+Open data
-Basic information
Entry | Database: PDB / ID: 7t2a | ||||||
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Title | Crystal structure of HLA-DP4 in complex with Ply | ||||||
Components |
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Keywords | IMMUNE SYSTEM / pHLA complex | ||||||
Function / homology | Function and homology information MHC class II receptor activity / transport vesicle membrane / cholesterol binding / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Generation of second messenger molecules / PD-1 signaling / positive regulation of T cell proliferation / MHC class II antigen presentation / trans-Golgi network membrane ...MHC class II receptor activity / transport vesicle membrane / cholesterol binding / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Generation of second messenger molecules / PD-1 signaling / positive regulation of T cell proliferation / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / cellular response to type II interferon / 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 / endocytic vesicle membrane / Interferon gamma signaling / positive regulation of immune response / positive regulation of type II interferon production / Downstream TCR signaling / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / toxin activity / adaptive immune response / killing of cells of another organism / immune response / lysosomal membrane / Golgi membrane / intracellular membrane-bounded organelle / host cell plasma membrane / cell surface / extracellular region / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.04 Å | ||||||
Authors | Ciacchi, L. / Farenc, C. / Petersen, J. / Reid, H.H. / Rossjohn, J. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Immunity / Year: 2023 Title: CD4 + T cell-mediated recognition of a conserved cholesterol-dependent cytolysin epitope generates broad antibacterial immunity. Authors: Ciacchi, L. / van de Garde, M.D.B. / Ladell, K. / Farenc, C. / Poelen, M.C.M. / Miners, K.L. / Llerena, C. / Reid, H.H. / Petersen, J. / Price, D.A. / Rossjohn, J. / van Els, C.A.C.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7t2a.cif.gz | 320.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7t2a.ent.gz | 261.3 KB | Display | PDB format |
PDBx/mmJSON format | 7t2a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7t2a_validation.pdf.gz | 491.1 KB | Display | wwPDB validaton report |
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Full document | 7t2a_full_validation.pdf.gz | 498.5 KB | Display | |
Data in XML | 7t2a_validation.xml.gz | 27.2 KB | Display | |
Data in CIF | 7t2a_validation.cif.gz | 36 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t2/7t2a ftp://data.pdbj.org/pub/pdb/validation_reports/t2/7t2a | HTTPS FTP |
-Related structure data
Related structure data | 7t2bC 7t2cC 7t2dC 4p5kS S: Starting model for refinement C: citing same article (ref.) |
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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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 20943.336 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DPA1, HLA-DP1A, HLASB / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P20036 #2: Protein | Mass: 21916.570 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DPB1, HLA-DP1B / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P04440 #3: Protein/peptide | Mass: 1825.995 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: ply, SPD_1726 / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q04IN8 #4: Sugar | ChemComp-NAG / Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.79 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: Sodium chloride, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 16, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 3→38.4 Å / Num. obs: 22483 / % possible obs: 99.8 % / Redundancy: 2 % / CC1/2: 0.996 / Net I/σ(I): 8 |
Reflection shell | Resolution: 3→3.1 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2197 / CC1/2: 0.661 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4P5K Resolution: 3.04→38.4 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.65 / Stereochemistry target values: ML
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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 max: 177.42 Å2 / Biso mean: 82.0719 Å2 / Biso min: 48.64 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.04→38.4 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: -24.7614 Å / Origin y: -23.275 Å / Origin z: -27.1993 Å
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Refinement TLS group |
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