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

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Basic information

Entry
Database: PDB / ID: 3mrf
TitleCrystal Structure of MHC class I HLA-A2 molecule complexed with EBV bmlf1-280-288 nonapeptide T4P variant
Components
  • 9-meric peptide from mRNA export factor EB2
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
KeywordsIMMUNE SYSTEM / MHC class I / HLA / IMMUNE RESPONSE / NONAPEPTIDE / VIRAL PEPTIDE / EPSTEIN-BARR VIRUS / BMLF1 PROTEIN / EB2 protein
Function / homology
Function and homology information


symbiont-mediated suppression of host PKR/eIFalpha signaling / 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 ...symbiont-mediated suppression of host PKR/eIFalpha signaling / 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 / protein serine/threonine kinase inhibitor activity / 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 / mRNA transport / 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 / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / 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 / 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 / positive regulation of cellular senescence / antibacterial humoral response / 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 / host cell cytoplasm / learning or memory / defense response to Gram-positive bacterium / immune response / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / Neutrophil degranulation / regulation of DNA-templated transcription / endoplasmic reticulum membrane / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses
Similarity search - Function
Herpesvirus ICP27-like / Herpesvirus transcriptional regulator family / 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 / : ...Herpesvirus ICP27-like / Herpesvirus transcriptional regulator family / 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 / mRNA export factor ICP27 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
Epstein-Barr virus EBV (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTrudel, E. / Gras, S. / Chouquet, A. / Debeaupuis, E. / Echasserieau, K. / Saulquin, X. / Bonneville, M. / Housset, D.
CitationJournal: To be Published
Title: Crystal Structure of MHC class I HLA-A2 molecule complexed with EBV bmlf1-280-288 nonapeptide T4P variant
Authors: Trudel, E. / Gras, S. / Chouquet, A. / Debeaupuis, E. / Echasserieau, K. / Saulquin, X. / Bonneville, M. / 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 1.2Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
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 1.4Oct 30, 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: 9-meric peptide from mRNA export factor EB2


Theoretical massNumber of molelcules
Total (without water)46,8043
Polymers46,8043
Non-polymers00
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-23 kcal/mol
Surface area18800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.622, 79.392, 55.661
Angle α, β, γ (deg.)90.000, 112.020, 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 9-meric peptide from mRNA export factor EB2 / 9-MERIC PEPTIDE FROM MRNA EXPORT FACTOR EB2 (BSFL2/BMLF1)


Mass: 916.202 Da / Num. of mol.: 1
Fragment: EB2 PROTEIN FRAGMENT (BMLF1 280-288), UNP residues 300-308
Mutation: T4P / Source method: obtained synthetically
Details: Variant of a sequence occuring in Epstein-Barr virus bmlf1 protein
Source: (synth.) Epstein-Barr virus EBV (Epstein-Barr virus)
References: UniProt: Q3KSU1
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Compound detailsEBV BSFL2 AND BMLF1 ORFS ARE JOINED TO ENCODE THE EB2 PROTEIN. EB2 PROTEIN IS ALSO CALLED ...EBV BSFL2 AND BMLF1 ORFS ARE JOINED TO ENCODE THE EB2 PROTEIN. EB2 PROTEIN IS ALSO CALLED BSFL2/BMLF1, MTA OR SM.
Has protein modificationY
Sequence detailsTHE GLCTLVAML NONAPEPTIDE WAS FIRST IDENTIFIED AS AN HLA-A2 RESTRICTED T CELL EPITOPE ON A ...THE GLCTLVAML NONAPEPTIDE WAS FIRST IDENTIFIED AS AN HLA-A2 RESTRICTED T CELL EPITOPE ON A TRUNCATED FORM OF THE EB2 PROTEIN, EXPRESSED IN VACCINIA RECOMBINANTS, LACKING THE FIRST 20 AMINO ACIDS ENCODED BY THE BSFL2 ORF (STEVEN ET AL., J. EXP. MED., 185:1605-1617 (1997)), AND NAMED BMLF1 OR VACBMLF1. THEREFORE, THIS PEPTIDE WAS NAMED BMLF1 280-288. IT CORRESPONDS TO RESIDUES 300 TO 308 OF THE FULL LENGTH EB2 PROTEIN.

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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: 2.26 Å3/Da / Density % sol: 45.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12% PEG 6000, 0.1M NaCacodylate, 0.1M NaCl, 7.5mg/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: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 21, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 18522 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 3.74 % / Biso Wilson estimate: 23.69 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.3-2.380.4013.66519176397.6
2.38-2.470.354.16659176799.4
2.47-2.570.3014.76329167499.8
2.57-2.690.2415.86347168099.8
2.69-2.820.1947.15767152599.9
2.82-2.970.1548.75499145799.2
2.97-3.150.12510.75274139799.9
3.15-3.370.09513.84973131499.4
3.37-3.640.07616.44596122199.4
3.64-3.980.05920.34175112199.4
3.98-4.450.05322.837681010100
4.45-5.140.04724.9339091299.2
5.14-6.30.04622.9285977099.4
6.3-8.910.04324.3215359699.2
8.910.02932.5102131592.9

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.5.0044refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3MRE

3mre


Resolution: 2.3→15 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.869 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 5.319 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES: REFINED INDIVIDUALLY; 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. ...Details: U VALUES: REFINED INDIVIDUALLY; 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
Rfree0.257 1782 10.1 %RANDOM
Rwork0.186 ---
obs0.189 17664 95.29 %-
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: 56.86 Å2 / Biso mean: 17.549 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å2-0 Å2-1.25 Å2
2---0.96 Å20 Å2
3---0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3138 0 0 153 3291
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0213321
X-RAY DIFFRACTIONr_angle_refined_deg1.1421.9254521
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.245398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.48522.898176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.16215544
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4681531
X-RAY DIFFRACTIONr_chiral_restr0.0830.2459
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212636
X-RAY DIFFRACTIONr_mcbond_it0.86421962
X-RAY DIFFRACTIONr_mcangle_it1.57833178
X-RAY DIFFRACTIONr_scbond_it1.52531359
X-RAY DIFFRACTIONr_scangle_it2.35841343
LS refinement shellResolution: 2.3→2.358 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 123 -
Rwork0.243 1058 -
all-1181 -
obs--86.97 %

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