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- PDB-4mji: T cell response to a HIV reverse transcriptase epitope presented ... -

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Basic information

Entry
Database: PDB / ID: 4mji
TitleT cell response to a HIV reverse transcriptase epitope presented by the protective allele HLA-B*51:01
Components
  • Beta-2-microglobulin
  • HIV Reverse Transcriptase peptide Marker
  • HLA class I histocompatibility antigen, B-51 alpha chain
  • T-Cell Receptor Chain alpha
  • T-cell Receptor Beta chain
KeywordsIMMUNE SYSTEM / HIV / peptide-major histocompatibility complex / pMHC / surface plasmon resonance / SPR / T-cell / T-cell receptor / TCR / Immunoglobulin / Class I MHC / Antigen Presentation
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 / alpha-beta T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / protection from natural killer cell mediated cytotoxicity / alpha-beta T cell activation / Generation of second messenger molecules ...regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / alpha-beta T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / protection from natural killer cell mediated cytotoxicity / alpha-beta T cell activation / Generation of second messenger molecules / TAP binding / Co-inhibition by PD-1 / detection of bacterium / 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 / beta-2-microglobulin binding / regulation of natural killer cell mediated immunity / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / positive regulation of T cell mediated cytotoxicity / DAP12 interactions / secretory granule membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / defense response / HFE-transferrin receptor complex / MHC class I peptide loading complex / transferrin transport / 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 / viral genome integration into host DNA / peptide antigen assembly with MHC class II protein complex / establishment of integrated proviral latency / negative regulation of epithelial cell proliferation / cellular response to nicotine / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / positive regulation of immune response / specific granule lumen / antigen processing and presentation of exogenous peptide antigen via MHC class II / RNA-directed DNA polymerase activity / peptide antigen binding / T cell receptor signaling pathway / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of T cell activation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / sensory perception of smell / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / tertiary granule lumen / positive regulation of cellular senescence / MHC class II protein complex binding / DAP12 signaling / Downstream TCR signaling / late endosome membrane / viral nucleocapsid / protein-folding chaperone binding / endonuclease activity / ER-Phagosome pathway / early endosome membrane / aspartic-type endopeptidase activity / amyloid fibril formation / protein homotetramerization / adaptive immune response / intracellular iron ion homeostasis / learning or memory / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / external side of plasma membrane / signaling receptor binding / Golgi membrane / innate immune response / focal adhesion / lysosomal membrane / Neutrophil degranulation / symbiont entry into host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / proteolysis / DNA binding / : / extracellular exosome
Similarity search - Function
: / : / 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 ...: / : / 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 / Retropepsin-like catalytic domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / MHC classes I/II-like antigen recognition protein / Peptidase A2A, retrovirus, catalytic / Immunoglobulin V-set domain / : / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 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 / Reverse transcriptase/Diguanylate cyclase domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Human nkt tcr alpha chain / T cell receptor beta constant 1 / HLA class I histocompatibility antigen, B alpha chain / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin / Polyprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.99 Å
AuthorsRizkallah, P.J. / Cole, D.K. / Sewell, A.K. / Motozono, C. / Takiguchi, M.
CitationJournal: J.Immunol. / Year: 2014
Title: Molecular basis of a dominant T cell response to an HIV reverse transcriptase 8-mer epitope presented by the protective allele HLA-B*51:01
Authors: Motozono, C. / Kuse, N. / Sun, X. / Rizkallah, P.J. / Fuller, A. / Oka, S. / Cole, D.K. / Sewell, A.K. / Takiguchi, M.
History
DepositionSep 3, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, B-51 alpha chain
B: Beta-2-microglobulin
C: HIV Reverse Transcriptase peptide Marker
D: T-Cell Receptor Chain alpha
E: T-cell Receptor Beta chain
F: HLA class I histocompatibility antigen, B-51 alpha chain
G: Beta-2-microglobulin
H: HIV Reverse Transcriptase peptide Marker
I: T-Cell Receptor Chain alpha
J: T-cell Receptor Beta chain


Theoretical massNumber of molelcules
Total (without water)186,35410
Polymers186,35410
Non-polymers00
Water00
1
A: HLA class I histocompatibility antigen, B-51 alpha chain
B: Beta-2-microglobulin
C: HIV Reverse Transcriptase peptide Marker
D: T-Cell Receptor Chain alpha
E: T-cell Receptor Beta chain


Theoretical massNumber of molelcules
Total (without water)93,1775
Polymers93,1775
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: HLA class I histocompatibility antigen, B-51 alpha chain
G: Beta-2-microglobulin
H: HIV Reverse Transcriptase peptide Marker
I: T-Cell Receptor Chain alpha
J: T-cell Receptor Beta chain


Theoretical massNumber of molelcules
Total (without water)93,1775
Polymers93,1775
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.510, 88.870, 129.270
Angle α, β, γ (deg.)102.910, 95.920, 90.090
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
12
13
14
/ NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein HLA class I histocompatibility antigen, B-51 alpha chain / MHC class I antigen B*51


Mass: 32051.305 Da / Num. of mol.: 2 / Fragment: UNP residues 25-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B / Plasmid: pGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: P18464, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11748.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Plasmid: pGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: P61769
#3: Protein/peptide HIV Reverse Transcriptase peptide Marker


Mass: 848.983 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence naturally occurs in HIV / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: R4WL38
#4: Protein T-Cell Receptor Chain alpha


Mass: 21629.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: K7N5M3*PLUS
#5: Protein T-cell Receptor Beta chain


Mass: 26898.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: P01850*PLUS
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: 2.72 Å3/Da / Density % sol: 54.77 % / Mosaicity: 0 °
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5
Details: 20% PEG 3350, 0.2M NaSO4, 0.1M Bis-Tris Propane, pH 6.5, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.99→64.753 Å / Num. all: 39174 / Num. obs: 39174 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Rsym value: 0.123 / Net I/σ(I): 4.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.99-3.0720.4240.3631.8590729180.2840.4240.3632.598.1
3.07-3.152.10.3580.3172565527500.240.3580.317398.1
3.15-3.2420.2990.2652.4552127940.20.2990.2653.397.4
3.24-3.341.90.2750.2223498026470.1860.2750.2223.599.6
3.34-3.451.90.2420.1773.6498625850.1620.2420.1773.998.7
3.45-3.5720.2070.1684511325040.1390.2070.1684.498.8
3.57-3.7120.1780.1374.9497224370.1190.1780.1374.899.1
3.71-3.8620.1690.1364.8464922830.1150.1690.1365.296.9
3.86-4.0320.1720.1285443622460.1160.1720.1285.399.7
4.03-4.231.80.1770.1085.8391021170.120.1770.1085.598.5
4.23-4.4620.1590.0995.7411820390.1070.1590.0995.999.2
4.46-4.7320.1550.0896.7388619160.1050.1550.0896.199
4.73-5.051.90.1660.0915.7353318240.1130.1660.091699
5.05-5.461.90.1670.0837.6322016690.1140.1670.0835.899.8
5.46-5.982.10.1630.0867320215450.1110.1630.086698.6
5.98-6.6920.1640.1065.7279914020.1110.1640.1065.898.5
6.69-7.721.80.1590.0936.3226012230.1080.1590.0935.998.6
7.72-9.462.10.1380.0748.2216410370.0940.1380.0746.899.4
9.46-13.3720.1350.0886.915898050.0920.1350.0886.899.3
13.37-64.7532.10.0970.096.68914330.0650.0970.096.996.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 48.42 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.99 Å64.75 Å
Translation2.99 Å64.75 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.99→64.75 Å / Cor.coef. Fo:Fc: 0.882 / Cor.coef. Fo:Fc free: 0.814 / WRfactor Rfree: 0.3401 / WRfactor Rwork: 0.267 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7203 / SU B: 60.769 / SU ML: 0.502 / SU R Cruickshank DPI: 0.4425 / SU Rfree: 0.5502 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.55 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.3038 1965 5 %RANDOM
Rwork0.2417 ---
all0.2448 39174 --
obs0.2448 39174 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 141.18 Å2 / Biso mean: 65.7253 Å2 / Biso min: 33.41 Å2
Baniso -1Baniso -2Baniso -3
1--6.81 Å21.66 Å24.34 Å2
2---9.9 Å26.18 Å2
3---13.12 Å2
Refinement stepCycle: LAST / Resolution: 2.99→64.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13067 0 0 0 13067
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01913410
X-RAY DIFFRACTIONr_angle_refined_deg1.7131.93618230
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.01951622
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.89623.818694
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.621152164
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.68115108
X-RAY DIFFRACTIONr_chiral_restr0.1210.21929
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110515
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeWeight position
11A434X-RAY DIFFRACTIONTIGHT THERMAL0.5
21A161X-RAY DIFFRACTIONTIGHT THERMAL0.5
31A315X-RAY DIFFRACTIONTIGHT THERMAL0.5
41A367X-RAY DIFFRACTIONTIGHT THERMAL0.5
LS refinement shellResolution: 2.99→3.068 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 157 -
Rwork0.343 2756 -
all-2913 -
obs--98.11 %
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)
111.26660.334-1.59452.97460.58841.6493-0.09660.0005-0.5295-0.3540.1578-0.23290.00970.1953-0.06120.5522-0.0084-0.06820.6026-0.16970.101740.9311-1.4252-149.5192
21.1247-0.58810.25822.79010.71350.58170.03120.24010.2877-0.36190.0637-0.5716-0.32830.2662-0.09490.686-0.0809-0.00120.8316-0.11910.185242.893213.5007-148.6992
32.00741.18150.07632.00230.81182.8688-0.06980.62150.7457-0.7455-0.00380.5619-0.9384-0.07940.07361.3142-0.12740.00821.2740.06890.597138.654312.8055-184.0997
42.5442-0.5422-1.59672.2972.26455.82520.0730.2507-0.2959-0.6157-0.10490.1209-0.00540.01150.03190.9144-0.0531-0.08280.8721-0.11950.057634.6038-6.3507-172.3726
51.0746-3.2111-0.00779.61820.02010.00380.06440.0174-0.023-0.1805-0.04390.1876-0.03720.0282-0.02040.6017-0.06990.04140.4921-0.07920.660541.35725.3832-142.1055
62.70540.56781.09394.01081.62756.02060.0281-0.10820.07580.30580.0545-0.4720.15790.2601-0.08270.6189-0.0006-0.11350.6743-0.17580.155555.45914.5513-123.0906
73.2686-1.33020.36375.0085-1.88323.40610.2112-0.2504-0.49530.3742-0.2598-0.88430.37470.44220.04861.3001-0.0064-0.31691.1442-0.17150.636864.58159.0072-90.8842
81.5776-0.19830.71423.4918-1.42972.12460.0959-0.1227-0.30520.3554-0.0198-0.3210.00010.0652-0.07610.6222-0.0508-0.13860.7001-0.13270.148844.8509-6.5396-122.718
91.88540.5555-0.65758.19632.87472.80380.0877-0.3099-0.04430.96040.0318-0.0430.350.0434-0.11951.251-0.0248-0.29271.0703-0.01410.231251.1995-2.1444-93.7898
108.1548-0.6137-0.92493.7156-0.91071.6533-0.0892-0.1951-0.7230.20780.21970.3919-0.0909-0.2086-0.13050.5992-0.0073-0.06810.66750.01070.126234.9103-45.8057-117.4322
112.09520.5248-0.26682.1463-1.34740.91750.0733-0.25320.22860.31620.17240.4752-0.2545-0.1931-0.24570.69670.0238-0.04630.7718-0.07580.156833.0388-30.913-118.3205
123.1284-0.65011.32713.7293-0.73114.1723-0.0662-0.53490.75490.8261-0.0312-0.4455-0.75450.15750.09741.23590.11690.04911.1864-0.18520.278837.394-31.372-82.9891
132.4084-0.469-1.33571.3792-2.1996.27980.0194-0.2442-0.36680.43520.03340.1569-0.0515-0.0573-0.05290.96650.0074-0.09260.9089-0.06940.090941.3183-50.6193-94.5595
140.015-0.1820.09147.3191-2.31150.9599-0.00390.02260.0703-0.0514-0.1226-0.0084-0.03550.04740.12650.51930.04490.04940.4461-0.0050.654234.4733-39.0452-124.8736
152.148-1.42190.44273.9318-1.36825.36960.0690.1524-0.2941-0.23210.06760.46140.2303-0.395-0.13660.6143-0.0693-0.15220.6936-0.05850.200820.1216-30.1997-143.8365
163.11172.8931-1.14124.41151.06523.9248-0.09030.18730.0154-0.2259-0.15060.78570.235-0.41170.24091.34310.0227-0.39951.168-0.06610.887211.3877-35.6889-176.0938
171.46770.67770.49464.99811.13991.09330.03450.0846-0.3315-0.25650.0740.28680.0355-0.0567-0.10860.6347-0.0051-0.11320.6992-0.10440.147630.9999-51.1434-144.2024
181.8122-0.4068-0.93698.5568-3.7293.79060.160.4468-0.1688-0.8710.01930.23560.33770.0684-0.17931.1751-0.0156-0.29741.0771-0.18810.148724.6232-46.7565-173.2558
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 100
2X-RAY DIFFRACTION2A101 - 183
3X-RAY DIFFRACTION3A184 - 276
4X-RAY DIFFRACTION4B1 - 99
5X-RAY DIFFRACTION5C1 - 8
6X-RAY DIFFRACTION6D7 - 113
7X-RAY DIFFRACTION7D114 - 198
8X-RAY DIFFRACTION8E5 - 114
9X-RAY DIFFRACTION9E115 - 243
10X-RAY DIFFRACTION10F1 - 100
11X-RAY DIFFRACTION11F101 - 183
12X-RAY DIFFRACTION12F184 - 275
13X-RAY DIFFRACTION13G1 - 99
14X-RAY DIFFRACTION14H1 - 8
15X-RAY DIFFRACTION15I4 - 113
16X-RAY DIFFRACTION16I114 - 197
17X-RAY DIFFRACTION17J6 - 114
18X-RAY DIFFRACTION18J115 - 243

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