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Yorodumi- PDB-3ftl: NVGSNTY segment from Islet Amyloid Polypeptide (IAPP or Amylin), ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ftl | ||||||
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Title | NVGSNTY segment from Islet Amyloid Polypeptide (IAPP or Amylin), dehydrated crystal form | ||||||
Components | NVGSNTY heptapeptide segment from Islet Amyloid Polypeptide | ||||||
Keywords | PROTEIN FIBRIL / amyloid-like protofibril / MEMBRANE PROTEIN | ||||||
Function / homology | Function and homology information : / amylin receptor signaling pathway / Calcitonin-like ligand receptors / negative regulation of amyloid fibril formation / negative regulation of bone resorption / eating behavior / negative regulation of osteoclast differentiation / positive regulation of protein kinase A signaling / Regulation of gene expression in beta cells / negative regulation of protein-containing complex assembly ...: / amylin receptor signaling pathway / Calcitonin-like ligand receptors / negative regulation of amyloid fibril formation / negative regulation of bone resorption / eating behavior / negative regulation of osteoclast differentiation / positive regulation of protein kinase A signaling / Regulation of gene expression in beta cells / negative regulation of protein-containing complex assembly / positive regulation of cAMP-mediated signaling / positive regulation of calcium-mediated signaling / bone resorption / sensory perception of pain / osteoclast differentiation / hormone activity / cell-cell signaling / amyloid-beta binding / G alpha (s) signalling events / positive regulation of MAPK cascade / receptor ligand activity / positive regulation of apoptotic process / Amyloid fiber formation / signaling receptor binding / lipid binding / apoptotic process / signal transduction / extracellular space / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å | ||||||
Authors | Wiltzius, J.J.W. / Sawaya, M.R. / Eisenberg, D. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2009 Title: Molecular mechanisms for protein-encoded inheritance Authors: Wiltzius, J.J. / Landau, M. / Nelson, R. / Sawaya, M.R. / Apostol, M.I. / Goldschmidt, L. / Soriaga, A.B. / Cascio, D. / Rajashankar, K. / Eisenberg, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ftl.cif.gz | 10.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ftl.ent.gz | 6.2 KB | Display | PDB format |
PDBx/mmJSON format | 3ftl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ft/3ftl ftp://data.pdbj.org/pub/pdb/validation_reports/ft/3ftl | HTTPS FTP |
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-Related structure data
Related structure data | 3fodC 3fpoC 3fr1C 3fthC 3ftkSC 3ftrC 3fvaC 4np8C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Details | THE AUTHORS STATE THAT THE BIOLOGICAL UNIT IS A INDEFINITELY LONG PAIR OF SHEETS (A PROTOFIBRIL). ONE SHEET FORMED BY CHAIN A AND CRYSTALLOGRAPHIC TRANSLATIONS ALONG THE "B" CELL DIMENSION (E.G. X,Y,Z AND X,Y+1,Z). THE SECOND SHEET IS CONSTRUCTED FROM 1-X, Y+1/2,1-Z AND CRYSTALLOGRAPHIC TRANSLATIONS ALONG THE "B" CELL DIMENSION (E.G. 1-X, Y+3/2,1-Z). A SECOND BIOLOGICAL UNIT, SIMILAR TO THE FIRST, IS AN INDEFINITELY LONG PAIR OF SHEETS. ONE SHEET FORMED BY CHAIN B AND CRYSTALLOGRAPHIC TRANSLATIONS ALONG THE "B" CELL DIMENSION (E.G. X,Y,Z AND X,Y+1,Z). THE SECOND SHEET IS CONSTRUCTED FROM -X, Y+1/2,-Z AND CRYSTALLOGRAPHIC TRANSLATIONS ALONG THE "B" CELL DIMENSION (E.G. -X, Y+3/2,-Z). |
-Components
#1: Protein/peptide | Mass: 753.759 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10997*PLUS #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES pH 7.5, 25% PEG 3350, vapor diffusion, hanging drop, temperature 298K |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 8, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→90 Å / Num. all: 1103 / Num. obs: 1103 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 12 Å2 / Rmerge(I) obs: 0.155 / Χ2: 1.005 |
Reflection shell | Resolution: 1.6→1.72 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.7 / Num. unique all: 187 / Χ2: 1.045 / % possible all: 94 |
-Phasing
Phasing | Method: molecular replacement |
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Phasing MR | Model details: Phaser MODE: MR_AUTO |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3FTK Resolution: 1.6→28.51 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.975 / WRfactor Rfree: 0.155 / WRfactor Rwork: 0.117 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.907 / SU B: 1.143 / SU ML: 0.039 / SU R Cruickshank DPI: 0.093 / SU Rfree: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.089 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 40.33 Å2 / Biso mean: 2.75 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→28.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.784 Å / Total num. of bins used: 5
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