+
Open data
-
Basic information
Entry | Database: PDB / ID: 7tug | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Tapasin in complex with PaSta2-Fab | ||||||
![]() |
| ||||||
![]() | IMMUNE SYSTEM / PaSta / Fab / Antibody / IgG / MHC-I / HLA / peptide loading complex / PLC / antigen presentation / immune response | ||||||
Function / homology | ![]() 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 / ER-Phagosome pathway / regulation of gene expression / protein-containing complex assembly / molecular adaptor activity / Golgi membrane / endoplasmic reticulum membrane / endoplasmic reticulum Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jiang, J. / Natarajan, K. / Taylor, D.K. / Boyd, L.F. / Margulies, D.H. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 186.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 115.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 474.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 480 KB | Display | |
Data in XML | ![]() | 26.5 KB | Display | |
Data in CIF | ![]() | 35.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7tucC ![]() 7tudC ![]() 7tueC ![]() 7tufC ![]() 7tuhC ![]() 3f8uS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 44739.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#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.) ![]() ![]() ![]() |
#3: Antibody | Mass: 24278.922 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#4: Sugar | ChemComp-NAG / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.22 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
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 |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() 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
| ||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||
LS refinement shell |
|