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Yorodumi- PDB-5e6r: Structures of leukocyte integrin aLb2: The aI domain, the headpie... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5e6r | ||||||
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Title | Structures of leukocyte integrin aLb2: The aI domain, the headpiece, and the pocket for the internal ligand | ||||||
Components |
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Keywords | CELL ADHESION / lymphocyte function-associated antigen-1 / LFA-1 | ||||||
Function / homology | Function and homology information integrin alphaX-beta2 complex / integrin alphaM-beta2 complex / positive regulation of prostaglandin-E synthase activity / memory T cell extravasation / positive regulation of neutrophil degranulation / integrin alphaL-beta2 complex / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / ICAM-3 receptor activity / complement component C3b binding / neutrophil migration ...integrin alphaX-beta2 complex / integrin alphaM-beta2 complex / positive regulation of prostaglandin-E synthase activity / memory T cell extravasation / positive regulation of neutrophil degranulation / integrin alphaL-beta2 complex / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / ICAM-3 receptor activity / complement component C3b binding / neutrophil migration / Toll Like Receptor 4 (TLR4) Cascade / negative regulation of dopamine metabolic process / cell-cell adhesion via plasma-membrane adhesion molecules / RUNX3 Regulates Immune Response and Cell Migration / heterotypic cell-cell adhesion / integrin complex / positive regulation of leukocyte adhesion to vascular endothelial cell / cell adhesion mediated by integrin / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / phagocytosis, engulfment / leukocyte cell-cell adhesion / receptor clustering / amyloid-beta clearance / endodermal cell differentiation / plasma membrane raft / tertiary granule membrane / ficolin-1-rich granule membrane / cellular response to low-density lipoprotein particle stimulus / positive regulation of protein targeting to membrane / Integrin cell surface interactions / specific granule membrane / phagocytosis / regulation of peptidyl-tyrosine phosphorylation / heat shock protein binding / receptor-mediated endocytosis / cell adhesion molecule binding / cell-matrix adhesion / neutrophil chemotaxis / positive regulation of superoxide anion generation / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / microglial cell activation / receptor internalization / cell-cell adhesion / extracellular vesicle / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / integrin binding / cell-cell signaling / amyloid-beta binding / regulation of cell shape / Interleukin-4 and Interleukin-13 signaling / receptor complex / cell adhesion / inflammatory response / external side of plasma membrane / focal adhesion / apoptotic process / Neutrophil degranulation / protein kinase binding / cell surface / signal transduction / extracellular exosome / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.901 Å | ||||||
Authors | Sen, M. / Springer, T.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 Title: Leukocyte integrin alpha L beta 2 headpiece structures: The alpha I domain, the pocket for the internal ligand, and concerted movements of its loops. Authors: Sen, M. / Springer, T.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5e6r.cif.gz | 428.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e6r.ent.gz | 350.1 KB | Display | PDB format |
PDBx/mmJSON format | 5e6r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e6/5e6r ftp://data.pdbj.org/pub/pdb/validation_reports/e6/5e6r | HTTPS FTP |
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-Related structure data
Related structure data | 5e6sC 5e6uC 5e6vC 5e6wC 5e6xC 5es4C 4nehS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 87841.086 Da / Num. of mol.: 1 / Fragment: UNP residues 26-615 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ITGAL, CD11A / Cell line (production host): HEK / Production host: Homo sapiens (human) / References: UniProt: P20701 |
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#2: Protein | Mass: 56899.809 Da / Num. of mol.: 1 / Fragment: UNP residues 23-482 / Mutation: N232R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB2, CD18, MFI7 / Cell line (production host): HEK / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: P05107 |
-Sugars , 1 types, 4 molecules
#5: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 211 molecules
#3: Chemical | ChemComp-MG / | ||
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#4: Chemical | ChemComp-CA / #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.3 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES pH 6.5, 15% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03321 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 7, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03321 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 33981 / % possible obs: 99.9 % / Redundancy: 3.11 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 9.47 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4neh Resolution: 2.901→46.242 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 24.7 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.901→46.242 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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