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- PDB-4jfq: A2 HLA complex with L8A heteroclitic variant of Melanoma peptide -

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Basic information

Entry
Database: PDB / ID: 4jfq
TitleA2 HLA complex with L8A heteroclitic variant of Melanoma peptide
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • L8A heteroclitic Melanoma peptide
KeywordsIMMUNE SYSTEM / Immunoglobulin / HLA / TCR / Melanoma / High Affinity
Function / homology
Function and homology information


T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / 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 exogenous peptide antigen via MHC class I / endoplasmic reticulum exit site ...T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / 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 exogenous peptide antigen via MHC class I / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / protection from natural killer cell mediated cytotoxicity / beta-2-microglobulin binding / T cell receptor binding / detection of bacterium / 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 / DAP12 interactions / negative regulation of receptor binding / 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 / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / 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 / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / 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 / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / positive regulation of type II interferon production / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / E3 ubiquitin ligases ubiquitinate target proteins / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / iron ion transport / ER-Phagosome pathway / early endosome membrane / antibacterial humoral response / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / innate immune response / focal adhesion / signaling receptor binding / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum
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 classes I/II-like antigen recognition protein ...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 classes I/II-like antigen recognition 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsRizkallah, P.J. / Cole, D.K. / Madura, F. / Sewell, A.K. / Baker, B.M.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: T-cell receptor specificity maintained by altered thermodynamics.
Authors: Madura, F. / Rizkallah, P.J. / Miles, K.M. / Holland, C.J. / Bulek, A.M. / Fuller, A. / Schauenburg, A.J. / Miles, J.J. / Liddy, N. / Sami, M. / Li, Y. / Hossain, M. / Baker, B.M. / ...Authors: Madura, F. / Rizkallah, P.J. / Miles, K.M. / Holland, C.J. / Bulek, A.M. / Fuller, A. / Schauenburg, A.J. / Miles, J.J. / Liddy, N. / Sami, M. / Li, Y. / Hossain, M. / Baker, B.M. / Jakobsen, B.K. / Sewell, A.K. / Cole, D.K.
History
DepositionFeb 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2013Group: Database references
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Jul 17, 2013Group: Database references

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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: L8A heteroclitic Melanoma peptide
D: HLA class I histocompatibility antigen, A-2 alpha chain
E: Beta-2-microglobulin
F: L8A heteroclitic Melanoma peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,68827
Polymers89,5486
Non-polymers2,14021
Water14,142785
1
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: L8A heteroclitic Melanoma peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,98215
Polymers44,7743
Non-polymers1,20812
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7220 Å2
ΔGint-23 kcal/mol
Surface area18710 Å2
MethodPISA
2
D: HLA class I histocompatibility antigen, A-2 alpha chain
E: Beta-2-microglobulin
F: L8A heteroclitic Melanoma peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,70612
Polymers44,7743
Non-polymers9329
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6410 Å2
ΔGint-20 kcal/mol
Surface area18930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.096, 58.359, 89.432
Angle α, β, γ (deg.)90.000, 109.820, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21A
12E
22B
13F
23C
/ NCS ensembles :
ID
1
2
3

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Components

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Protein , 2 types, 4 molecules ADBE

#1: Protein HLA class I histocompatibility antigen, A-2 alpha chain / 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) / Gene: HLA-A, HLAA / Plasmid: pGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): Roseatta DE3 / References: UniProt: P61769

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Protein/peptide , 1 types, 2 molecules CF

#3: Protein/peptide L8A heteroclitic Melanoma peptide


Mass: 943.096 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: L8A Heteroclitic variant of Melanoma motif

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Non-polymers , 3 types, 806 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 785 / 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: 2.31 Å3/Da / Density % sol: 46.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25 mM MES, 24% PEG 3350, 10 mM NaCl, pH 6.5, vapor diffusion, sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 1-BM-C
DetectorDetector: CCD / Date: Nov 16, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→84.22 Å / Num. all: 64546 / Num. obs: 64546 / % possible obs: 100 %

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→84.22 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.861 / WRfactor Rfree: 0.2739 / WRfactor Rwork: 0.2015 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7815 / SU B: 9.895 / SU ML: 0.157 / SU R Cruickshank DPI: 0.1989 / SU Rfree: 0.198 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.199 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2966 3275 5.1 %RANDOM
Rwork0.2156 ---
obs0.2198 64546 99.58 %-
all-64546 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 61.07 Å2 / Biso mean: 19.2976 Å2 / Biso min: 3.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å20.91 Å2
2---1.03 Å20 Å2
3---2.24 Å2
Refinement stepCycle: LAST / Resolution: 1.9→84.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6305 0 138 785 7228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0216688
X-RAY DIFFRACTIONr_bond_other_d0.0020.024620
X-RAY DIFFRACTIONr_angle_refined_deg1.7971.9389058
X-RAY DIFFRACTIONr_angle_other_deg0.989311116
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7025783
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.65623.171350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.636151067
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.241557
X-RAY DIFFRACTIONr_chiral_restr0.1140.2914
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217448
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021457
X-RAY DIFFRACTIONr_mcbond_it0.8891.53890
X-RAY DIFFRACTIONr_mcbond_other0.3091.51571
X-RAY DIFFRACTIONr_mcangle_it1.47826281
X-RAY DIFFRACTIONr_scbond_it2.54332798
X-RAY DIFFRACTIONr_scangle_it3.7754.52777
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1D3784MEDIUM POSITIONAL0.40.5
1D3784MEDIUM THERMAL0.682
2E1393MEDIUM POSITIONAL0.340.5
2E1393MEDIUM THERMAL0.652
3F102MEDIUM POSITIONAL0.340.5
3F102MEDIUM THERMAL1.352
LS refinement shellResolution: 1.9→1.947 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 247 -
Rwork0.266 4395 -
all-4642 -
obs--97.42 %
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)
12.13731.35730.35292.4643-0.18650.53710.0198-0.02670.08210.1199-0.0651-0.18190.05430.06250.04520.04060.026-0.01880.0424-0.0040.04421.1053-25.0444-38.4389
25.3688-2.3898-0.91822.86050.51481.2824-0.0661-0.2164-0.08250.22270.01630.0118-0.0189-0.05870.04980.0302-0.0094-0.00870.02630.00690.0075-14.82335.8781-34.967
31.58410.7669-0.19565.0005-0.66152.0858-0.01750.14520.0743-0.2971-0.0163-0.2011-0.07840.01110.03380.02670.00950.00970.041-0.00170.0223-7.3328-3.9656-53.1813
42.1891-1.3028-0.33943.2324-0.07220.28160.03310.0477-0.0762-0.1576-0.0253-0.285-0.02170.02-0.00780.0437-0.02490.02410.0367-0.01360.064-14.0441-6.1475-3.5246
52.56912.49920.31493.90070.38990.3564-0.07730.1477-0.0314-0.25920.1017-0.0118-0.0026-0.0602-0.02440.03490.01230.00830.06370.0210.0164-28.6944-34.6138-7.0847
62.0574-0.95530.10545.1744-0.32711.3928-0.0198-0.1993-0.15530.43620.1033-0.16240.02210.0351-0.08350.0417-0.0011-0.02150.04610.00550.0306-22.5193-26.948911.0536
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 180
2X-RAY DIFFRACTION1C1 - 9
3X-RAY DIFFRACTION2A181 - 275
4X-RAY DIFFRACTION3B0 - 99
5X-RAY DIFFRACTION4D1 - 180
6X-RAY DIFFRACTION5D181 - 276
7X-RAY DIFFRACTION5F1 - 9
8X-RAY DIFFRACTION6E0 - 99

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