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Yorodumi- PDB-8voh: HADDOCK models of human alphaM I-domain bound to the the N-termin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8voh | |||||||||
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Title | HADDOCK models of human alphaM I-domain bound to the the N-terminal domain of the cytokine pleiotrophin | |||||||||
Components |
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Keywords | CELL ADHESION / integrin / Mac-1 / pleiotrophin | |||||||||
Function / homology | Function and homology information dendrite regeneration / ossification involved in bone remodeling / ectodermal cell differentiation / cell surface receptor protein tyrosine phosphatase signaling pathway / leukocyte chemotaxis involved in inflammatory response / integrin alphaM-beta2 complex / positive regulation of prostaglandin-E synthase activity / response to curcumin / positive regulation of neutrophil degranulation / chondroitin sulfate binding ...dendrite regeneration / ossification involved in bone remodeling / ectodermal cell differentiation / cell surface receptor protein tyrosine phosphatase signaling pathway / leukocyte chemotaxis involved in inflammatory response / integrin alphaM-beta2 complex / positive regulation of prostaglandin-E synthase activity / response to curcumin / positive regulation of neutrophil degranulation / chondroitin sulfate binding / response to Gram-positive bacterium / positive regulation of microglial cell mediated cytotoxicity / regulation of stem cell population maintenance / regulation of endothelial cell migration / dendrite arborization / positive regulation of stem cell differentiation / complement component C3b binding / response to auditory stimulus / vertebrate eye-specific patterning / complement-mediated synapse pruning / Toll Like Receptor 4 (TLR4) Cascade / negative regulation of dopamine metabolic process / cell-cell adhesion via plasma-membrane adhesion molecules / tissue regeneration / complement receptor mediated signaling pathway / positive regulation of ossification / positive regulation of hepatocyte proliferation / positive regulation of dendrite development / heterotypic cell-cell adhesion / integrin complex / cargo receptor activity / positive regulation of leukocyte chemotaxis / protein phosphatase inhibitor activity / regulation of myelination / negative regulation of neuroblast proliferation / cell adhesion mediated by integrin / regulation of hemopoiesis / phagocytosis, engulfment / oogenesis / positive regulation of oligodendrocyte differentiation / Signaling by ALK / positive regulation of axon regeneration / bone mineralization / amyloid-beta clearance / receptor clustering / plasma membrane raft / tertiary granule membrane / positive regulation of cell division / decidualization / negative regulation of long-term synaptic potentiation / estrous cycle / positive regulation of protein targeting to membrane / Integrin cell surface interactions / positive regulation of bone mineralization / specific granule membrane / response to mechanical stimulus / forebrain development / heat shock protein binding / receptor-mediated endocytosis / cell-matrix adhesion / positive regulation of superoxide anion generation / learning / molecular function activator activity / integrin-mediated signaling pathway / response to ischemia / Cell surface interactions at the vascular wall / microglial cell activation / growth factor activity / Schaffer collateral - CA1 synapse / regulation of synaptic plasticity / memory / positive regulation of neuron projection development / cell-cell adhesion / integrin binding / response to estradiol / heparin binding / nervous system development / amyloid-beta binding / carbohydrate binding / Interleukin-4 and Interleukin-13 signaling / cell adhesion / external side of plasma membrane / innate immune response / Neutrophil degranulation / positive regulation of cell population proliferation / protein kinase binding / cell surface / endoplasmic reticulum / protein-containing complex / extracellular space / extracellular exosome / extracellular region / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | SOLUTION NMR / simulated annealing | |||||||||
Authors | Wang, X. / Nguyen, H. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published Title: NMR structure of alphaM I-domain of integrin Mac-1 in complex with the Cytokine Pleiotrophin Authors: Wang, X. / Nguyen, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8voh.cif.gz | 787.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8voh.ent.gz | 656.8 KB | Display | PDB format |
PDBx/mmJSON format | 8voh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vo/8voh ftp://data.pdbj.org/pub/pdb/validation_reports/vo/8voh | HTTPS FTP |
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-Related structure data
Related structure data | 8voiC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 22238.340 Da / Num. of mol.: 1 / Fragment: I-domain, residues 147-340 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ITGAM, CD11B, CR3A / Production host: Escherichia coli (E. coli) / References: UniProt: P11215 |
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#2: Protein | Mass: 6431.449 Da / Num. of mol.: 1 / Fragment: N-terminal domain, residues 33-90 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTN, HBNF1, NEGF1 / Production host: Escherichia coli (E. coli) / References: UniProt: P21246 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 0.1 M / Ionic strength err: 0.01 / Label: HEPES / pH: 7 / PH err: 0.1 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 298 K / Temperature err: 0.1 |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE III HD / Manufacturer: Bruker / Model: AVANCE III HD / Field strength: 850 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 2 Details: The Integrin alpha-M starting structure is 1JLM. The Pleiotrophin starting structure is 2N6F. | |||||||||
NMR representative | Selection criteria: target function | |||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 10 |