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- PDB-5hhm: Crystal Structure of the JM22 TCR in complex with HLA-A*0201 in c... -

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Basic information

Entry
Database: PDB / ID: 5hhm
TitleCrystal Structure of the JM22 TCR in complex with HLA-A*0201 in complex with M1-F5L
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • JM22 TCR alpha chain
  • JM22 TCR beta chain
  • M1-F5L, GILGLVFTL
KeywordsIMMUNE SYSTEM / HLA A*0201 / influenza / M1 / TCR / T cell
Function / homology
Function and homology information


alpha-beta T cell receptor complex / 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 ...alpha-beta T cell receptor complex / 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 / 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 / T cell receptor binding / detection of bacterium / : / : / 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 / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / response to bacterium / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / 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 receptor-mediated endocytosis / positive regulation of T cell mediated cytotoxicity / positive regulation of T cell activation / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / specific granule lumen / positive regulation of type II interferon production / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / late endosome membrane / sensory perception of smell / antibacterial humoral response / tertiary granule lumen / DAP12 signaling / positive regulation of protein binding / E3 ubiquitin ligases ubiquitinate target proteins / T cell receptor signaling pathway / iron ion transport / negative regulation of neuron projection development / T cell differentiation in thymus / ER-Phagosome pathway / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / adaptive immune response / learning or memory / cell surface receptor signaling pathway / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / lysosomal membrane / signaling receptor binding / innate immune response / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses
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 / Immunoglobulin V-Type / Beta-2-Microglobulin ...: / : / 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 / Immunoglobulin V-Type / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / : / 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
T cell receptor beta variable 19 / T cell receptor alpha variable 27 / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsGras, S. / Josephs, T.M. / Rossjohn, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Molecular basis for universal HLA-A*0201-restricted CD8+ T-cell immunity against influenza viruses.
Authors: Valkenburg, S.A. / Josephs, T.M. / Clemens, E.B. / Grant, E.J. / Nguyen, T.H. / Wang, G.C. / Price, D.A. / Miller, A. / Tong, S.Y. / Thomas, P.G. / Doherty, P.C. / Rossjohn, J. / Gras, S. / Kedzierska, K.
History
DepositionJan 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2Apr 13, 2016Group: Database references
Revision 1.3May 4, 2016Group: Database references
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: M1-F5L, GILGLVFTL
D: JM22 TCR alpha chain
E: JM22 TCR beta chain
F: HLA class I histocompatibility antigen, A-2 alpha chain
G: Beta-2-microglobulin
H: M1-F5L, GILGLVFTL
I: JM22 TCR alpha chain
J: JM22 TCR beta chain


Theoretical massNumber of molelcules
Total (without water)188,10910
Polymers188,10910
Non-polymers00
Water10,593588
1
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: M1-F5L, GILGLVFTL
D: JM22 TCR alpha chain
E: JM22 TCR beta chain


Theoretical massNumber of molelcules
Total (without water)94,0545
Polymers94,0545
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: HLA class I histocompatibility antigen, A-2 alpha chain
G: Beta-2-microglobulin
H: M1-F5L, GILGLVFTL
I: JM22 TCR alpha chain
J: JM22 TCR beta chain


Theoretical massNumber of molelcules
Total (without water)94,0545
Polymers94,0545
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)242.876, 47.296, 185.945
Angle α, β, γ (deg.)90.00, 115.49, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 4 types, 8 molecules AFBGDIEJ

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


Mass: 31951.316 Da / Num. of mol.: 2 / Fragment: UNP residues 25-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61769
#4: Protein JM22 TCR alpha chain


Mass: 21867.275 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A087WT01*PLUS
#5: Protein JM22 TCR beta chain


Mass: 27424.307 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A075B6N1*PLUS

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Protein/peptide / Non-polymers , 2 types, 590 molecules CH

#3: Protein/peptide M1-F5L, GILGLVFTL


Mass: 932.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic source / Source: (synth.) synthetic construct (others)
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 588 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.57 Å3/Da / Density % sol: 52.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 50mM Tris-HCl, 70mM NaCl, 16%PEG10K, 14% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.5→46.53 Å / Num. obs: 67001 / % possible obs: 99.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 48.15 Å2 / Rmerge(I) obs: 0.121 / Rsym value: 0.121 / Net I/σ(I): 7.7
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.682 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.051 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER-TNTBUSTER 2.10.0refinement
SCALA3.3.21data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OGA

1oga


Resolution: 2.5→43.58 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.89 / SU R Cruickshank DPI: 0.484 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.511 / SU Rfree Blow DPI: 0.315 / SU Rfree Cruickshank DPI: 0.315
RfactorNum. reflection% reflectionSelection details
Rfree0.289 3250 4.85 %RANDOM
Rwork0.216 ---
obs0.22 66994 99.8 %-
Displacement parametersBiso mean: 42.7 Å2
Baniso -1Baniso -2Baniso -3
1-8.3368 Å20 Å2-1.3012 Å2
2---2.7288 Å20 Å2
3----5.608 Å2
Refine analyzeLuzzati coordinate error obs: 0.345 Å
Refinement stepCycle: LAST / Resolution: 2.5→43.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12084 0 0 588 12672
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112388HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1716798HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4220SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes332HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1792HARMONIC5
X-RAY DIFFRACTIONt_it12388HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.13
X-RAY DIFFRACTIONt_other_torsion20.09
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1553SEMIHARMONIC5
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_contact13461SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3034 235 4.84 %
Rwork0.2278 4624 -
all0.2314 4859 -
obs--99.78 %

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