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- PDB-5wjn: Crystal Structure of HLA-A*11:01-GTS3 -

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Basic information

Entry
Database: PDB / ID: 5wjn
TitleCrystal Structure of HLA-A*11:01-GTS3
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • GTS3 peptide
  • HLA class I histocompatibility antigen, A-11 alpha chain
KeywordsIMMUNE SYSTEM / HLA / TCR / dengue / CD8 T cells
Function / homology
Function and homology information


peptide antigen assembly with MHC class I protein 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 ...peptide antigen assembly with MHC class I protein 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 / 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 / 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 / RNA helicase activity / host cell endoplasmic reticulum membrane
Similarity search - Function
: / 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 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 / 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 / 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/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
: / 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: 2.85 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 23, 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

Downloads & links

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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: HLA class I histocompatibility antigen, A-11 alpha chain
E: Beta-2-microglobulin
F: GTS3 peptide
G: HLA class I histocompatibility antigen, A-11 alpha chain
H: Beta-2-microglobulin
I: GTS3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,86110
Polymers133,8229
Non-polymers391
Water6,107339
1
A: HLA class I histocompatibility antigen, A-11 alpha chain
B: Beta-2-microglobulin
C: GTS3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6464
Polymers44,6073
Non-polymers391
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-11 kcal/mol
Surface area18740 Å2
MethodPISA
2
D: HLA class I histocompatibility antigen, A-11 alpha chain
E: Beta-2-microglobulin
F: GTS3 peptide


Theoretical massNumber of molelcules
Total (without water)44,6073
Polymers44,6073
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-12 kcal/mol
Surface area18720 Å2
MethodPISA
3
G: HLA class I histocompatibility antigen, A-11 alpha chain
H: Beta-2-microglobulin
I: GTS3 peptide


Theoretical massNumber of molelcules
Total (without water)44,6073
Polymers44,6073
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-13 kcal/mol
Surface area19000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.325, 145.522, 106.303
Angle α, β, γ (deg.)90.00, 121.14, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 31725.936 Da / Num. of mol.: 3
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.: 3
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
#3: Protein/peptide GTS3 peptide


Mass: 1002.105 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: GL Biochem / Source: (synth.) Dengue virus 3 / References: UniProt: Q6YMS4*PLUS
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 3.92 Å3/Da / Density % sol: 68.59 % / Mosaicity: 0.49 °
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8.5
Details: 1.4-1.8M NH4SO4, 0.1M Na-cacodylate pH6.5, 200mM NaCl, 2% Ethylen glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.85→45.67 Å / Num. obs: 47263 / % possible obs: 98.2 % / Redundancy: 3.8 % / Biso Wilson estimate: 65.69 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.088 / Rsym value: 0.147 / Net I/σ(I): 6.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.85-33.90.5992707270230.670.0310.0610.0522.1100
9.01-48.973.60.052534714960.9930.0430.0830.07114.495.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
SCALA3.3.21data scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
XDSdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→45.67 Å / Cor.coef. Fo:Fc: 0.9245 / Cor.coef. Fo:Fc free: 0.901 / SU R Cruickshank DPI: 0.631 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.598 / SU Rfree Blow DPI: 0.292 / SU Rfree Cruickshank DPI: 0.299
RfactorNum. reflection% reflectionSelection details
Rfree0.2299 2388 5.06 %RANDOM
Rwork0.2005 ---
obs0.202 47215 98.09 %-
Displacement parametersBiso mean: 57.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.2132 Å20 Å2-0.5022 Å2
2--0.9734 Å20 Å2
3----1.1866 Å2
Refine analyzeLuzzati coordinate error obs: 0.402 Å
Refinement stepCycle: 1 / Resolution: 2.85→45.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9439 0 1 339 9779
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0079695HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9913148HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3354SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes279HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1406HARMONIC5
X-RAY DIFFRACTIONt_it9695HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.45
X-RAY DIFFRACTIONt_other_torsion19.72
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1201SEMIHARMONIC5
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_contact10569SEMIHARMONIC4
LS refinement shellResolution: 2.85→2.92 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2884 143 4.01 %
Rwork0.2536 3424 -
all0.2549 3567 -
obs--98.09 %

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