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- PDB-6amu: Crystal structure of DMF5 TCR bound to HLA-A2 presenting syntheti... -

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Basic information

Entry
Database: PDB / ID: 6amu
TitleCrystal structure of DMF5 TCR bound to HLA-A2 presenting synthetic peptide MMWDRGLGMM
Components
  • Beta-2-microglobulin
  • DMF5 TCR alpha chain
  • DMF5 TCR beta chain
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • MET-MET-TRP-ASP-ARG-GLY-LEU-GLY-MET-MET
KeywordsIMMUNE SYSTEM / pMHC / TCR
Function / homology
Function and homology information


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 ...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 / detection of bacterium / T cell receptor binding / : / : / 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 / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / 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 / 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 T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / positive regulation of type II interferon production / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / MHC class II protein complex binding / Interferon alpha/beta signaling / positive regulation of protein binding / antibacterial humoral response / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / E3 ubiquitin ligases ubiquitinate target proteins / T cell receptor signaling pathway / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / signaling receptor binding / lysosomal membrane / innate immune response / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus
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 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily ...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 / 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 / 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 / Resolution: 2.151 Å
AuthorsRiley, T.P. / Baker, B.M.
CitationJournal: To Be Published
Title: Crystal structure of DMF5 TCR bound to HLA-A2 presenting synthetic peptide MMWDRGLGMM
Authors: Riley, T.P. / Baker, B.M.
History
DepositionAug 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: MET-MET-TRP-ASP-ARG-GLY-LEU-GLY-MET-MET
D: DMF5 TCR alpha chain
E: DMF5 TCR beta chain


Theoretical massNumber of molelcules
Total (without water)93,3805
Polymers93,3805
Non-polymers00
Water8,647480
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10730 Å2
ΔGint-57 kcal/mol
Surface area37370 Å2
Unit cell
Length a, b, c (Å)232.078, 50.326, 84.361
Angle α, β, γ (deg.)90.00, 99.52, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 4 types, 4 molecules ABDE

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


Mass: 31668.033 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Production host: Escherichia coli (E. coli) / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1
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
#4: Protein DMF5 TCR alpha chain


Mass: 21790.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#5: Protein DMF5 TCR beta chain


Mass: 26812.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Protein/peptide / Non-polymers , 2 types, 481 molecules C

#3: Protein/peptide MET-MET-TRP-ASP-ARG-GLY-LEU-GLY-MET-MET


Mass: 1228.551 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 480 / 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: 2.62 Å3/Da / Density % sol: 53.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 18% PEG3350, 0.25 M magnesium chloride, 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 7, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→20 Å / Num. obs: 52057 / % possible obs: 98.8 % / Redundancy: 2.7 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.069 / Rrim(I) all: 0.119 / Χ2: 1.016 / Net I/σ(I): 9.9 / Num. measured all: 141798
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.15-2.232.20.45450550.6880.3780.5941.06396.4
2.23-2.322.40.44751160.7370.3510.5711.01998.3
2.32-2.422.70.44351720.7730.320.5491.01798.6
2.42-2.552.80.37951360.8470.2610.4621.01798.8
2.55-2.712.90.27952030.9140.1910.341.02498.9
2.71-2.922.90.18551990.960.1260.2250.99699
2.92-3.212.90.11452030.9820.0790.1391.0299.2
3.21-3.672.90.07552540.990.0520.0921.00299.5
3.67-4.612.80.04852950.9950.0340.0590.99999.5
4.61-202.80.0454240.9960.0280.0491.0299.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementResolution: 2.151→19.94 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2262 1888 3.85 %
Rwork0.1799 --
obs0.1817 49062 93.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.151→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6527 0 0 480 7007
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036704
X-RAY DIFFRACTIONf_angle_d0.5979100
X-RAY DIFFRACTIONf_dihedral_angle_d18.5212452
X-RAY DIFFRACTIONf_chiral_restr0.043953
X-RAY DIFFRACTIONf_plane_restr0.0041188
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1507-2.20880.30991240.25053143X-RAY DIFFRACTION81
2.2088-2.27370.30491280.23193323X-RAY DIFFRACTION85
2.2737-2.34690.27291440.23453365X-RAY DIFFRACTION87
2.3469-2.43070.29621410.22043418X-RAY DIFFRACTION89
2.4307-2.52780.27061430.20593554X-RAY DIFFRACTION91
2.5278-2.64260.2191440.20713554X-RAY DIFFRACTION92
2.6426-2.78160.24431390.23640X-RAY DIFFRACTION94
2.7816-2.95540.23831500.19563720X-RAY DIFFRACTION96
2.9554-3.18270.22011520.18413778X-RAY DIFFRACTION97
3.1827-3.50140.21631520.17013851X-RAY DIFFRACTION98
3.5014-4.00450.2221540.15263879X-RAY DIFFRACTION99
4.0045-5.03180.16821570.1313938X-RAY DIFFRACTION99
5.0318-19.94060.19251600.1684011X-RAY DIFFRACTION99

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