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- PDB-7t5m: Structure of HLA-A*02:01-FLPTPEELGLLGPPRPQVLA complex -

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Basic information

Entry
Database: PDB / ID: 7t5m
TitleStructure of HLA-A*02:01-FLPTPEELGLLGPPRPQVLA complex
Components
  • Beta-2-microglobulin
  • Interleukin-27 receptor subunit alpha
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / HLA / long epitope / 20mer / T cell recognition
Function / homology
Function and homology information


negative regulation of T cell extravasation / negative regulation of T-helper 17 type immune response / interleukin-27 receptor activity / negative regulation of type 2 immune response / regulation of isotype switching to IgG isotypes / positive regulation of T-helper 1 type immune response / negative regulation of interleukin-17 production / Interleukin-35 Signalling / Interleukin-27 signaling / cytokine binding ...negative regulation of T cell extravasation / negative regulation of T-helper 17 type immune response / interleukin-27 receptor activity / negative regulation of type 2 immune response / regulation of isotype switching to IgG isotypes / positive regulation of T-helper 1 type immune response / negative regulation of interleukin-17 production / Interleukin-35 Signalling / Interleukin-27 signaling / cytokine binding / negative regulation of interleukin-6 production / negative regulation of tumor necrosis factor production / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / 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 / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / cytokine-mediated signaling pathway / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / transmembrane signaling receptor activity / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / positive regulation of type II interferon production / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / ER-Phagosome pathway / iron ion transport / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / negative regulation of neuron apoptotic process / amyloid fibril formation / learning or memory / cell surface receptor signaling pathway / receptor complex / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / signaling receptor binding / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding
Similarity search - Function
MHC class I, alpha chain, C-terminal / MHC_I C-terminus / Fibronectin type III domain / MHC class I alpha chain, alpha1 alpha2 domains / Fibronectin type 3 domain / Class I Histocompatibility antigen, domains alpha 1 and 2 / Fibronectin type-III domain profile. / Beta-2-Microglobulin / Fibronectin type III / MHC class I-like antigen recognition-like ...MHC class I, alpha chain, C-terminal / MHC_I C-terminus / Fibronectin type III domain / MHC class I alpha chain, alpha1 alpha2 domains / Fibronectin type 3 domain / Class I Histocompatibility antigen, domains alpha 1 and 2 / Fibronectin type-III domain profile. / Beta-2-Microglobulin / Fibronectin type III / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Fibronectin type III 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
Similarity search - Domain/homology
Beta-2-microglobulin / Interleukin-27 receptor subunit alpha / MHC class I antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsGras, S.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1159272 Australia
CitationJournal: J Immunol. / Year: 2022
Title: Cutting Edge: Unconventional CD8 + T Cell Recognition of a Naturally Occurring HLA-A*02:01-Restricted 20mer Epitope.
Authors: Meeuwsen, M.H. / Wouters, A.K. / Hagedoorn, R.S. / Kester, M.G.D. / Remst, D.F.G. / van der Steen, D.M. / de Ru, A. / van Veelen, P.A. / Rossjohn, J. / Gras, S. / Falkenburg, J.H.F. / Heemskerk, M.H.M.
History
DepositionDec 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Jan 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: MHC class I antigen
D: Beta-2-microglobulin
E: Interleukin-27 receptor subunit alpha
F: Interleukin-27 receptor subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,2099
Polymers92,0386
Non-polymers1713
Water21,9421218
1
A: MHC class I antigen
B: Beta-2-microglobulin
E: Interleukin-27 receptor subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1665
Polymers46,0193
Non-polymers1462
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-26 kcal/mol
Surface area19440 Å2
MethodPISA
2
C: MHC class I antigen
D: Beta-2-microglobulin
F: Interleukin-27 receptor subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0434
Polymers46,0193
Non-polymers241
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-31 kcal/mol
Surface area19280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.178, 99.903, 135.464
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein MHC class I antigen


Mass: 32125.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Production host: Escherichia coli (E. coli) / References: UniProt: Q861F7
#2: Protein Beta-2-microglobulin


Mass: 11748.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769

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Protein/peptide , 1 types, 2 molecules EF

#3: Protein/peptide Interleukin-27 receptor subunit alpha / IL-27 receptor subunit alpha / IL-27R subunit alpha / IL-27R-alpha / IL-27RA / Cytokine receptor ...IL-27 receptor subunit alpha / IL-27R subunit alpha / IL-27R-alpha / IL-27RA / Cytokine receptor WSX-1 / Cytokine receptor-like 1 / Type I T-cell cytokine receptor / TCCR / ZcytoR1


Mass: 2145.518 Da / Num. of mol.: 2 / Fragment: residues 617-636 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q6UWB1

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Non-polymers , 3 types, 1221 molecules

#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1218 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.58 Å3/Da / Density % sol: 52.29 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop
Details: 0.12M Monosaccharides (D-Glucose; D-Mannose; D-Galactose; L-Fucose; D-Xylose; N-Acetyl-D-Glucosamine), 0.1M of Na-HEPES and MOPS buffer at pH 7.5, 20% W/V Glycerol and 10% W/V PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.67→48.74 Å / Num. obs: 111273 / % possible obs: 99.8 % / Redundancy: 7.4 % / CC1/2: 0.998 / Rpim(I) all: 0.041 / Net I/σ(I): 13.2
Reflection shellResolution: 1.67→1.7 Å / Num. unique obs: 5154 / CC1/2: 0.72 / Rpim(I) all: 0.351

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.27data extraction
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GSO

3gso


Resolution: 1.67→43.8 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.943 / SU R Cruickshank DPI: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.112 / SU Rfree Blow DPI: 0.1 / SU Rfree Cruickshank DPI: 0.094
RfactorNum. reflection% reflectionSelection details
Rfree0.208 5546 4.99 %RANDOM
Rwork0.187 ---
obs0.188 111197 99.7 %-
Displacement parametersBiso max: 86.59 Å2 / Biso mean: 21.57 Å2 / Biso min: 4.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.9336 Å20 Å20 Å2
2---0.7927 Å20 Å2
3----0.1409 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: final / Resolution: 1.67→43.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6417 0 10 1222 7649
Biso mean--22.17 34.39 -
Num. residues----783
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2463SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1250HARMONIC5
X-RAY DIFFRACTIONt_it7097HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion865SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9527SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7097HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg9717HARMONIC20.98
X-RAY DIFFRACTIONt_omega_torsion3.6
X-RAY DIFFRACTIONt_other_torsion15.81
LS refinement shellResolution: 1.67→1.68 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2616 106 4.77 %
Rwork0.2449 2118 -
all0.2457 2224 -
obs--85.92 %

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