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- PDB-2ypk: Structural features underlying T-cell receptor sensitivity to con... -

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Basic information

Entry
Database: PDB / ID: 2ypk
TitleStructural features underlying T-cell receptor sensitivity to concealed MHC class I micropolymorphisms
Components
  • BETA-2-MICROGLOBULINBeta-2 microglobulin
  • HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, B-57 ALPHA CHAIN
  • KF11 P24 GAG PEPTIDE
KeywordsIMMUNE SYSTEM / MICROPOLYMORPHISM
Function / homology
Function and homology information


regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / viral budding via host ESCRT complex / 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 ...regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / viral budding via host ESCRT complex / 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 / secretory granule membrane / 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 / 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 / defense response / ER to Golgi transport vesicle membrane / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / exoribonuclease H activity / 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 / DNA integration / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / viral genome integration into host DNA / peptide antigen binding / viral penetration into host nucleus / establishment of integrated proviral latency / 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 / RNA-directed DNA polymerase activity / 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 / sensory perception of smell / RNA-DNA hybrid ribonuclease activity / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization / viral nucleocapsid / DNA recombination / intracellular iron ion homeostasis / host cell cytoplasm / amyloid fibril formation / adaptive immune response / aspartic-type endopeptidase activity / learning or memory / DNA-directed DNA polymerase activity / immune response / symbiont entry into host cell / Amyloid fiber formation / symbiont-mediated suppression of host gene expression / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response / Neutrophil degranulation / structural molecule activity / SARS-CoV-2 activates/modulates innate and adaptive immune responses
Similarity search - Function
Gag protein p6 / Gag protein p6 / 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 / Reverse transcriptase connection ...Gag protein p6 / Gag protein p6 / 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 / Reverse transcriptase connection / Reverse transcriptase connection domain / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / MHC classes I/II-like antigen recognition protein / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / DNA/RNA polymerase superfamily / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, B alpha chain / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin / Gag polyprotein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
HUMAN IMMUNODEFICIENCY VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsStewart-Jones, G.B. / Simpson, P. / Van Der Merwe, P.A. / Easterbrook, P. / Mcmichael, A.J. / Rowland-Jones, S.L. / Jones, E.Y. / Gillespie, G.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural Features Underlying T-Cell Receptor Sensitivity to Concealed Mhc Class I Micropolymorphisms.
Authors: Stewart-Jones, G.B. / Simpson, P. / Anton Van Der Merwe, P. / Easterbrook, P. / Mcmichael, A.J. / Rowland-Jones, S.L. / Jones, E.Y. / Gillespie, G.M.
History
DepositionOct 30, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2012Group: Database references
Revision 1.2Jan 16, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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, B-57 ALPHA CHAIN
B: BETA-2-MICROGLOBULIN
C: KF11 P24 GAG PEPTIDE


Theoretical massNumber of molelcules
Total (without water)44,5253
Polymers44,5253
Non-polymers00
Water8,899494
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-21.2 kcal/mol
Surface area19310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.829, 82.067, 110.489
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, B-57 ALPHA CHAIN / BW-57 / MHC CLASS I ANTIGEN B*57 / HLA-B5701


Mass: 31509.943 Da / Num. of mol.: 1 / Fragment: RESIDUES 25-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P18465, UniProt: P01889*PLUS
#2: Protein BETA-2-MICROGLOBULIN / Beta-2 microglobulin


Mass: 11748.160 Da / Num. of mol.: 1 / Fragment: RESIDUES 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61769
#3: Protein/peptide KF11 P24 GAG PEPTIDE


Mass: 1266.526 Da / Num. of mol.: 1 / Fragment: RESIDUES 162-172 / Source method: obtained synthetically / Source: (synth.) HUMAN IMMUNODEFICIENCY VIRUS / References: UniProt: Q70XD7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 494 / 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: 2.59 Å3/Da / Density % sol: 52.47 % / Description: NONE
Crystal growpH: 6.5 / Details: 16% PEG 8000, 50MM MES PH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 34422 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 2.99 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 19.4
Reflection shellResolution: 1.95→2.02 Å / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.4 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BVO

2bvo


Resolution: 1.95→29.84 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.912 / SU B: 7.705 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25182 1737 5 %RANDOM
Rwork0.19125 ---
obs0.19427 32685 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.235 Å2
Baniso -1Baniso -2Baniso -3
1--1.33 Å20 Å20 Å2
2---2.13 Å20 Å2
3---3.46 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3139 0 0 494 3633
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193229
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5391.9364387
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3635381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.43623.198172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.22815523
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7651530
X-RAY DIFFRACTIONr_chiral_restr0.1190.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212553
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 122 -
Rwork0.261 2358 -
obs--99.56 %
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)
10.77360.1527-0.19760.448-0.02370.0667-0.0064-0.0509-0.00630.06060.0074-0.0209-0.0023-0.0059-0.0010.13670.0060.00160.1343-0.00280.0015-4.6052-12.531830.7099
20.1261-0.04570.30910.49260.16471.76840.02080.00830.0115-0.06710.01690.04270.03820.0183-0.03770.1433-0.0207-0.01340.15940.00910.0163-25.0301-15.59171.8585
31.3875-0.49180.43380.7029-0.08040.2716-0.07670.08590.1269-0.02790.03410.03670.00630.04260.04260.1272-0.0187-0.02620.12810.03250.0272-15.20572.585110.9116
44.8405-2.1298-1.83261.8948-0.50682.4980.0392-0.3052-0.1770.12470.020.1572-0.21260.2346-0.05920.1546-0.0185-0.0330.153-0.00350.02771.0231-13.768137.9432
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 181
2X-RAY DIFFRACTION2A182 - 274
3X-RAY DIFFRACTION3B1 - 99
4X-RAY DIFFRACTION4C1 - 11

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