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Open data
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Basic information
Entry | Database: PDB / ID: 1iao | ||||||
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Title | CLASS II MHC I-AD IN COMPLEX WITH OVALBUMIN PEPTIDE 323-339 | ||||||
![]() | (MHC CLASS II I-AD) x 2 | ||||||
![]() | MHC II / CLASS II MHC / I-A / OVALBUMIN PEPTIDE | ||||||
Function / homology | ![]() Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / PD-1 signaling / Generation of second messenger molecules / Downstream TCR signaling / antigen processing and presentation of peptide antigen / MHC class II antigen presentation / positive regulation of T cell differentiation / antigen processing and presentation / negative regulation of T cell proliferation ...Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / PD-1 signaling / Generation of second messenger molecules / Downstream TCR signaling / antigen processing and presentation of peptide antigen / MHC class II antigen presentation / positive regulation of T cell differentiation / antigen processing and presentation / negative regulation of T cell proliferation / multivesicular body / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / adaptive immune response / early endosome / lysosome / immune response / external side of plasma membrane / lysosomal membrane / protein-containing complex binding / Golgi apparatus / cell surface / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Scott, C.A. / Peterson, P.A. / Teyton, L. / Wilson, I.A. | ||||||
![]() | ![]() Title: Crystal structures of two I-Ad-peptide complexes reveal that high affinity can be achieved without large anchor residues. Authors: Scott, C.A. / Peterson, P.A. / Teyton, L. / Wilson, I.A. #1: ![]() Title: Erratum. Crystal Structures of Two I-Ad-Peptide Complexes Reveal that High Affinity Can be Achieved without Large Anchor Residues Authors: Scott, C.A. / Peterson, P.A. / Teyton, L. / Wilson, I.A. #2: ![]() Title: Engineering Protein for X-Ray Crystallography: The Murine Major Histocompatibility Complex Class II Molecule I-Ad Authors: Scott, C.A. / Garcia, K.C. / Stura, E.A. / Peterson, P.A. / Wilson, I.A. / Teyton, L. #3: ![]() Title: Role of Chain Pairing for the Production of Functional Soluble Ia Major Histocompatibility Complex Class II Molecules Authors: Scott, C.A. / Garcia, K.C. / Carbone, F.R. / Wilson, I.A. / Teyton, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 86.6 KB | Display | ![]() |
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PDB format | ![]() | 67.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2iadC ![]() 1dlhS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 22091.631 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: BOTH THE A AND B CHAINS HAVE AN 8-RESIDUE (SSADLVPR) PEPTIDE BOUND TO THE C-TERMINUS. THE B CHAIN ALSO HAS A 24-RESIDUE PEPTIDE CONSISTING OF A 2-RESIDUE (RG) SIGNAL SEQUENCE, RESIDUES 323 - ...Details: BOTH THE A AND B CHAINS HAVE AN 8-RESIDUE (SSADLVPR) PEPTIDE BOUND TO THE C-TERMINUS. THE B CHAIN ALSO HAS A 24-RESIDUE PEPTIDE CONSISTING OF A 2-RESIDUE (RG) SIGNAL SEQUENCE, RESIDUES 323 - 339 OF HEN EGG OVALBUMIN AND A 6-RESIDUE (GSGSGS) LINKER, COVALENTLY BONDED TO THE N-TERMINUS. Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 25324.998 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: BOTH THE A AND B CHAINS HAVE AN 8-RESIDUE (SSADLVPR) PEPTIDE BOUND TO THE C-TERMINUS. THE B CHAIN ALSO HAS A 24-RESIDUE PEPTIDE CONSISTING OF A 2-RESIDUE (RG) SIGNAL SEQUENCE, RESIDUES 323 - ...Details: BOTH THE A AND B CHAINS HAVE AN 8-RESIDUE (SSADLVPR) PEPTIDE BOUND TO THE C-TERMINUS. THE B CHAIN ALSO HAS A 24-RESIDUE PEPTIDE CONSISTING OF A 2-RESIDUE (RG) SIGNAL SEQUENCE, RESIDUES 323 - 339 OF HEN EGG OVALBUMIN AND A 6-RESIDUE (GSGSGS) LINKER, COVALENTLY BONDED TO THE N-TERMINUS. Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Sugar | ChemComp-NAG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 56 % | ||||||||||||||||||||
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Crystal grow | pH: 5.5 / Details: 32% PEG 600, 0.1 IMIDAZOLE MALATE, PH 5.5 | ||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / Method: vapor diffusion, sitting drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1997 Details: 58 CM LONG, PT-COATED, FUSED SILICA, VERTICAL FOCUS |
Radiation | Monochromator: CYLINDRICALLY BENT TRIANGULAR SI(111) ASYMMETRIC CUT, HORIZONTAL FOCUS Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→27 Å / Num. obs: 14777 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 9 % / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.6→2.7 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 2 / Rsym value: 0.383 / % possible all: 91 |
Reflection shell | *PLUS % possible obs: 91 % / Num. unique obs: 1690 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1DLH Resolution: 2.6→27 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.01 / σ(F): 0
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Displacement parameters | Biso mean: 51 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.72 Å / Total num. of bins used: 8
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.32 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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