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- PDB-1i4f: CRYSTAL STRUCTURE OF HLA-A*0201/MAGE-A4-PEPTIDE COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1i4f
TitleCRYSTAL STRUCTURE OF HLA-A*0201/MAGE-A4-PEPTIDE COMPLEX
Components
  • BETA-2-MICROGLOBULIN
  • HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
  • MELANOMA-ASSOCIATED ANTIGEN 4
KeywordsIMMUNE SYSTEM / MAJOR HISTOCOMPATIBILITY COMPLEX / HUMAN LEUKOCYTE ANTIGEN / MELANOMA-ASSOCIATED ANTIGEN
Function / homology
Function and homology information


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 ...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 / 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 / positive regulation of cell cycle / 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 / 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 / histone deacetylase binding / 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 / 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 / negative regulation of apoptotic process / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / Golgi apparatus
Similarity search - Function
Melanoma associated antigen, N-terminal / Melanoma associated antigen family N terminal / Melanoma associated antigen family N terminal / MAGE conserved domain profile. / MAGE homology domain / Melanoma-associated antigen / MAGE homology domain, winged helix WH1 motif / MAGE homology domain, winged helix WH2 motif / MAGE homology domain / Melanoma-associated antigen ...Melanoma associated antigen, N-terminal / Melanoma associated antigen family N terminal / Melanoma associated antigen family N terminal / MAGE conserved domain profile. / MAGE homology domain / Melanoma-associated antigen / MAGE homology domain, winged helix WH1 motif / MAGE homology domain, winged helix WH2 motif / MAGE homology domain / Melanoma-associated antigen / 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
Chem-1PG / HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Melanoma-associated antigen 4 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsHillig, R.C. / Coulie, P.G. / Stroobant, V. / Saenger, W. / Ziegler, A. / Huelsmeyer, M.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: High-resolution structure of HLA-A*0201 in complex with a tumour-specific antigenic peptide encoded by the MAGE-A4 gene.
Authors: Hillig, R.C. / Coulie, P.G. / Stroobant, V. / Saenger, W. / Ziegler, A. / Hulsmeyer, M.
#1: Journal: Eur.J.Immunol. / Year: 1999
Title: A MAGE-A4 Peptide Presented by HLA-A2 is Recognized by Cytolytic T Lymphocytes
Authors: Duffour, M.T. / Chaux, P. / Lurquin, C. / Cornelis, G. / Boon, T. / van der Bruggen, P.
History
DepositionFeb 21, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 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-ASSOCIATED ANTIGEN 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3725
Polymers44,8683
Non-polymers5052
Water7,782432
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-3 kcal/mol
Surface area18840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.467, 80.222, 54.009
Angle α, β, γ (deg.)90.00, 111.06, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a heterotrimeric complex consisting of one HLA-A2 (heavy) chain, one beta-2-microglobulin (light) chain and one MAGE-A4-peptide chain.

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Components

#1: Protein HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN


Mass: 31854.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Production host: Escherichia coli (E. coli) / Strain (production host): SURE / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein BETA-2-MICROGLOBULIN


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Production host: Escherichia coli (E. coli) / Strain (production host): SURE / References: UniProt: P61769
#3: Protein/peptide MELANOMA-ASSOCIATED ANTIGEN 4 / MAGE-4 ANTIGEN


Mass: 1134.200 Da / Num. of mol.: 1 / Fragment: RESIDUES 230-239 / Source method: obtained synthetically
Details: This peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (humans).
References: UniProt: P43358
#4: Chemical ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL


Mass: 252.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H24O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 432 / 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: 1.9 Å3/Da / Density % sol: 35.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 8000, Tris-HCl, NaCl. PEG 400 as cryo protectant., pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
pH: 7.5 / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
2150 mM1dropNaCl
320 mMTris-HCl1drop
423-27 %PEG80001reservoir
5100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.782 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 21, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.782 Å / Relative weight: 1
ReflectionResolution: 1.4→19.9 Å / Num. all: 324813 / Num. obs: 75194 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 15.25 Å2 / Rsym value: 0.084 / Net I/σ(I): 15.2
Reflection shellResolution: 1.4→1.44 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 4563 / Rsym value: 0.369 / % possible all: 80.1
Reflection
*PLUS
Rmerge(I) obs: 0.084
Reflection shell
*PLUS
% possible obs: 80.1 % / Rmerge(I) obs: 0.369

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1hhg

1hhg


Resolution: 1.4→19.9 Å / SU B: 2.42983 / SU ML: 0.04954 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09996 / ESU R Free: 0.07691 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1732 3712 5 %RANDOM
Rwork0.1358 ---
all0.1376 74439 --
obs0.138 70727 94.3 %-
Displacement parametersBiso mean: 17.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å2-0.29 Å2
2---0.42 Å20 Å2
3---0.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.4→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3238 0 34 432 3704
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0210.021
X-RAY DIFFRACTIONp_mcbond_it2.5021.5
X-RAY DIFFRACTIONp_mcangle_it3.4172
X-RAY DIFFRACTIONp_scbond_it3.9223
X-RAY DIFFRACTIONp_scangle_it5.2374.5
X-RAY DIFFRACTIONp_plane_restr0.0130.02
X-RAY DIFFRACTIONp_chiral_restr0.1570.2
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
1.42-1.460.231910.15X-RAY DIFFRACTION365187
1.46-1.50.192410.15X-RAY DIFFRACTION434679.6
1.5-1.540.232190.14X-RAY DIFFRACTION424679
1.54-1.590.192260.13X-RAY DIFFRACTION405678.7
1.59-1.640.172540.12X-RAY DIFFRACTION487296.5
1.64-1.70.162560.11X-RAY DIFFRACTION484099.5
1.7-1.770.182270.1X-RAY DIFFRACTION469799.8
1.77-1.840.162130.11X-RAY DIFFRACTION452799.8
1.84-1.930.162280.11X-RAY DIFFRACTION430899.9
1.93-2.030.172320.11X-RAY DIFFRACTION4162100
2.03-2.150.182170.12X-RAY DIFFRACTION3926100
2.15-2.280.182020.12X-RAY DIFFRACTION3732100
2.28-2.450.151970.12X-RAY DIFFRACTION3510100
2.45-2.660.182010.13X-RAY DIFFRACTION3240100
2.66-2.950.161410.14X-RAY DIFFRACTION3025100
2.95-3.330.181430.15X-RAY DIFFRACTION2747100
3.33-3.950.151040.15X-RAY DIFFRACTION243999.9
3.95-5.060.151060.15X-RAY DIFFRACTION203199.1
5.06-8.770.18750.17X-RAY DIFFRACTION155897.3
8.77-19.80.25390.22X-RAY DIFFRACTION81488.6
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.4 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor all: 0.138 / Rfactor obs: 0.136
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.09

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