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- PDB-5wkh: D30 TCR in complex with HLA-A*11:01-GTS3 -

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Entry
Database: PDB / ID: 5wkh
TitleD30 TCR in complex with HLA-A*11:01-GTS3
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • D30 TCR beta chain
  • GTS3 peptide
  • HLA class I histocompatibility antigen, A-11 alpha chain
  • T-cell receptor alpha variable 30,T-cell receptor, sp3.4 alpha chain
KeywordsIMMUNE SYSTEM / HLA / TCR / dengue / CD8 T cells
Function / homology
Function and homology information


T cell receptor complex / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna ...T cell receptor complex / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / 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 / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / endoplasmic reticulum exit site / beta-2-microglobulin binding / 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / detection of bacterium / T cell receptor binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / response to bacterium / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / 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 / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / viral capsid / : / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / positive regulation of type II interferon production / sensory perception of smell / nucleoside-triphosphate phosphatase / negative regulation of neuron projection development / double-stranded RNA binding / E3 ubiquitin ligases ubiquitinate target proteins / tertiary granule lumen / DAP12 signaling / protein complex oligomerization / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / monoatomic ion channel activity / positive regulation of protein binding / ER-Phagosome pathway / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / protein refolding / early endosome membrane / protein homotetramerization / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / intracellular iron ion homeostasis / amyloid fibril formation
Similarity search - Function
T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / : / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / : / Flavivirus non-structural protein NS2B / Flavivirus NS3 helicase, C-terminal helical domain ...T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / : / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / : / Flavivirus non-structural protein NS2B / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / DEAD box, Flavivirus / Flavivirus DEAD domain / 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 / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
T cell receptor alpha variable 30 / T-cell receptor, sp3.4 alpha chain / HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin / Genome polyprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Dengue virus 3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å
AuthorsGras, S. / Rossjohn, J.
CitationJournal: Nat. Immunol. / Year: 2017
Title: Germline bias dictates cross-serotype reactivity in a common dengue-virus-specific CD8(+) T cell response.
Authors: Culshaw, A. / Ladell, K. / Gras, S. / McLaren, J.E. / Miners, K.L. / Farenc, C. / van den Heuvel, H. / Gostick, E. / Dejnirattisai, W. / Wangteeraprasert, A. / Duangchinda, T. / ...Authors: Culshaw, A. / Ladell, K. / Gras, S. / McLaren, J.E. / Miners, K.L. / Farenc, C. / van den Heuvel, H. / Gostick, E. / Dejnirattisai, W. / Wangteeraprasert, A. / Duangchinda, T. / Chotiyarnwong, P. / Limpitikul, W. / Vasanawathana, S. / Malasit, P. / Dong, T. / Rossjohn, J. / Mongkolsapaya, J. / Price, D.A. / Screaton, G.R.
History
DepositionJul 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A-11 alpha chain
B: Beta-2-microglobulin
C: GTS3 peptide
D: T-cell receptor alpha variable 30,T-cell receptor, sp3.4 alpha chain
E: D30 TCR beta chain
F: HLA class I histocompatibility antigen, A-11 alpha chain
G: Beta-2-microglobulin
H: GTS3 peptide
I: T-cell receptor alpha variable 30,T-cell receptor, sp3.4 alpha chain
J: D30 TCR beta chain


Theoretical massNumber of molelcules
Total (without water)187,78310
Polymers187,78310
Non-polymers00
Water362
1
A: HLA class I histocompatibility antigen, A-11 alpha chain
B: Beta-2-microglobulin
C: GTS3 peptide
D: T-cell receptor alpha variable 30,T-cell receptor, sp3.4 alpha chain
E: D30 TCR beta chain


Theoretical massNumber of molelcules
Total (without water)93,8925
Polymers93,8925
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: HLA class I histocompatibility antigen, A-11 alpha chain
G: Beta-2-microglobulin
H: GTS3 peptide
I: T-cell receptor alpha variable 30,T-cell receptor, sp3.4 alpha chain
J: D30 TCR beta chain


Theoretical massNumber of molelcules
Total (without water)93,8925
Polymers93,8925
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.389, 170.536, 85.692
Angle α, β, γ (deg.)90.00, 113.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 4 types, 8 molecules AFBGDIEJ

#1: Protein HLA class I histocompatibility antigen, A-11 alpha chain / MHC class I antigen A*11


Mass: 31725.936 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P13746, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61769
#4: Protein T-cell receptor alpha variable 30,T-cell receptor, sp3.4 alpha chain / T-cell receptor / sp3.4 beta chain


Mass: 21888.479 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAV30 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A087WSZ9, UniProt: K7N5N2
#5: Protein D30 TCR beta chain


Mass: 27395.740 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)

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Protein/peptide / Non-polymers , 2 types, 4 molecules CH

#3: Protein/peptide GTS3 peptide


Mass: 1002.105 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: GL Biochem / Source: (synth.) Dengue virus 3 / References: UniProt: Q6YMS4*PLUS
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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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: 2.75 Å3/Da / Density % sol: 55.32 % / Mosaicity: 0.23 °
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.5 / Details: 17%PEG8000, 2% Ethylen glycol, 0.1M HEPES pH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 3.2→46.01 Å / Num. obs: 33473 / % possible obs: 99.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 46.46 Å2 / Rpim(I) all: 0.131 / Net I/σ(I): 6.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym value% possible all
3.2-3.373.70.5992.748650.7240.3640.050.04299.9
10.12-46.013.60.0420.9960.0380.0720.06297.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
SCALA3.3.21data scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
XDSdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→46.01 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.788 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.472
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1663 4.97 %RANDOM
Rwork0.177 ---
obs0.18 33448 99.8 %-
Displacement parametersBiso mean: 39.82 Å2
Baniso -1Baniso -2Baniso -3
1--20.6746 Å20 Å29.1206 Å2
2--15.0822 Å20 Å2
3---5.5924 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: 1 / Resolution: 3.2→46.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13218 0 0 2 13220
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00813559HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0818396HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4654SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes380HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1959HARMONIC5
X-RAY DIFFRACTIONt_it13559HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.63
X-RAY DIFFRACTIONt_other_torsion22.02
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1703SEMIHARMONIC5
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_contact14376SEMIHARMONIC4
LS refinement shellResolution: 3.2→3.3 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2912 145 5 %
Rwork0.224 2756 -
all0.2274 2901 -
obs--99.83 %

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