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- PDB-4gks: A2-MHC Complex carrying FLTGIGIITV -

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Basic information

Entry
Database: PDB / ID: 4gks
TitleA2-MHC Complex carrying FLTGIGIITV
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • FLT Cognate peptide
  • HLA class I histocompatibility antigen, A-2 alpha chain
KeywordsIMMUNE SYSTEM / Major Histocompatibility Complex / T-Cell Receptor / Immuno / Immunoglobulin / Recognition / MHC / TCR
Function / homology
Function and homology information


T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / 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 / T cell mediated cytotoxicity / antigen processing and presentation of exogenous peptide antigen via MHC class I / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP complex binding / Golgi medial cisterna ...T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / 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 / T cell mediated cytotoxicity / antigen processing and presentation of exogenous peptide antigen via MHC class I / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP complex binding / Golgi medial cisterna / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / protection from natural killer cell mediated cytotoxicity / CD8 receptor binding / endoplasmic reticulum exit site / beta-2-microglobulin binding / detection of bacterium / TAP binding / T cell receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / early endosome lumen / Interferon alpha/beta signaling / integral component of lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen binding / Endosomal/Vacuolar pathway / type I interferon signaling pathway / antigen processing and presentation of peptide antigen via MHC class I / ER to Golgi transport vesicle membrane / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / regulation of defense response to virus by virus / positive regulation of transferrin receptor binding / positive regulation of ferrous iron binding / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent / regulation of membrane depolarization / MHC class I peptide loading complex / negative regulation of receptor binding / response to molecule of bacterial origin / regulation of iron ion transport / MHC class I protein complex / HFE-transferrin receptor complex / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / recycling endosome membrane / positive regulation of T cell cytokine production / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor binding / phagocytic vesicle membrane / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / E3 ubiquitin ligases ubiquitinate target proteins / Interferon gamma signaling / positive regulation of interferon-gamma production / positive regulation of cellular senescence / specific granule lumen / modulation by symbiont of host defense response / Modulation by Mtb of host immune system / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / retina homeostasis / negative regulation of neuron projection development / iron ion homeostasis / interferon-gamma-mediated signaling pathway / response to cadmium ion / DAP12 signaling / modulation of age-related behavioral decline / T cell differentiation in thymus / ER-Phagosome pathway / early endosome membrane / tertiary granule lumen / regulation of immune response / iron ion transport / protein refolding / protein homotetramerization / antibacterial humoral response / T cell receptor signaling pathway / positive regulation of protein binding / learning or memory / antimicrobial humoral immune response mediated by antimicrobial peptide / cellular response to lipopolysaccharide / immune response / protein ubiquitination / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / external side of plasma membrane / Amyloid fiber formation / Golgi membrane / amyloid fibril formation / signaling receptor binding / focal adhesion / response to xenobiotic stimulus => GO:0009410 / endoplasmic reticulum lumen / endoplasmic reticulum membrane / innate immune response / Neutrophil degranulation
Similarity search - Function
MHC_I C-terminus / MHC class I, alpha chain, C-terminal / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Beta-2-Microglobulin / MHC classes I/II-like antigen recognition protein ...MHC_I C-terminus / MHC class I, alpha chain, C-terminal / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Beta-2-Microglobulin / 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)
Synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.346 Å
AuthorsSewell, A.K. / Rizkallah, P.J. / Cole, D.K. / Wooldridge, L. / Price, D.A.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: T-cell Receptor-optimized Peptide Skewing of the T-cell Repertoire Can Enhance Antigen Targeting.
Authors: Ekeruche-Makinde, J. / Clement, M. / Cole, D.K. / Edwards, E.S. / Ladell, K. / Miles, J.J. / Matthews, K.K. / Fuller, A. / Lloyd, K.A. / Madura, F. / Dolton, G.M. / Pentier, J. / Lissina, A. ...Authors: Ekeruche-Makinde, J. / Clement, M. / Cole, D.K. / Edwards, E.S. / Ladell, K. / Miles, J.J. / Matthews, K.K. / Fuller, A. / Lloyd, K.A. / Madura, F. / Dolton, G.M. / Pentier, J. / Lissina, A. / Gostick, E. / Baxter, T.K. / Baker, B.M. / Rizkallah, P.J. / Price, D.A. / Wooldridge, L. / Sewell, A.K.
History
DepositionAug 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Database references
Revision 1.2Nov 14, 2012Group: Database references

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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: FLT Cognate peptide
D: HLA class I histocompatibility antigen, A-2 alpha chain
E: Beta-2-microglobulin
F: FLT Cognate peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,81522
Polymers89,7286
Non-polymers1,08716
Water1,802100
1
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: FLT Cognate peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,48712
Polymers44,8643
Non-polymers6239
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint-18 kcal/mol
Surface area18700 Å2
MethodPISA
2
D: HLA class I histocompatibility antigen, A-2 alpha chain
E: Beta-2-microglobulin
F: FLT Cognate peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,32810
Polymers44,8643
Non-polymers4657
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-7 kcal/mol
Surface area18960 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)201.540, 46.780, 115.860
Angle α, β, γ (deg.)90.00, 121.66, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 4 molecules ADBE

#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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin / Beta-2-microglobulin form pI 5.3


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 / References: UniProt: P61769

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Protein/peptide , 1 types, 2 molecules CF

#3: Protein/peptide FLT Cognate peptide


Mass: 1033.262 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)

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Non-polymers , 4 types, 116 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.59 Å3/Da / Density % sol: 52.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG 8000, 200 mM Ammonium Sulphate, 200 mM Cacodylate Buffer, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.346→39.049 Å / Num. all: 36005 / Num. obs: 36005 / % possible obs: 92.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2.2 / Redundancy: 4 % / Biso Wilson estimate: 66.4 Å2 / Rsym value: 0.09 / Net I/σ(I): 8.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.346-2.4140.70111078027020.70194.2
2.41-2.4740.6191.21044426350.61994.8
2.47-2.5440.5071.41018925280.50794.5
2.54-2.624.10.4641.61005024810.46494.2
2.62-2.714.10.3252.2986824170.32594
2.71-2.84.20.2712.7958323030.27193.6
2.8-2.914.10.2243.3909622370.22493.5
2.91-3.0340.1654.5847121040.16592.6
3.03-3.1640.1355.4810420350.13592.5
3.16-3.323.90.0987.4762119480.09891.2
3.32-3.53.90.0858.3702417860.08589.8
3.5-3.7140.06810.1664016670.06887.3
3.71-3.973.90.05911.1563714610.05981.1
3.97-4.283.90.05411.7500412890.05476.2
4.28-4.694.10.05112.2631815230.05198.6
4.69-5.254.10.04713.6564113680.04798.4
5.25-6.064.10.0513505712250.0598.3
6.06-7.4240.04713.7416010370.04798.1
7.42-10.493.80.04612.331268150.04697.2
10.49-39.0493.60.04612.415784440.04692.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
GDAdata collection
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4GKN
Resolution: 2.346→39.049 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.893 / WRfactor Rfree: 0.2864 / WRfactor Rwork: 0.2125 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7926 / SU B: 15.275 / SU ML: 0.238 / SU R Cruickshank DPI: 0.4552 / SU Rfree: 0.2977 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.455 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2852 1798 5 %RANDOM
Rwork0.2113 ---
obs0.215 36000 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 111.77 Å2 / Biso mean: 45.7261 Å2 / Biso min: 14.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å2-0.05 Å2
2--0.15 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 2.346→39.049 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6327 0 69 100 6496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0216613
X-RAY DIFFRACTIONr_angle_refined_deg1.6641.9298946
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0845774
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.56723.066349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.745151069
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.361558
X-RAY DIFFRACTIONr_chiral_restr0.1170.2908
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215162
X-RAY DIFFRACTIONr_mcbond_it1.7651.53867
X-RAY DIFFRACTIONr_mcangle_it2.99526244
X-RAY DIFFRACTIONr_scbond_it5.21832746
X-RAY DIFFRACTIONr_scangle_it7.4944.52702
LS refinement shellResolution: 2.346→2.407 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 122 -
Rwork0.268 2571 -
all-2693 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.91130.0911-3.77241.0063-0.15064.853-0.1325-0.334-0.61550.0681-0.1279-0.0588-0.01420.12970.26040.0410.0049-0.0350.08060.06030.239-40.724-15.13711.688
22.0716-0.1633-2.1021.077-0.35218.0238-0.1277-0.12920.02120.0145-0.05560.0676-0.5613-0.21970.18330.13090.0448-0.10060.0616-0.01880.14555.226-12.42945.924
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 100
2X-RAY DIFFRACTION1A101 - 183
3X-RAY DIFFRACTION1B0 - 99
4X-RAY DIFFRACTION1C1 - 10
5X-RAY DIFFRACTION2D1 - 100
6X-RAY DIFFRACTION2D101 - 183
7X-RAY DIFFRACTION2E0 - 99
8X-RAY DIFFRACTION2F1 - 10

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