93 / SU B: 12.081 / SU ML: 0.179 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1.127 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25293 6421 5 %RANDOM
Rwork0.21887 ---
all0.23 122580 --
obs0.22058 121366 99.99 %-
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 mean: 14.229 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20 Å20.98 Å2
2--0.59 Å20 Å2
3----1.69 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13136 0 0 416 13552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02113162
X-RAY DIFFRACTIONr_bond_other_d0.0070.0211197
X-RAY DIFFRACTIONr_angle_refined_deg1.4351.92317822
X-RAY DIFFRACTIONr_angle_other_deg0.811326030
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.28831592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.406152188
X-RAY DIFFRACTIONr_chiral_restr0.090.21886
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214685
X-RAY DIFFRACTIONr_gen_planes_other0.0490.022807
X-RAY DIFFRACTIONr_nbd_refined0.2840.32540
X-RAY DIFFRACTIONr_nbd_other0.2290.310602
X-RAY DIFFRACTIONr_nbtor_other0.0650.53
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.5972
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.3570.513
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3340.345
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3280.3111
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3710.515
X-RAY DIFFRACTIONr_symmetry_hbond_other0.5320.51
X-RAY DIFFRACTIONr_mcbond_it0.6581.58030
X-RAY DIFFRACTIONr_mcangle_it1.067212887
X-RAY DIFFRACTIONr_scbond_it1.50735132
X-RAY DIFFRACTIONr_scangle_it2.2284.54935
X-RAY DIFFRACTIONr_rigid_bond_restr0.902213162
X-RAY DIFFRACTIONr_sphericity_free3.6122438
X-RAY DIFFRACTIONr_sphericity_bonded1.083212817
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.294 480
Rwork0.244 8863
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)
11.73060.43550.2022.24670.7231.78190.0582-0.0495-0.0864-0.05280.0066-0.0007-0.0196-0.0692-0.06470.060.00270.00330.00690.02240.073516.2634-1.764619.7157
22.1688-0.2655-0.55984.464-4.85587.78270.0952-0.3513-0.2667-0.24830.0090.07510.48260.1308-0.10420.21140.0347-0.02590.22820.02070.154713.0646-2.374354.3849
31.9128-1.0877-1.55213.37993.2165.8064-0.03260.0492-0.05650.1915-0.22270.32020.1176-0.69040.25530.091-0.00930.01260.22980.03290.114-0.95635.545539.0128
43.0415-0.6245-2.03140.30360.65353.61520.0247-0.0116-0.0584-0.0212-0.01430.004-0.07090.1171-0.01040.1136-0.0181-0.0080.05090.00790.100835.8693-5.7792-5.4835
57.2395-1.92821.08224.5119-1.46717.2950.03980.60710.5514-0.2655-0.1864-0.3335-0.38140.35660.14660.13020.02970.00320.35510.02070.199144.3314-1.3568-37.9132
60.77670.32780.16222.1909-2.56013.82750.02970.09510.1178-0.01870.130.176-0.3396-0.2813-0.15970.22160.03730.03090.0998-0.0060.143218.1196.7533-9.4874
72.7372-2.4294-0.69314.54631.49892.14190.17120.367-0.0601-0.2085-0.24260.2933-0.11210.11990.07140.14910.0318-0.04710.30320.02970.189727.68591.3177-38.9042
81.72170.1135-0.30331.70850.34362.496-0.033-0.0562-0.00140.0051-0.01370.0450.2426-0.18460.04670.0846-0.03280.02570.02290.01420.069516.277740.813524.2165
91.65440.2606-0.76264.7298-5.1587.75540.035-0.0694-0.1854-0.05870.14490.03620.30220.0201-0.17980.1510.0323-0.03470.1545-0.02550.137113.296239.964958.9928
101.7963-0.5925-1.45532.77161.93875.7057-0.04060.08570.02590.11370.01620.19870.0106-0.54740.02440.06380.00740.00490.17980.06360.104-0.873248.227343.6282
113.2974-0.6492-2.45190.62440.62953.3901-0.05140.0458-0.067-0.00640.032-0.01230.08210.11790.01940.10610.0052-0.00290.04380.00840.092835.755336.6042-1.102
127.0978-3.50021.15545.5435-1.38346.26220.04130.3790.5203-0.1118-0.3049-0.456-0.33960.34840.26350.08040.0093-0.01610.24430.03130.176644.505841.9228-33.2143
130.8987-0.71510.46252.6469-1.9033.3857-0.02030.00650.028-0.05690.12690.2368-0.1074-0.2951-0.10660.0896-0.00260.00010.0709-0.00550.110718.060449.3128-4.9619
142.7921-1.9302-0.7713.68881.38022.92780.13930.1504-0.0173-0.1677-0.12810.0786-0.2461-0.0044-0.01120.10950.0101-0.04720.17590.02820.122928.019944.8936-34.3048
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1831 - 183
2X-RAY DIFFRACTION1CC1 - 91 - 9
3X-RAY DIFFRACTION2AA184 - 275184 - 275
4X-RAY DIFFRACTION3BB0 - 991 - 100
5X-RAY DIFFRACTION4ED0 - 1161 - 114
6X-RAY DIFFRACTION5ED117 - 198115 - 194
7X-RAY DIFFRACTION6FE1 - 1162 - 112
8X-RAY DIFFRACTION7FE117 - 245114 - 238
9X-RAY DIFFRACTION8HF1 - 1831 - 183
10X-RAY DIFFRACTION8JH1 - 91 - 9
11X-RAY DIFFRACTION9HF184 - 275184 - 275
12X-RAY DIFFRACTION10IG0 - 991 - 100
13X-RAY DIFFRACTION11LI0 - 1161 - 114
14X-RAY DIFFRACTION12LI117 - 198115 - 194
15X-RAY DIFFRACTION13MJ1 - 1162 - 112
16X-RAY DIFFRACTION14MJ117 - 245114 - 238
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 30 Å / Rfactor Rfree: 0.253 / Rfactor Rwork: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.012
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.435

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