+Open data
-Basic information
Entry | Database: PDB / ID: 1w72 | ||||||
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Title | Crystal structure of HLA-A1:MAGE-A1 in complex with Fab-Hyb3 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / HLA/FAB FRAGMENT / HUMAN LEUCOCYTE ANTIGEN / PEPTIDE-SPECIFIC FAB / TCR-LIKE BINDING / MHC-I | ||||||
Function / homology | Function and homology information peptide antigen assembly with MHC class I protein complex / negative regulation of Notch signaling pathway / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation ...peptide antigen assembly with MHC class I protein complex / negative regulation of Notch signaling pathway / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / 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 / endoplasmic reticulum exit site / beta-2-microglobulin binding / 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 ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / histone deacetylase binding / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / 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 / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / positive regulation of type II interferon production / sensory perception of smell / negative regulation of neuron projection development / E3 ubiquitin ligases ubiquitinate target proteins / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / Golgi apparatus / negative regulation of transcription by RNA polymerase II Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Hulsmeyer, M. / Chames, P. / Hillig, R.C. / Stanfield, R.L. / Held, G. / Coulie, P.G. / Alings, C. / Wille, G. / Saenger, W. / Uchanska-Ziegler, B. ...Hulsmeyer, M. / Chames, P. / Hillig, R.C. / Stanfield, R.L. / Held, G. / Coulie, P.G. / Alings, C. / Wille, G. / Saenger, W. / Uchanska-Ziegler, B. / Hoogenboom, H.R. / Ziegler, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: A Major Histocompatibility Complex.Peptide- Restricted Antibody and T Cell Receptor Molecules Recognize Their Target by Distinct Binding Modes: Crystal Structure of Human Leukocyte Antigen ...Title: A Major Histocompatibility Complex.Peptide- Restricted Antibody and T Cell Receptor Molecules Recognize Their Target by Distinct Binding Modes: Crystal Structure of Human Leukocyte Antigen (Hla)-A1.Mage-A1 in Complex with Fab-Hyb3 Authors: Hulsmeyer, M. / Chames, P. / Hillig, R.C. / Stanfield, R.L. / Held, G. / Coulie, P.G. / Alings, C. / Wille, G. / Saenger, W. / Uchanska-Ziegler, B. / Hoogenboom, H.R. / Ziegler, A. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 Title: Direct Selection of a Human Antibody Fragment Directed Against the Tumor T-Cell Epitope Hla-A1- Mage-A1 from a Nonimmunized Phage-Fab Library Authors: Chames, P. / Hufton, S.E. / Coulie, P.G. / Uchanska-Ziegler, B. / Hoogenboom, H.R. #2: Journal: J.Immunol. / Year: 2002 Title: Tcr-Like Human Antibodies Expressed on Human Ctls Mediate Antibody Affinity-Dependent Cytolytic Activity Authors: Chames, P. / Willemsen, R.A. / Rojas, G. / Dieckmann, D. / Rem, L. / Schuler, G. / Bolhuis, R.L. / Hoogenboom, H.R. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1w72.cif.gz | 337.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w72.ent.gz | 274.4 KB | Display | PDB format |
PDBx/mmJSON format | 1w72.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w7/1w72 ftp://data.pdbj.org/pub/pdb/validation_reports/w7/1w72 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | SUBUNIT: DIMER OF ALPHA CHAIN AND A BETA CHAIN(BETA-2-MICROGLOBULIN). |
-Components
-Protein , 2 types, 4 molecules ADBE
#1: Protein | Mass: 31636.955 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 25-298 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P30443, UniProt: P04439*PLUS #2: Protein | Mass: 11879.356 Da / Num. of mol.: 2 / Fragment: RESIDUES 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P61769 |
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-Protein/peptide , 1 types, 2 molecules CF
#3: Protein/peptide | Mass: 976.964 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P43355 |
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-Antibody , 2 types, 4 molecules HILM
#4: Antibody | Mass: 23845.672 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT, RESIDUES 1-211 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) #5: Antibody | Mass: 22523.867 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT, RESIDUES 1-228 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) |
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-Non-polymers , 2 types, 657 molecules
#6: Chemical | ChemComp-GOL / #7: Water | ChemComp-HOH / | |
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-Details
Compound details | INVOLVED IN THE PRESENTATION OF FOREIGN ANTIGENS TO THE IMMUNE SYSTEM. BETA-2-MICROGLOBULIN IS THE ...INVOLVED IN THE PRESENTATI |
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Sequence details | N-TERMINAL MET IS A CLONING ARTIFACT FRAGMENT. THE NUMBERING IN CHAINS L,M,H AND I FOLLOW THE ...N-TERMINAL MET IS A CLONING ARTIFACT FRAGMENT. THE NUMBERING IN CHAINS L,M,H AND I FOLLOW THE STANDARD KABAT NUMBERING SCHEME. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 42 % Description: A DATABASE OF 125 ANTIBODIES WAS USED AS SEARCH MODELS |
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Crystal grow | pH: 6.5 / Details: MES PH 6.5, NACL 600MM, 19% PEG3350, 80MM DIOXANE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 14, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→30 Å / Num. obs: 78453 / % possible obs: 90 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2.3 / % possible all: 90 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1DUZ, 7FAB, 2GFB, 2FB4 Resolution: 2.15→120 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.908 / SU B: 12.789 / SU ML: 0.173 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.335 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.22 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→120 Å
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Refine LS restraints |
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