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- PDB-3mro: Crystal Structure of MHC class I HLA-A2 molecule complexed with M... -

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Basic information

Entry
Database: PDB / ID: 3mro
TitleCrystal Structure of MHC class I HLA-A2 molecule complexed with Melan-A MART1 decapeptide variant
Components
  • 10-meric peptide from Melanoma antigen recognized by T-cells 1
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
KeywordsIMMUNE SYSTEM / MHC class I / HLA / IMMUNE RESPONSE / DECAPEPTIDE / TUMORAL PEPTIDE / MELAN-A / MART1
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 / Regulation of MITF-M-dependent genes involved in pigmentation / 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 / 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 receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / 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 / trans-Golgi network / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / positive regulation of type II interferon production / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / Interferon alpha/beta signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / antibacterial humoral response / late endosome membrane / sensory perception of smell / tertiary granule lumen / melanosome / DAP12 signaling / E3 ubiquitin ligases ubiquitinate target proteins / T cell receptor signaling pathway / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / 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 / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / signaling receptor binding / lysosomal membrane / innate immune response / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses
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 / Resolution: 2.35 Å
AuthorsReiser, J.-B. / Le Gorrec, M. / Chouquet, A. / Debeaupuis, E. / Echasserieau, K. / Saulquin, X. / Bonneville, M. / Housset, D.
CitationJournal: J.Immunol. / Year: 2014
Title: Analysis of Relationships between Peptide/MHC Structural Features and Naive T Cell Frequency in Humans.
Authors: Reiser, J.B. / Legoux, F. / Gras, S. / Trudel, E. / Chouquet, A. / Leger, A. / Le Gorrec, M. / Machillot, P. / Bonneville, M. / Saulquin, X. / Housset, D.
History
DepositionApr 29, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 28, 2015Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
P: 10-meric peptide from Melanoma antigen recognized by T-cells 1


Theoretical massNumber of molelcules
Total (without water)46,9463
Polymers46,9463
Non-polymers00
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-24 kcal/mol
Surface area18990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.881, 81.076, 57.276
Angle α, β, γ (deg.)90.000, 113.800, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 34008.711 Da / Num. of mol.: 1 / Fragment: HLA-A*0201 alpha chain, UNP resiude 25-300 / Mutation: A245V
Source method: isolated from a genetically manipulated source
Details: C-terminal biotin acceptor peptide sequence tag (GSLHHILDAQKMVWNHR)
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA, HLA-A, HLAA / Plasmid: pHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): X90F LAQQ1 / 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.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, BETA-2 MICROGLUBULIN, CDABP0092, HDCMA22P / Plasmid: pHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): X90F LAQQ1 / References: UniProt: P61769
#3: Protein/peptide 10-meric peptide from Melanoma antigen recognized by T-cells 1


Mass: 1058.228 Da / Num. of mol.: 1
Fragment: Melan-A MART1 protein fragment, UNP residues 26-35
Mutation: I5W / Source method: obtained synthetically
Details: chemical synthesis; Variant of a sequence occurring in Human Melan-A MART1 protein
Source: (synth.) Homo sapiens (human) / References: UniProt: Q16655
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsFOR THE MELAN-A MART1 DECAPEPTIDE, A27L(A2L) ANALOGUE WAS USED IN THIS STUDY.

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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: 2.44 Å3/Da / Density % sol: 49.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12% PEG 6000, 0.1M NaCitrate, 0.1M NaCl, 3mg/ml protein conc., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.072 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 25, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 18709 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.53 % / Biso Wilson estimate: 32.027 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.95
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.35-2.430.3153.86221175297.3
2.43-2.520.2754.56341174399.5
2.52-2.630.24756681183899.4
2.63-2.740.215.95602154699.5
2.74-2.880.16775880163799.2
2.88-3.030.1418.25142143999.6
3.03-3.220.1189.75141146398.9
3.22-3.440.10610.74543129599.5
3.44-3.720.10211.74263123899
3.72-4.070.08612.83933114798.8
4.07-4.550.07614.43427101898.9
4.55-5.250.07714.6302590698.3
5.25-6.440.0614.7275377999.4
6.44-9.10.06315.8212260196.9
9.10.05216.9104830789.8

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3MRP

3mrp


Resolution: 2.35→14.47 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.841 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.328 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 10 to 20 refinement cycles with all observed reflections were performed at the end of the refinement procedure, in order to obtain the most accurate model. Rwork and Rfree values corresponds ...Details: 10 to 20 refinement cycles with all observed reflections were performed at the end of the refinement procedure, in order to obtain the most accurate model. Rwork and Rfree values corresponds to the coordinates just before these very last cycles.
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1866 10 %RANDOM
Rwork0.219 ---
obs0.224 18655 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 45.34 Å2 / Biso mean: 17.33 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.01 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.35→14.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3160 0 0 31 3191
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0213252
X-RAY DIFFRACTIONr_angle_refined_deg1.2651.9214414
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4055382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.32923.161174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.81315529
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7531528
X-RAY DIFFRACTIONr_chiral_restr0.090.2450
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022555
X-RAY DIFFRACTIONr_nbd_refined0.2040.21255
X-RAY DIFFRACTIONr_nbtor_refined0.2980.22136
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2136
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.25
X-RAY DIFFRACTIONr_mcbond_it0.7021.51980
X-RAY DIFFRACTIONr_mcangle_it1.223086
X-RAY DIFFRACTIONr_scbond_it1.64131506
X-RAY DIFFRACTIONr_scangle_it2.5194.51328
LS refinement shellResolution: 2.35→2.409 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 131 -
Rwork0.236 1185 -
all-1316 -
obs--100 %

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