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- PDB-3gsw: Crystal structure of the binary complex between HLA-A2 and HCMV N... -

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Basic information

Entry
Database: PDB / ID: 3gsw
TitleCrystal structure of the binary complex between HLA-A2 and HCMV NLV-T8A peptide variant
Components
  • Beta-2-microglobulin
  • HCMV pp65 fragment 495-503, variant T8A (NLVPMVAAV)
  • HLA class I histocompatibility antigen, A-2 alpha chain
KeywordsIMMUNE SYSTEM / HLA / HUMAN CYTOMEGALOVIRUS / PP65 / T CELL RECEPTOR (TCR) / IMMUNE RESPONSE / PUBLIC RESPONSE / IMMUNODOMINANCE / RESTRAINED RESPONSE / HOST-VIRUS INTERACTION / MEMBRANE / MHC I / POLYMORPHISM / IMMUNOGLOBULIN DOMAIN
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 / 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 / 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 / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / RNA binding / extracellular exosome
Similarity search - Function
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 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.81 Å
AuthorsReiser, J.-B. / Saulquin, X. / Gras, S. / Debeaupuis, E. / Echasserieau, K. / Kissenpfennig, A. / Legoux, F. / Chouquet, A. / Le Gorrec, M. / Machillot, P. ...Reiser, J.-B. / Saulquin, X. / Gras, S. / Debeaupuis, E. / Echasserieau, K. / Kissenpfennig, A. / Legoux, F. / Chouquet, A. / Le Gorrec, M. / Machillot, P. / Neveu, B. / Thielens, N. / Malissen, B. / Bonneville, M. / Housset, D.
CitationJournal: J.Immunol. / Year: 2009
Title: Structural bases for the affinity-driven selection of a public TCR against a dominant human cytomegalovirus epitope.
Authors: Gras, S. / Saulquin, X. / Reiser, J.B. / Debeaupuis, E. / Echasserieau, K. / Kissenpfennig, A. / Legoux, F. / Chouquet, A. / Le Gorrec, M. / Machillot, P. / Neveu, B. / Thielens, N. / ...Authors: Gras, S. / Saulquin, X. / Reiser, J.B. / Debeaupuis, E. / Echasserieau, K. / Kissenpfennig, A. / Legoux, F. / Chouquet, A. / Le Gorrec, M. / Machillot, P. / Neveu, B. / Thielens, N. / Malissen, B. / Bonneville, M. / Housset, D.
History
DepositionMar 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 27, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: HCMV pp65 fragment 495-503, variant T8A (NLVPMVAAV)


Theoretical massNumber of molelcules
Total (without water)44,5463
Polymers44,5463
Non-polymers00
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-18 kcal/mol
Surface area18890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.610, 79.879, 57.893
Angle α, β, γ (deg.)90.000, 116.330, 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: 31753.139 Da / Num. of mol.: 1 / Mutation: A245V
Source method: isolated from a genetically manipulated source
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 HCMV pp65 fragment 495-503, variant T8A (NLVPMVAAV)


Mass: 913.135 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.63 Å3/Da / Density % sol: 53.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 9-20% PEG 6000, 0.1M tri-Na Citrate, 0-0.1M NaCl, 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: May 17, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 46082 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 25.566 Å2 / Rmerge(I) obs: 0.034 / Rsym value: 0.034 / Net I/σ(I): 28.45
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 5.7 / Num. measured obs: 11542 / Num. unique all: 3043 / Num. unique obs: 3191 / Rsym value: 0.258 / % possible all: 76.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
AMoREphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→14.5 Å / Cor.coef. Fo:Fc: 0.947 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.296 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.227 4184 10 %RANDOM
Rwork0.194 ---
all0.195 46082 --
obs0.195 41305 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 68.48 Å2 / Biso mean: 23.282 Å2 / Biso min: 11.43 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.81→14.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3307 0 0 304 3611
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0213428
X-RAY DIFFRACTIONr_angle_refined_deg1.0621.9224692
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4365435
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.48922.88191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.26515579
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4321536
X-RAY DIFFRACTIONr_chiral_restr0.0810.2479
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022745
X-RAY DIFFRACTIONr_nbd_refined0.1870.21479
X-RAY DIFFRACTIONr_nbtor_refined0.2940.22295
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.2299
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.227
X-RAY DIFFRACTIONr_mcbond_it0.611.52061
X-RAY DIFFRACTIONr_mcangle_it1.03523258
X-RAY DIFFRACTIONr_scbond_it1.40731589
X-RAY DIFFRACTIONr_scangle_it2.1114.51408
LS refinement shellResolution: 1.81→1.857 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 305 -
Rwork0.235 2986 -
all-3291 -
obs--97.52 %

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