+Open data
-Basic information
Entry | Database: PDB / ID: 2g2b | ||||||
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Title | NMR structure of the human allograft inflammatory factor 1 | ||||||
Components | Allograft inflammatory factor 1 | ||||||
Keywords | IMMUNE SYSTEM / AIF-1 / Allograft Inflammatory Factor 1 / Structural Genomics / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG | ||||||
Function / homology | Function and homology information negative regulation of smooth muscle cell chemotaxis / positive regulation of smooth muscle cell chemotaxis / parallel actin filament bundle assembly / positive regulation of fibroblast growth factor production / actin crosslink formation / ruffle assembly / positive regulation of chemotaxis / positive regulation of mononuclear cell migration / positive regulation of monocyte chemotaxis / phagocytosis, engulfment ...negative regulation of smooth muscle cell chemotaxis / positive regulation of smooth muscle cell chemotaxis / parallel actin filament bundle assembly / positive regulation of fibroblast growth factor production / actin crosslink formation / ruffle assembly / positive regulation of chemotaxis / positive regulation of mononuclear cell migration / positive regulation of monocyte chemotaxis / phagocytosis, engulfment / Rac protein signal transduction / glial cell projection / actin filament bundle assembly / phagocytic cup / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of T cell migration / positive regulation of chemokine production / ruffle / positive regulation of T cell proliferation / actin filament polymerization / actin filament / negative regulation of smooth muscle cell proliferation / microglial cell activation / positive regulation of smooth muscle cell proliferation / cellular response to type II interferon / positive regulation of interleukin-6 production / ruffle membrane / actin filament binding / lamellipodium / cellular response to oxidative stress / regulation of gene expression / positive regulation of cell migration / inflammatory response / calcium ion binding / positive regulation of cell population proliferation / perinuclear region of cytoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics,simulated annealing,distance geometry | ||||||
Authors | Song, J. / Tyler, R.C. / Newman, C.L. / Vinarov, D. / Markley, J.L. / Center for Eukaryotic Structural Genomics (CESG) | ||||||
Citation | Journal: To be published Title: NMR structure of the human allograft inflammatory factor 1 Authors: Song, J. / Tyler, R.C. / Newman, C.L. / Vinarov, D. / Markley, J.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2g2b.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2g2b.ent.gz | 889.9 KB | Display | PDB format |
PDBx/mmJSON format | 2g2b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/2g2b ftp://data.pdbj.org/pub/pdb/validation_reports/g2/2g2b | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 16994.590 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: WHEAT GERM CELL-FREE, IN VITRO EXPRESSION / Gene: AIF1, G1, IBA1 / Plasmid: pEU-HIS / Production host: CELL-FREE SYNTHESIS (others) / References: UniProt: P55008 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 10 mM MOPS,100mM NaCl, 5 mM DTT, 0.7 mM 13C,15N-LABELED AIF1_HUMAN Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 100 mM NaCl / pH: 7.0 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | ||||||||||||||||||||
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Radiation wavelength | Relative weight: 1 | ||||||||||||||||||||
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics,simulated annealing,distance geometry Software ordinal: 1 Details: STRUCTURES ARE BASED ON A TOTAL OF 2152 NOE RESTRAINTS (797 INTRA, 462 SEQUENTIAL, 431 MEDIUM, AND 381 LONG RANGE INTERMOLECULR), 81 HBOND RESTRAINTS, AND 162 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 |