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Basic information

Entry
Database: PDB / ID: 2ypl
TitleStructural features underlying T-cell receptor sensitivity to concealed MHC class I micropolymorphisms
Components
  • (AGA T-CELL RECEPTOR ...) x 2
  • BETA-2-MICROGLOBULIN
  • HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, B-57 ALPHA CHAIN
  • KF11 P24 GAG PEPTIDE
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / IMMUNE SYSTEM-VIRAL PROTEIN COMPLEX / 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 / detection of bacterium / secretory granule membrane / positive regulation of ferrous iron binding ...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 / detection of bacterium / secretory granule membrane / 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 / negative regulation of receptor binding / DAP12 interactions / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / exoribonuclease H activity / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / 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 / MHC class I protein complex / defense response / DNA integration / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / viral genome integration into host DNA / MHC class II protein complex / cellular response to nicotine / establishment of integrated proviral latency / viral penetration into host nucleus / symbiont-mediated suppression of host gene expression / positive regulation of T cell mediated cytotoxicity / specific granule lumen / RNA stem-loop binding / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / RNA-directed DNA polymerase activity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / RNA-DNA hybrid ribonuclease activity / positive regulation of T cell activation / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / sensory perception of smell / host cell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / protein-folding chaperone binding / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / viral nucleocapsid / protein homotetramerization / intracellular iron ion homeostasis / DNA recombination / host cell cytoplasm / adaptive immune response / amyloid fibril formation / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / learning or memory / immune response / symbiont entry into host cell / Amyloid fiber formation / viral translational frameshifting / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / lysosomal membrane / innate immune response / signaling receptor binding
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 / Reverse transcriptase connection / Reverse transcriptase connection domain ...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 / Reverse transcriptase connection / Reverse transcriptase connection domain / Beta-2-Microglobulin / : / 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 / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / MHC classes I/II-like antigen recognition protein / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / 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 / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / DNA/RNA polymerase superfamily / 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: 2.4 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
Revision 1.4Nov 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: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, B-57 ALPHA CHAIN
B: BETA-2-MICROGLOBULIN
C: KF11 P24 GAG PEPTIDE
D: AGA T-CELL RECEPTOR ALPHA CHAIN
E: AGA T-CELL RECEPTOR BETA CHAIN


Theoretical massNumber of molelcules
Total (without water)93,7255
Polymers93,7255
Non-polymers00
Water3,513195
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10140 Å2
ΔGint-53.1 kcal/mol
Surface area39060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.348, 75.605, 241.527
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, B-57 ALPHA CHAIN / BW-57 / MHC CLASS I ANTIGEN B*57 / HLA-B5703


Mass: 31598.096 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): DE3 / References: UniProt: P18465, UniProt: P01889*PLUS
#2: Protein BETA-2-MICROGLOBULIN / BETA-2-MICROGLOBULIN FORM PI 5.3


Mass: 11748.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DE3 / References: UniProt: P61769

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

#4: Protein AGA T-CELL RECEPTOR ALPHA CHAIN


Mass: 22307.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DE3
#5: Protein AGA T-CELL RECEPTOR BETA CHAIN


Mass: 26804.928 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DE3

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Protein/peptide / Non-polymers , 2 types, 196 molecules C

#3: Protein/peptide KF11 P24 GAG PEPTIDE


Mass: 1266.526 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HUMAN IMMUNODEFICIENCY VIRUS / References: UniProt: Q70XD7*PLUS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.74 Å3/Da / Density % sol: 55.18 % / Description: NONE
Crystal growpH: 7.3 / Details: pH 7.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 41023 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 13.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 40.1
Reflection shellResolution: 2.4→2.51 Å / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 5.5 / % possible all: 94.7

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Processing

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

2bvo


Resolution: 2.4→29.77 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.916 / SU B: 21.049 / SU ML: 0.236 / Cross valid method: THROUGHOUT / ESU R: 0.412 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27746 2054 5 %RANDOM
Rwork0.22072 ---
obs0.22358 38896 98.68 %-
Displacement parametersBiso mean: 66.1 Å2
Baniso -1Baniso -2Baniso -3
1-3.21 Å20 Å20 Å2
2--0.07 Å20 Å2
3----3.29 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6601 0 0 195 6796
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0196778
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2221.949208
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5725816
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.62723.848343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.836151107
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.941549
X-RAY DIFFRACTIONr_chiral_restr0.0910.2969
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215292
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: 2.399→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.425 157 -
Rwork0.346 2603 -
obs--91.24 %
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)
10.39990.0524-0.38970.1154-0.33991.8377-0.01470.09740.04140.01910.1205-0.0540.0313-0.2812-0.10570.0850.13090.09270.29550.12720.3684-3.4308-33.301431.6149
21.67430.8449-0.42471.0529-1.63393.6736-0.24030.37980.1051-0.0790.27260.07910.09170.015-0.03220.16620.0050.07030.36860.08280.30339.9511-28.5795-1.6937
30.9074-0.5916-0.01940.8720.39782.8225-0.0268-0.2032-0.151-0.13160.4694-0.03330.3665-0.6143-0.44250.1462-0.25910.0020.59980.11470.2449-8.1969-39.93765.8727
40.38-0.33711.0850.3175-0.99313.15340.1567-0.3897-0.1462-0.24150.25370.07390.6946-1.0663-0.41040.2744-0.10270.09040.52430.34340.4076-5.8941-32.699140.4108
50.75180.1884-0.48480.10990.31795.29360.1723-0.11880.06760.0217-0.06090.00210.09240.5249-0.11140.1380.10840.06350.27080.09640.33155.6309-34.638462.857
60.4871-0.1409-0.43561.9482-0.44483.1870.1037-0.2039-0.03120.2409-0.0941-0.08680.21950.4802-0.00960.2236-0.00170.01110.19060.02970.2749-0.4277-38.367396.595
73.48351.0295-2.81280.4018-0.76124.18160.23410.8233-0.08390.13780.016-0.13420.2663-1.1625-0.25010.1907-0.1789-0.05130.70380.15220.3074-18.1527-42.044461.0613
80.92691.1526-0.16651.4775-0.15921.6830.00020.09780.08490.08410.09560.08330.0092-0.2426-0.09580.1794-0.06070.05570.1705-0.01340.3336-15.2213-34.794390.3973
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
5X-RAY DIFFRACTION5D1 - 115
6X-RAY DIFFRACTION6D116 - 199
7X-RAY DIFFRACTION7E4 - 115
8X-RAY DIFFRACTION8E116 - 241

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