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- PDB-8qfy: Crystal structure of high affinity TCR in complex with pHLA harbo... -

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Basic information

Entry
Database: PDB / ID: 8qfy
TitleCrystal structure of high affinity TCR in complex with pHLA harbouring bacterial peptide
Components
  • (T-cell receptor ...) x 2
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, alpha chain E
  • Peptide from inhA
KeywordsIMMUNE SYSTEM / T-cell receptor / HLA-E
Function / homology
Function and homology information


positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell lectin-like receptor binding / natural killer cell tolerance induction / negative regulation of natural killer cell activation ...positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell lectin-like receptor binding / natural killer cell tolerance induction / negative regulation of natural killer cell activation / positive regulation of natural killer cell activation / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of interleukin-13 production / negative regulation of natural killer cell mediated cytotoxicity / 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 / positive regulation of immunoglobulin production / positive regulation of interleukin-4 production / beta-2-microglobulin binding / positive regulation of natural killer cell proliferation / MHC class I protein 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 / negative regulation of T cell proliferation / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / 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 / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / positive regulation of tumor necrosis factor production / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / antibacterial humoral response / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / adaptive immune response / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / receptor ligand activity / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / Neutrophil degranulation / 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 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 / : ...MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 / : / 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
ACETATE ION / HLA class I histocompatibility antigen, alpha chain E / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Mycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsPengelly, R.J. / Robinson, R.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: An HLA-E-targeted TCR bispecific molecule redirects T cell immunity against Mycobacterium tuberculosis.
Authors: Paterson, R.L. / La Manna, M.P. / Arena De Souza, V. / Walker, A. / Gibbs-Howe, D. / Kulkarni, R. / Fergusson, J.R. / Mulakkal, N.C. / Monteiro, M. / Bunjobpol, W. / Dembek, M. / Martin- ...Authors: Paterson, R.L. / La Manna, M.P. / Arena De Souza, V. / Walker, A. / Gibbs-Howe, D. / Kulkarni, R. / Fergusson, J.R. / Mulakkal, N.C. / Monteiro, M. / Bunjobpol, W. / Dembek, M. / Martin-Urdiroz, M. / Grant, T. / Barber, C. / Garay-Baquero, D.J. / Tezera, L.B. / Lowne, D. / Britton-Rivet, C. / Pengelly, R. / Chepisiuk, N. / Singh, P.K. / Woon, A.P. / Powlesland, A.S. / McCully, M.L. / Caccamo, N. / Salio, M. / Badami, G.D. / Dorrell, L. / Knox, A. / Robinson, R. / Elkington, P. / Dieli, F. / Lepore, M. / Leonard, S. / Godinho, L.F.
History
DepositionSep 5, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: HLA class I histocompatibility antigen, alpha chain E
BBB: Beta-2-microglobulin
CCC: Peptide from inhA
DDD: T-cell receptor alpha chain
EEE: T-cell receptor beta chain
FFF: HLA class I histocompatibility antigen, alpha chain E
GGG: Beta-2-microglobulin
HHH: Peptide from inhA
III: T-cell receptor alpha chain
JJJ: T-cell receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,03212
Polymers188,91310
Non-polymers1182
Water5,062281
1
AAA: HLA class I histocompatibility antigen, alpha chain E
BBB: Beta-2-microglobulin
CCC: Peptide from inhA
DDD: T-cell receptor alpha chain
EEE: T-cell receptor beta chain


Theoretical massNumber of molelcules
Total (without water)94,4575
Polymers94,4575
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
FFF: HLA class I histocompatibility antigen, alpha chain E
GGG: Beta-2-microglobulin
HHH: Peptide from inhA
III: T-cell receptor alpha chain
JJJ: T-cell receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,5757
Polymers94,4575
Non-polymers1182
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)326.828, 79.879, 104.073
Angle α, β, γ (deg.)90.000, 96.894, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21FFF
32BBB
42GGG
53DDD
63III
74EEE
84JJJ

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLYGLYTHRTHRAAAA1 - 2711 - 271
221GLYGLYTHRTHRFFFF1 - 2711 - 271
332METMETMETMETBBBB0 - 991 - 100
442METMETMETMETGGGG0 - 991 - 100
553LYSLYSASNASNDDDD3 - 1893 - 189
663LYSLYSASNASNIIII3 - 1893 - 189
774THRTHRASPASPEEEE3 - 2433 - 243
884THRTHRASPASPJJJJ3 - 2433 - 243

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8

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Components

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Protein , 2 types, 4 molecules AAAFFFBBBGGG

#1: Protein HLA class I histocompatibility antigen, alpha chain E / MHC class I antigen E


Mass: 31824.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-E, HLA-6.2, HLAE / Production host: Escherichia coli (E. coli) / References: UniProt: P13747
#2: Protein 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 / Production host: Escherichia coli (E. coli) / References: UniProt: P61769

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Protein/peptide , 1 types, 2 molecules CCCHHH

#3: Protein/peptide Peptide from inhA


Mass: 980.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mycobacterium tuberculosis (bacteria)

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T-cell receptor ... , 2 types, 4 molecules DDDIIIEEEJJJ

#4: Protein T-cell receptor alpha chain


Mass: 22079.363 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#5: Protein T-cell receptor beta chain


Mass: 27693.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 2 types, 283 molecules

#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 3.57 Å3/Da / Density % sol: 65.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M calcium acetate, 0.1 M imidazole pH 8.0, 10% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.33→82.9 Å / Num. obs: 114168 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.987 / Rmerge(I) obs: 0.121 / Rrim(I) all: 0.131 / Net I/σ(I): 11.3
Reflection shellResolution: 2.33→2.37 Å / Redundancy: 6 % / Rmerge(I) obs: 3.209 / Num. unique obs: 5720 / CC1/2: 0.34 / Rrim(I) all: 3.521 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALS3.1.2data reduction
DIALS3.1.2data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GH1, 4WW2

6gh1

4ww2


Resolution: 2.33→82.9 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.921 / WRfactor Rfree: 0.253 / WRfactor Rwork: 0.206 / SU B: 15.989 / SU ML: 0.323 / Average fsc free: 0.6939 / Average fsc work: 0.7064 / Cross valid method: THROUGHOUT / ESU R: 0.279 / ESU R Free: 0.238
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2886 5685 4.981 %
Rwork0.2425 108459 -
all0.245 --
obs-114144 99.947 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 74.978 Å2
Baniso -1Baniso -2Baniso -3
1--2.741 Å20 Å2-2.502 Å2
2--6.869 Å20 Å2
3----3.423 Å2
Refinement stepCycle: LAST / Resolution: 2.33→82.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12837 0 8 281 13126
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01313218
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711866
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.65217946
X-RAY DIFFRACTIONr_angle_other_deg1.1531.58327379
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.37751586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.32421.828793
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.572152164
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.08915107
X-RAY DIFFRACTIONr_chiral_restr0.0530.21653
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215161
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023245
X-RAY DIFFRACTIONr_nbd_refined0.1990.22262
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.210749
X-RAY DIFFRACTIONr_nbtor_refined0.1640.25908
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.26500
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2347
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1340.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2860.217
X-RAY DIFFRACTIONr_nbd_other0.2640.280
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2080.28
X-RAY DIFFRACTIONr_mcbond_it5.6497.8146367
X-RAY DIFFRACTIONr_mcbond_other5.657.8136365
X-RAY DIFFRACTIONr_mcangle_it8.54511.7037938
X-RAY DIFFRACTIONr_mcangle_other8.54411.7047939
X-RAY DIFFRACTIONr_scbond_it5.2728.2176851
X-RAY DIFFRACTIONr_scbond_other5.2718.2176852
X-RAY DIFFRACTIONr_scangle_it8.32212.17210006
X-RAY DIFFRACTIONr_scangle_other8.32212.17210007
X-RAY DIFFRACTIONr_lrange_it12.21386.12213827
X-RAY DIFFRACTIONr_lrange_other12.21386.12513828
X-RAY DIFFRACTIONr_ncsr_local_group_10.0820.057792
X-RAY DIFFRACTIONr_ncsr_local_group_20.0350.053056
X-RAY DIFFRACTIONr_ncsr_local_group_30.0910.055476
X-RAY DIFFRACTIONr_ncsr_local_group_40.0660.057526
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.081750.05009
12FFFX-RAY DIFFRACTIONLocal ncs0.081750.05009
23BBBX-RAY DIFFRACTIONLocal ncs0.034560.0501
24GGGX-RAY DIFFRACTIONLocal ncs0.034560.0501
35DDDX-RAY DIFFRACTIONLocal ncs0.090930.0501
36IIIX-RAY DIFFRACTIONLocal ncs0.090930.0501
47EEEX-RAY DIFFRACTIONLocal ncs0.066070.05009
48JJJX-RAY DIFFRACTIONLocal ncs0.066070.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.390.4334000.4347969X-RAY DIFFRACTION99.5835
2.39-2.4550.414210.4057744X-RAY DIFFRACTION100
2.455-2.5270.4153840.3957597X-RAY DIFFRACTION99.9875
2.527-2.6040.4053980.3827337X-RAY DIFFRACTION99.9225
2.604-2.690.4063540.387136X-RAY DIFFRACTION99.96
2.69-2.7840.3883760.3566859X-RAY DIFFRACTION99.9171
2.784-2.8890.343500.3226670X-RAY DIFFRACTION99.9715
2.889-3.0070.3113120.2986438X-RAY DIFFRACTION99.9704
3.007-3.1410.3233400.2676128X-RAY DIFFRACTION99.9845
3.141-3.2940.2633310.2385862X-RAY DIFFRACTION100
3.294-3.4720.2843290.2375601X-RAY DIFFRACTION99.9831
3.472-3.6830.2982680.2325266X-RAY DIFFRACTION100
3.683-3.9370.2732700.2194981X-RAY DIFFRACTION100
3.937-4.2520.2532280.1944687X-RAY DIFFRACTION99.9797
4.252-4.6580.2062240.1654300X-RAY DIFFRACTION100
4.658-5.2070.2241990.1683899X-RAY DIFFRACTION100
5.207-6.0110.2711640.193457X-RAY DIFFRACTION100
6.011-7.360.3281580.2122921X-RAY DIFFRACTION100
7.36-10.3980.2061130.1782303X-RAY DIFFRACTION100
10.398-82.90.303660.2931305X-RAY DIFFRACTION99.7817

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