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Yorodumi- PDB-7bg0: Fusion of MBP and the backbone of the long-acting amylin analog AM833. -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bg0 | ||||||
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Title | Fusion of MBP and the backbone of the long-acting amylin analog AM833. | ||||||
Components | Maltose/maltodextrin-binding periplasmic protein,Islet amyloid polypeptide | ||||||
Keywords | HORMONE / Amylin / AM833 / cagrilintide | ||||||
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 / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport ...: / amylin receptor signaling pathway / Calcitonin-like ligand receptors / negative regulation of amyloid fibril formation / negative regulation of bone resorption / eating behavior / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / negative regulation of osteoclast differentiation / positive regulation of protein kinase A signaling / Regulation of gene expression in beta cells / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / 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 / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / osteoclast differentiation / hormone activity / cell-cell signaling / outer membrane-bounded periplasmic space / amyloid-beta binding / G alpha (s) signalling events / positive regulation of MAPK cascade / receptor ligand activity / periplasmic space / positive regulation of apoptotic process / Amyloid fiber formation / signaling receptor binding / lipid binding / apoptotic process / DNA damage response / signal transduction / extracellular space / extracellular region / membrane / identical protein binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.89 Å | ||||||
Authors | Johansson, E. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2021 Title: Development of Cagrilintide, a Long-Acting Amylin Analogue. Authors: Kruse, T. / Hansen, J.L. / Dahl, K. / Schaffer, L. / Sensfuss, U. / Poulsen, C. / Schlein, M. / Hansen, A.M.K. / Jeppesen, C.B. / Dornonville de la Cour, C. / Clausen, T.R. / Johansson, E. / ...Authors: Kruse, T. / Hansen, J.L. / Dahl, K. / Schaffer, L. / Sensfuss, U. / Poulsen, C. / Schlein, M. / Hansen, A.M.K. / Jeppesen, C.B. / Dornonville de la Cour, C. / Clausen, T.R. / Johansson, E. / Fulle, S. / Skyggebjerg, R.B. / Raun, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bg0.cif.gz | 369.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bg0.ent.gz | 243.8 KB | Display | PDB format |
PDBx/mmJSON format | 7bg0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bg/7bg0 ftp://data.pdbj.org/pub/pdb/validation_reports/bg/7bg0 | HTTPS FTP |
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-Related structure data
Related structure data | 3g7vS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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-Components
#1: Protein | Mass: 44495.297 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Homo sapiens (human) Strain: K12 / Gene: malE, b4034, JW3994, IAPP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AEX9, UniProt: P10997 #2: Polysaccharide | 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: 2.61 Å3/Da / Density % sol: 52.8 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20mM Tris pH 7.4, 50mM NaCl, 0.02 M magnesium chloride, 0.1 M HEPES pH 7.5, 22 %(w/v) polyacrylic acid 5100 sodium salt |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 11, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.89→37.55 Å / Num. obs: 40035 / % possible obs: 99.77 % / Redundancy: 5.7 % / Biso Wilson estimate: 63.76 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.09446 / Rpim(I) all: 0.04386 / Rrim(I) all: 0.1042 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 2.895→2.998 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.5807 / Mean I/σ(I) obs: 2.43 / Num. unique obs: 3961 / CC1/2: 0.887 / CC star: 0.969 / Rpim(I) all: 0.2675 / Rrim(I) all: 0.6397 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3G7V Resolution: 2.89→37.55 Å / SU ML: 0.4209 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 31.0437 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.32 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.89→37.55 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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