+Open data
-Basic information
Entry | Database: PDB / ID: 7tug | ||||||
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Title | Crystal structure of Tapasin in complex with PaSta2-Fab | ||||||
Components |
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Keywords | IMMUNE SYSTEM / PaSta / Fab / Antibody / IgG / MHC-I / HLA / peptide loading complex / PLC / antigen presentation / immune response | ||||||
Function / homology | Function and homology information MHC class Ib protein complex assembly / peptide antigen stabilization / Tapasin-ERp57 complex / MHC class I protein complex binding / TAP1 binding / TAP2 binding / regulation of protein complex stability / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / TAP complex binding / MHC class I protein binding ...MHC class Ib protein complex assembly / peptide antigen stabilization / Tapasin-ERp57 complex / MHC class I protein complex binding / TAP1 binding / TAP2 binding / regulation of protein complex stability / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / TAP complex binding / MHC class I protein binding / protein folding chaperone / endoplasmic reticulum-Golgi intermediate compartment membrane / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class I protein complex / MHC class I peptide loading complex / antigen processing and presentation of endogenous peptide antigen via MHC class I / phagocytic vesicle membrane / peptide antigen binding / unfolded protein binding / regulation of gene expression / ER-Phagosome pathway / protein-containing complex assembly / molecular adaptor activity / Golgi membrane / endoplasmic reticulum membrane / endoplasmic reticulum Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å | ||||||
Authors | Jiang, J. / Natarajan, K. / Taylor, D.K. / Boyd, L.F. / Margulies, D.H. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structural mechanism of tapasin-mediated MHC-I peptide loading in antigen presentation. Authors: Jiang, J. / Taylor, D.K. / Kim, E.J. / Boyd, L.F. / Ahmad, J. / Mage, M.G. / Truong, H.V. / Woodward, C.H. / Sgourakis, N.G. / Cresswell, P. / Margulies, D.H. / Natarajan, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tug.cif.gz | 186.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tug.ent.gz | 115.9 KB | Display | PDB format |
PDBx/mmJSON format | 7tug.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tug_validation.pdf.gz | 474.9 KB | Display | wwPDB validaton report |
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Full document | 7tug_full_validation.pdf.gz | 480 KB | Display | |
Data in XML | 7tug_validation.xml.gz | 26.5 KB | Display | |
Data in CIF | 7tug_validation.cif.gz | 35.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tu/7tug ftp://data.pdbj.org/pub/pdb/validation_reports/tu/7tug | HTTPS FTP |
-Related structure data
Related structure data | 7tucC 7tudC 7tueC 7tufC 7tuhC 3f8uS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 44739.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TAPBP, NGS17, TAPA / Plasmid: pET21b / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: O15533 |
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#2: Antibody | Mass: 24792.748 Da / Num. of mol.: 1 / Fragment: Variable and Constant CH1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET21b / Cell line (production host): Expi 293S / Production host: Homo sapiens (human) |
#3: Antibody | Mass: 24278.922 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET21b / Cell line (production host): Expi 293S / Production host: Homo sapiens (human) |
#4: Sugar | ChemComp-NAG / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.22 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 17% PEG 10000, 0.1M Bis-Tris, 0.1M Am Acetate / PH range: 5.5-8.5 |
-Data collection
Diffraction | Mean temperature: 273 K / Ambient temp details: LN blow / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 20, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.9→54.33 Å / Num. obs: 8241 / % possible obs: 95.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 67.65 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.065 / Rrim(I) all: 0.127 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 3.9→4.04 Å / Mean I/σ(I) obs: 0.85 / Num. unique obs: 692 / CC1/2: 0.477 / Rpim(I) all: 0.851 / % possible all: 80.75 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3F8U Resolution: 3.9→54.33 Å / SU ML: 0.6412 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 34.8533 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 78.23 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.9→54.33 Å
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Refine LS restraints |
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LS refinement shell |
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