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- PDB-1hsb: DIFFERENT LENGTH PEPTIDES BIND TO HLA-AW68 SIMILARLY AT THEIR END... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1hsb | ||||||
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Title | DIFFERENT LENGTH PEPTIDES BIND TO HLA-AW68 SIMILARLY AT THEIR ENDS BUT BULGE OUT IN THE MIDDLE | ||||||
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![]() | IMMUNE SYSTEM / HISTOCOMPATIBILITY ANTIGEN | ||||||
Function / homology | ![]() T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / 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 / endoplasmic reticulum exit site ...T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / 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 / 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 / beta-2-microglobulin binding / T cell receptor binding / detection of bacterium / positive regulation of ferrous iron binding / positive regulation of transferrin 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 / 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 / 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 / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / 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 / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of type II interferon production / peptide antigen binding / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / E3 ubiquitin ligases ubiquitinate target proteins / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / iron ion transport / antibacterial humoral response / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / lysosomal membrane / innate immune response / signaling receptor binding / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Guo, H.-C. / Strominger, J.L. / Wiley, D.C. | ||||||
![]() | ![]() Title: Different length peptides bind to HLA-Aw68 similarly at their ends but bulge out in the middle. Authors: Guo, H.C. / Jardetzky, T.S. / Garrett, T.P. / Lane, W.S. / Strominger, J.L. / Wiley, D.C. #1: ![]() Title: Comparison of a Specificity Pocket in Three Human Histocompatibility Antigens: Hla-Aw68, Hla-A2 and Hla-B27 Authors: Guo, H.-C. / Madden, D.R. / Strominger, J.L. / Wiley, D.C. #2: ![]() Title: Different Length Peptides Bind to Hla-Aw68 Similarly at Their Ends But Bulge Out in the Middle Authors: Guo, H.-C. / Jardetzky, T.S. / Garrett, T.P.J. / Lane, W.S. / Strominger, J.L. / Wiley, D.C. #3: ![]() Title: Atomic Structure of a Human Mhc Molecule Presenting an Influenza Virus Peptide Authors: Silver, M.L. / Guo, H.-C. / Strominger, J.L. / Wiley, D.C. #4: ![]() Title: The Three-Dimensional Structure of Hla-B27 at 2.1 Angstroms Resolution Suggests a General Mechanism for Tight Peptide Binding to Mhc Authors: Madden, D.R. / Gorga, J.C. / Strominger, J.L. / Wiley, D.C. #5: ![]() Title: Refined Structure of the Human Histocompatibility Antigen Hla-A2 at 2.6 Angstroms Resolution Authors: Saper, M.A. / Bjorkman, P.J. / Wiley, D.C. #6: ![]() Title: The Structure of Hla-B27 Reveals Nonamer Self-Peptides Bound in an Extended Conformation Authors: Madden, D.R. / Gorga, J.C. / Strominger, J.L. / Wiley, D.C. #7: ![]() Title: Specificity Pockets for the Side Chains of Peptide Antigens in Hla-Aw68 Authors: Garrett, T.P.J. / Saper, M.A. / Bjorkman, P.J. / Strominger, J.L. / Wiley, D.C. #8: ![]() Title: Structure of the Human Class I Histocompatibility Antigen, Hla-A2 Authors: Bjorkman, P.J. / Saper, M.A. / Samraoui, B. / Bennett, W.S. / Strominger, J.L. / Wiley, D.C. #9: ![]() Title: The Foreign Antigen Binding Site and T Cell Recognition Regions of Class I Histocompatibility Antigens Authors: Bjorkman, P.J. / Saper, M.A. / Samraoui, B. / Bennett, W.S. / Strominger, J.L. / Wiley, D.C. #10: ![]() Title: Crystallization and X-Ray Diffraction Studies on the Histocompatibility Antigens Hla-A2 and Hla-A28 from Human Cell Membranes Authors: Bjorkman, P.J. / Strominger, J.L. / Wiley, D.C. | ||||||
History |
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Remark 700 | SHEET SHEETS 2 AND 4 EACH HAVE ONE STRAND THAT IS BIFURCATED. THIS IS REPRESENTED BY PRESENTING THE ...SHEET SHEETS 2 AND 4 EACH HAVE ONE STRAND THAT IS BIFURCATED. THIS IS REPRESENTED BY PRESENTING THE SHEETS TWICE (DESIGNATED SHEETS SB1, SB2 AND SD1, SD2 RESPECTIVELY) WHERE THE TWO REPRESENTATIONS DIFFER IN THEIR LAST STRAND. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 95.7 KB | Display | ![]() |
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PDB format | ![]() | 72.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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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Atom site foot note | 1: SIDE CHAIN ATOMS OF GLU A 58, GLU A 89, ASP A 106, ARG A 108, GLN A 115, GLU A 128, HIS A 151, ASP A 196, GLN A 255, ASP B 34, GLU B 36, LYS B 41, GLU B 44, GLU B 47, LYS B 48, LYS B 58, GLU B 69, ...1: SIDE CHAIN ATOMS OF GLU A 58, GLU A 89, ASP A 106, ARG A 108, GLN A 115, GLU A 128, HIS A 151, ASP A 196, GLN A 255, ASP B 34, GLU B 36, LYS B 41, GLU B 44, GLU B 47, LYS B 48, LYS B 58, GLU B 69, LYS B 75, GLU B 77, ASN B 83, GLN B 89, AND LYS B 94 ARE DISORDERED AND HAVE OCCUPANCIES EQUAL TO 0.01 IN THIS ENTRY. 2: RESIDUES PRO A 210 AND PRO B 32 ARE CIS PROLINES. 3: LYS A 268, PRO A 269, AND LEU A 270 ARE DISORDERED, AND HAVE OCCUPANCIES EQUAL TO 0.01 IN THIS ENTRY. 4: THESE SOLVENT MOLECULES ARE LOCATED WITHIN THE PEPTIDE-BINDING SITE OF HLA-AW68. | ||||||||
Details | THERE IS ONE COMPLEX PER ASYMMETRIC UNIT, WHICH COMPOSED OF FOUR POLYPEPTIDE CHAINS: HLA HEAVY CHAIN IDENTIFIED AS CHAIN *A* IN THIS ENTRY, BETA-2-MICROGLOBULIN IDENTIFIED AS CHAIN *B*, A MODEL OF BOUND N-TERMINAL TRI-PEPTIDE IDENTIFIED AS CHAIN *C*, A MODEL OF BOUND C-TERMINAL DI-PEPTIDE REPORTED AS RESIDUES 1001 AND 1002 IN THE ENTRY. |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 31151.334 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Protein | Mass: 11748.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 259.302 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
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-Non-polymers , 3 types, 272 molecules ![](data/chem/img/ALA.gif)
![](data/chem/img/ARG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ARG.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-ALA / |
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#5: Chemical | ChemComp-ARG / |
#6: Water | ChemComp-HOH / |
-Details
Compound details | SECONDARY STRUCTURE SPECIFICATIONS WERE MADE BY USE OF THE PROCEDURE OF W. KABSCH AND C. SANDER ...SECONDARY STRUCTURE SPECIFICAT |
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Nonpolymer details | THE RESIDUES 1001 AND 1002 REPRESENT THE BOUND, C-TERMINAL DIPEPTIDE (ALA-ARG) |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 59.06 % | ||||||||||||||||||||||||
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Crystal grow | *PLUS Method: vapor diffusion / Details: referred to J.Mol.Biol. 186.205-210 1985 / PH range low: 6.5 / PH range high: 6.2 | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.9 Å / Rmerge(I) obs: 0.073 |
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Processing
Software |
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Refinement | Rfactor Rwork: 0.22 / Rfactor obs: 0.22 / Highest resolution: 1.9 Å Details: LYS A 268, PRO A 269, AND LEU A 270 ARE DISORDERED, AND HAVE OCCUPANCIES EQUAL TO 0.01 IN THIS ENTRY | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.9 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 5.5 Å / σ(F): 3 / Rfactor obs: 0.22 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3.1 |