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- PDB-4wj5: Structure of HLA-A2 in complex with an altered peptide ligands ba... -

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Basic information

Entry
Database: PDB / ID: 4wj5
TitleStructure of HLA-A2 in complex with an altered peptide ligands based on Mart-1 variant epitope
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • Melanoma antigen recognized by T-cells 1
KeywordsIMMUNE SYSTEM / Antigen Presentation / Major histocompatibility complex / HLA-A2 Antigen / Altered peptide ligand
Function / homology
Function and homology information


melanosome membrane / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / 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 ...melanosome membrane / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / 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 / beta-2-microglobulin binding / endoplasmic reticulum exit site / Regulation of MITF-M-dependent genes involved in pigmentation / TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / 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 / T cell receptor binding / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / trans-Golgi network / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / positive regulation of type II interferon production / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / antibacterial humoral response / positive regulation of cellular senescence / tertiary granule lumen / melanosome / DAP12 signaling / T cell differentiation in thymus / T cell receptor signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / 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 / lysosomal membrane / innate immune response / external side of plasma 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
Similarity search - Function
Protein melan-A / Protein melan-A / 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 / : ...Protein melan-A / Protein melan-A / 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 / Immunoglobulin-like fold / Immunoglobulins / 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 / Melanoma antigen recognized by T-cells 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsCelie, P.H.N. / Rodenko, B. / Ovaa, H.
CitationJournal: J Immunol. / Year: 2014
Title: Altered Peptide Ligands Revisited: Vaccine Design through Chemically Modified HLA-A2-Restricted T Cell Epitopes.
Authors: Hoppes, R. / Oostvogels, R. / Luimstra, J.J. / Wals, K. / Toebes, M. / Bies, L. / Ekkebus, R. / Rijal, P. / Celie, P.H. / Huang, J.H. / Emmelot, M.E. / Spaapen, R.M. / Lokhorst, H. / ...Authors: Hoppes, R. / Oostvogels, R. / Luimstra, J.J. / Wals, K. / Toebes, M. / Bies, L. / Ekkebus, R. / Rijal, P. / Celie, P.H. / Huang, J.H. / Emmelot, M.E. / Spaapen, R.M. / Lokhorst, H. / Schumacher, T.N. / Mutis, T. / Rodenko, B. / Ovaa, H.
History
DepositionSep 29, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2014Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 9, 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, A-2 alpha chain
B: Beta-2-microglobulin
C: Melanoma antigen recognized by T-cells 1
D: HLA class I histocompatibility antigen, A-2 alpha chain
E: Beta-2-microglobulin
F: Melanoma antigen recognized by T-cells 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,63519
Polymers89,4376
Non-polymers1,19713
Water9,656536
1
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Melanoma antigen recognized by T-cells 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0877
Polymers44,7193
Non-polymers3684
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-21 kcal/mol
Surface area18530 Å2
MethodPISA
2
D: HLA class I histocompatibility antigen, A-2 alpha chain
E: Beta-2-microglobulin
F: Melanoma antigen recognized by T-cells 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,54812
Polymers44,7193
Non-polymers8299
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6390 Å2
ΔGint-21 kcal/mol
Surface area18390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.180, 87.140, 79.194
Angle α, β, γ (deg.)90.000, 90.150, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYGLUGLUAA1 - 2751 - 275
21GLYGLYGLUGLUDD1 - 2751 - 275
12METMETMETMETBB0 - 991 - 100
22METMETMETMETEE0 - 991 - 100

NCS ensembles :
ID
1
2

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Components

#1: Protein HLA class I histocompatibility antigen, A-2 alpha chain / MHC class I antigen A*2


Mass: 31854.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): pLysS / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2 / Fragment: UNP residues 21-119 / Mutation: Methionine residue is introduced as start codon
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769
#3: Protein/peptide Melanoma antigen recognized by T-cells 1 / MART-1 / Antigen LB39-AA / Antigen SK29-AA / Protein Melan-A


Mass: 985.178 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: DECAMERIC ALTERED PEPTIDE LIGNAD FROM THE MART-1/MELAN-A epitope EAAGIGILTV
Source: (synth.) Homo sapiens (human) / References: UniProt: Q16655
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 536 / Source method: isolated from a natural source / Formula: H2O
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: 2.45 Å3/Da / Density % sol: 49.85 %
Description: Crystal dimensions 0.2 (W) X 0.1 (L) X 0.1 (H).
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Good diffracting crystals were obtained by streak seeding
PH range: 6.0 - 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.747
11-h,-k,l20.253
ReflectionResolution: 1.65→79.194 Å / Num. all: 102600 / Num. obs: 102600 / % possible obs: 99.6 % / Redundancy: 3.4 % / Rpim(I) all: 0.026 / Rrim(I) all: 0.049 / Rsym value: 0.041 / Net I/av σ(I): 13.118 / Net I/σ(I): 17 / Num. measured all: 346375
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.65-1.743.50.4831.652522149760.3010.4832.799.8
1.74-1.843.50.2952.749286141610.1840.2954.299.9
1.84-1.973.40.1664.745196132860.1050.1667.299.6
1.97-2.133.20.095839145123990.0640.0951199.7
2.13-2.333.20.06510.437008114050.0430.06515.899.7
2.33-2.613.60.0441736645103160.0270.04421.999.7
2.61-3.013.40.03619.33108791200.0230.03628.899.5
3.01-3.693.30.02822.22499376900.0180.02839.399.3
3.69-5.223.10.0230.71871859650.0130.024799.3
5.22-19.9363.60.02325.71177532820.0140.0234897.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.453 / R rigid body: 0.357 / Cor.coef. Fo:Fc: 0.681 / Cor.coef. Io to Ic: 0.683
Highest resolutionLowest resolution
Translation3 Å15 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
SCALA3.3.21data scaling
XDSdata reduction
PDB_EXTRACT3.15data extraction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2X70

2x70


Resolution: 1.65→19.94 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.503 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.018 / ESU R Free: 0.018 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1787 5093 5 %RANDOM
Rwork0.1553 97482 --
obs0.1564 -98.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso max: 84.6 Å2 / Biso mean: 27.234 Å2 / Biso min: 7.43 Å2
Baniso -1Baniso -2Baniso -3
1--3.89 Å2-0 Å2-0.73 Å2
2--12.12 Å20 Å2
3----8.23 Å2
Refinement stepCycle: final / Resolution: 1.65→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6308 0 78 536 6922
Biso mean--45.65 31.67 -
Num. residues----770
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0197161
X-RAY DIFFRACTIONr_bond_other_d0.0040.026467
X-RAY DIFFRACTIONr_angle_refined_deg1.6871.9419781
X-RAY DIFFRACTIONr_angle_other_deg1.406314924
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.165881
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.02223.029373
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.901151173
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9021567
X-RAY DIFFRACTIONr_chiral_restr0.2430.2994
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028398
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021823
X-RAY DIFFRACTIONr_mcbond_it2.0161.3683389
X-RAY DIFFRACTIONr_mcbond_other2.0131.3683387
X-RAY DIFFRACTIONr_mcangle_it2.6852.054327
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A157180.11
12D157180.11
21B58960.09
22E58960.09
LS refinement shellResolution: 1.646→1.689 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 325 -
Rwork0.219 6548 -
all-6873 -
obs--89.67 %
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)
11.67620.12090.3120.5040.21350.95150.0918-0.0557-0.08570.0468-0.06720.0290.039-0.0779-0.02460.0549-0.0090.00180.0386-0.00160.009715.72-4.31725.53
24.71730.3382-0.45020.81-0.11381.21910.0593-0.1530.52430.0293-0.0375-0.0287-0.12320.0602-0.02170.0581-0.01520.01220.0328-0.02130.067726.06211.32128.572
35.8623-3.5012-3.65772.09252.24297.03780.10810.15390.1109-0.0588-0.0962-0.0555-0.0757-0.3736-0.01190.1055-0.00990.03650.1651-0.03120.1544-2.776-4.18717.279
41.5185-0.0825-0.62770.6867-0.1780.81660.0201-0.1681-0.04890.0217-0.0096-0.0525-0.00240.0686-0.01050.056-0.0305-0.00590.126-0.01440.016515.77449.32810.302
53.39830.22170.34730.7496-0.0921.22720.0384-0.2063-0.30170.030.01990.00270.13680.0083-0.05830.0524-0.0189-0.01830.1160.02640.03285.36833.71313.409
64.4011-4.70912.79255.7827-4.72065.8113-0.07520.0827-0.28240.153-0.26370.0694-0.21460.48120.33890.1035-0.0018-0.00550.1676-0.02440.212234.29348.9781.963
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 275
2X-RAY DIFFRACTION2B0 - 99
3X-RAY DIFFRACTION3C2 - 8
4X-RAY DIFFRACTION4D1 - 275
5X-RAY DIFFRACTION5E0 - 99
6X-RAY DIFFRACTION6F2 - 8

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