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- PDB-3mr9: Crystal Structure of MHC class I HLA-A2 molecule complexed with H... -

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Basic information

Entry
Database: PDB / ID: 3mr9
TitleCrystal Structure of MHC class I HLA-A2 molecule complexed with HCMV pp65-495-503 nonapeptide M5A variant
Components
  • 9-meric peptide from Tegument protein pp65
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
KeywordsIMMUNE SYSTEM / MHC class I / HLA / IMMUNE RESPONSE / NONAPEPTIDE / VIRAL PEPTIDE / CYTOMEGALOVIRUS / pp65 PROTEIN
Function / homology
Function and homology information


host cell viral assembly compartment / viral tegument / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / 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 / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I ...host cell viral assembly compartment / viral tegument / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / 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 / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / CD8 receptor binding / protection from natural killer cell mediated cytotoxicity / endoplasmic reticulum exit site / TAP binding / beta-2-microglobulin binding / detection of bacterium / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / T cell receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / T cell mediated cytotoxicity / Endosomal/Vacuolar pathway / HCMV Late Events / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / response to molecule of bacterial origin / HFE-transferrin receptor complex / MHC class I peptide loading complex / transferrin transport / negative regulation of receptor-mediated endocytosis / cellular response to iron ion / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / positive regulation of T cell mediated cytotoxicity / negative regulation of epithelial cell proliferation / specific granule lumen / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / phagocytic vesicle membrane / recycling endosome membrane / positive regulation of T cell activation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / HCMV Early Events / positive regulation of type II interferon production / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / MHC class II protein complex binding / T cell differentiation in thymus / DAP12 signaling / T cell receptor signaling pathway / late endosome membrane / negative regulation of neuron projection development / E3 ubiquitin ligases ubiquitinate target proteins / antibacterial humoral response / protein refolding / ER-Phagosome pathway / early endosome membrane / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / external side of plasma membrane / signaling receptor binding / innate immune response / lysosomal membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity
Similarity search - Function
Herpesvirus UL82/UL83 / Betaherpesvirus UL82/83 protein N terminus / dUTPase-like superfamily / 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 UL82/UL83 / Betaherpesvirus UL82/83 protein N terminus / dUTPase-like superfamily / 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 / 65 kDa phosphoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Human Cytomegalovirus HCMV
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsReiser, J.-B. / Le Gorrec, M. / 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 short peptide
Authors: Reiser, J.-B. / Le Gorrec, M. / 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 1.2Nov 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 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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 Tegument protein pp65


Theoretical massNumber of molelcules
Total (without water)46,7713
Polymers46,7713
Non-polymers00
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-21 kcal/mol
Surface area19090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.020, 81.100, 57.340
Angle α, β, γ (deg.)90.000, 113.900, 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 Tegument protein pp65


Mass: 883.042 Da / Num. of mol.: 1 / Fragment: UNP residues 495-503 / Mutation: M5A / Source method: obtained synthetically
Details: Variant of a sequence in Human Cytomegalovirus pp65 protein
Source: (synth.) Human Cytomegalovirus HCMV / References: UniProt: Q6SW59
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 2.46 Å3/Da / Density % sol: 49.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12% PEG 6000, 0.1M NaCitrate, 0.15M NaCl, 3.5mg/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: Sep 9, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 33491 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 3.49 % / Biso Wilson estimate: 26.876 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 13.77
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.93-20.2793.16211308590.1
2-2.070.2365.19958298899.5
2.07-2.160.2016.512246329199.7
2.16-2.250.20679794271896.6
2.25-2.360.1389.110242279298.7
2.36-2.490.11710.410238275499.8
2.49-2.640.09612.39436254899.8
2.64-2.830.07515.19280251899.8
2.83-3.050.05718.77950215399.6
3.05-3.340.04522.57619206199.8
3.34-3.740.04225.26964189399.2
3.74-4.320.03528.66128165299.3
4.32-5.290.03430.45042138399.6
5.29-7.470.03229.63976109499.1
7.470.03529.6176256190

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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 3GSO

3gso


Resolution: 1.93→14.06 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.893 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.15 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.181 / 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
Rfree0.266 3361 10.1 %RANDOM
Rwork0.209 ---
obs0.208 33426 98.48 %-
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: 67.81 Å2 / Biso mean: 25.312 Å2 / Biso min: 9.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.93→14.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3138 0 0 296 3434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0213262
X-RAY DIFFRACTIONr_angle_refined_deg1.1741.9214438
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7535390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.06923.239176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.90415530
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1611528
X-RAY DIFFRACTIONr_chiral_restr0.0810.2455
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022575
X-RAY DIFFRACTIONr_nbd_refined0.1890.21361
X-RAY DIFFRACTIONr_nbtor_refined0.2930.22151
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2274
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1030.212
X-RAY DIFFRACTIONr_mcbond_it1.31321992
X-RAY DIFFRACTIONr_mcangle_it1.98933109
X-RAY DIFFRACTIONr_scbond_it1.24721500
X-RAY DIFFRACTIONr_scangle_it1.77431324
LS refinement shellResolution: 1.93→1.979 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 204 -
Rwork0.301 1964 -
all-2168 -
obs--87.77 %

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