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- PDB-2c7u: Conflicting selective forces affect CD8 T-cell receptor contact s... -

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Basic information

Entry
Database: PDB / ID: 2c7u
TitleConflicting selective forces affect CD8 T-cell receptor contact sites in an HLA-A2 immunodominant HIV epitope.
Components
  • BETA-2-MICROGLOBULIN
  • GAG PROTEIN
  • HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
KeywordsGLYCOPROTEIN/PEPTIDE / GLYCOPROTEIN-PEPTIDE COMPLEX / MHC / TCR / HLA-A2 / HIV / GLYCOPROTEIN / IMMUNE RESPONSE / MHC I / TRANSMEMBRANE / IMMUNOGLOBULIN DOMAIN / PYRROLIDONE CARBOXYLIC ACID / AIDS
Function / homology
Function and homology information


positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / antigen processing and presentation of exogenous peptide antigen via MHC class I ...positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / endoplasmic reticulum exit site / TAP binding / protection from natural killer cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / detection of bacterium / T cell receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / T cell mediated cytotoxicity / lumenal side of endoplasmic reticulum membrane / negative regulation of iron ion transport / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / regulation of iron ion transport / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / transferrin transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / negative regulation of receptor-mediated endocytosis / cellular response to iron ion / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / phagocytic vesicle membrane / positive regulation of type II interferon production / positive regulation of immune response / recycling endosome membrane / Interferon gamma signaling / positive regulation of T cell activation / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / T cell receptor signaling pathway / late endosome membrane / negative regulation of neuron projection development / E3 ubiquitin ligases ubiquitinate target proteins / antibacterial humoral response / ER-Phagosome pathway / protein refolding / early endosome membrane / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / signaling receptor binding / external side of plasma membrane / innate immune response / lysosomal membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / RNA binding
Similarity search - Function
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 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 / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / MHC classes I/II-like antigen recognition protein / : / Retroviral matrix 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
Gag protein / HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
HUMAN IMMUNODEFICIENCY VIRUS 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.38 Å
AuthorsIversen, A.K. / Stewart-Jones, G. / Learn, G.H. / Christie, N. / Sylvester-Hviid, C. / Armitage, A.E. / Kaul, R. / Beattie, T. / Lee, J.K. / Li, Y. ...Iversen, A.K. / Stewart-Jones, G. / Learn, G.H. / Christie, N. / Sylvester-Hviid, C. / Armitage, A.E. / Kaul, R. / Beattie, T. / Lee, J.K. / Li, Y. / Chotiyarnwong, P. / Dong, T. / Xu, X. / Luscher, M.A. / MacDonald, K. / Ullum, H. / Klarlund-Pedersen, B. / Skinhoj, P. / Fugger, J.L. / Buus, S. / Mullins, J.I. / Jones, E.Y. / van der Merwe, P.A. / McMichael, A.J.
CitationJournal: Nat.Immunol. / Year: 2006
Title: Conflicting Selective Forces Affect T Cell Receptor Contacts in an Immunodominant Human Immunodeficiency Virus Epitope.
Authors: Iversen, A.K. / Stewart-Jones, G. / Learn, G.H. / Christie, N. / Sylvester-Hviid, C. / Armitage, A.E. / Kaul, R. / Beattie, T. / Lee, J.K. / Li, Y. / Chotiyarnwong, P. / Dong, T. / Xu, X. / ...Authors: Iversen, A.K. / Stewart-Jones, G. / Learn, G.H. / Christie, N. / Sylvester-Hviid, C. / Armitage, A.E. / Kaul, R. / Beattie, T. / Lee, J.K. / Li, Y. / Chotiyarnwong, P. / Dong, T. / Xu, X. / Luscher, M.A. / Macdonald, K. / Ullum, H. / Klarlund-Pedersen, B. / Skinhoj, P. / Fugger, L. / Buus, S. / Mullins, J.I. / Jones, E.Y. / Van Der Merwe, P.A. / Mcmichael, A.J.
History
DepositionNov 29, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
B: BETA-2-MICROGLOBULIN
C: GAG PROTEIN
D: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
E: BETA-2-MICROGLOBULIN
F: GAG PROTEIN


Theoretical massNumber of molelcules
Total (without water)89,6166
Polymers89,6166
Non-polymers00
Water3,945219
1
A: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
B: BETA-2-MICROGLOBULIN
C: GAG PROTEIN


Theoretical massNumber of molelcules
Total (without water)44,8083
Polymers44,8083
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
D: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
E: BETA-2-MICROGLOBULIN
F: GAG PROTEIN


Theoretical massNumber of molelcules
Total (without water)44,8083
Polymers44,8083
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)63.163, 93.854, 81.497
Angle α, β, γ (deg.)90.00, 89.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN / HLA-A2 / MHC CLASS I ANTIGEN A*2


Mass: 31951.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET-22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BLR / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein BETA-2-MICROGLOBULIN


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET-22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BLR / References: UniProt: P61769
#3: Protein/peptide GAG PROTEIN


Mass: 977.155 Da / Num. of mol.: 2 / Fragment: RESIDUES 7-15 / Source method: obtained synthetically / Source: (synth.) HUMAN IMMUNODEFICIENCY VIRUS 1 / References: UniProt: O11822
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O
Compound detailsINVOLVED IN THE PRESENTATION OF FOREIGN ANTIGENS TO THE IMMUNE SYSTEM
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.37 %
Crystal growpH: 6.5 / Details: pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.977
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 23, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 138420 / % possible obs: 96.8 % / Observed criterion σ(I): 0.9 / Redundancy: 3.7 % / Rmerge(I) obs: 0.07

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: OTHER / Resolution: 2.38→81.38 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.881 / SU B: 26.462 / SU ML: 0.326 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.513 / ESU R Free: 0.331 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.314 1851 5 %RANDOM
Rwork0.248 ---
obs0.251 35178 97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.48 Å2
Baniso -1Baniso -2Baniso -3
1--2.6 Å20 Å20.34 Å2
2--1.58 Å20 Å2
3---1.02 Å2
Refinement stepCycle: LAST / Resolution: 2.38→81.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6300 0 0 219 6519
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0216482
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.281.928794
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3855762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.35323.161348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.935151056
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1971556
X-RAY DIFFRACTIONr_chiral_restr0.0830.2900
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025080
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.22641
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2920.24160
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2307
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.222
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4621.53949
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.79926156
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.12132986
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.7054.52638
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.38→2.44 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.45 105
Rwork0.342 2019
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)
13.0331-0.35681.923.4393-0.21245.5274-0.1821-0.0931-0.10020.44020.59781.0341-0.5098-0.4387-0.41570.00130.20160.29770.17340.47850.072229.38948.69668.524
27.76351.684-6.73325.8468-6.588316.08250.52970.1690.90080.2207-0.4038-0.7697-1.07580.4563-0.1259-0.2534-0.01080.0486-0.27810.1808-0.056361.04353.22552.742
36.9619-1.06631.40855.9532-1.41633.9789-0.01270.1668-0.3635-0.03390.40780.21060.0661-0.1059-0.3951-0.3154-0.0607-0.0493-0.30.1237-0.410150.71434.53559.949
42.75840.1839-1.9443.63250.03885.6652-0.13270.18530.1143-0.31370.64360.96280.5254-0.5578-0.51090.0622-0.2701-0.27620.17030.5470.118860.96141.48494.52
59.3836-1.53817.64745.9706-5.880617.1860.5383-0.1851-0.9421-0.1797-0.3489-0.78331.20520.5646-0.1895-0.2328-0.0097-0.0733-0.32550.1795-0.064992.64936.923110.299
66.820.9623-1.17486.3066-1.44743.6786-0.0293-0.23380.3799-0.00110.430.2503-0.0052-0.0961-0.4007-0.30690.05580.0307-0.28590.1251-0.41982.26755.625103.031
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 180
2X-RAY DIFFRACTION2A181 - 275
3X-RAY DIFFRACTION3B0 - 99
4X-RAY DIFFRACTION4D1 - 180
5X-RAY DIFFRACTION5D181 - 275
6X-RAY DIFFRACTION6E0 - 99

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