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Yorodumi- PDB-1bte: CRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF THE TYPE II ACTI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bte | |||||||||
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Title | CRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF THE TYPE II ACTIVIN RECEPTOR | |||||||||
Components | PROTEIN (ACTIVIN RECEPTOR TYPE II) | |||||||||
Keywords | TRANSFERASE / RECEPTOR / SERINE KINASE / LIGAND BINDING DOMAIN / THREE-FINGER TOXIN | |||||||||
Function / homology | Function and homology information Signaling by Activin / inhibin-betaglycan-ActRII complex / inhibin binding / Signaling by BMP / penile erection / positive regulation of activin receptor signaling pathway / activin receptor activity / positive regulation of follicle-stimulating hormone secretion / cellular response to oxygen-glucose deprivation / Sertoli cell proliferation ...Signaling by Activin / inhibin-betaglycan-ActRII complex / inhibin binding / Signaling by BMP / penile erection / positive regulation of activin receptor signaling pathway / activin receptor activity / positive regulation of follicle-stimulating hormone secretion / cellular response to oxygen-glucose deprivation / Sertoli cell proliferation / sperm ejaculation / BMP receptor activity / embryonic skeletal system development / activin receptor complex / receptor protein serine/threonine kinase / activin binding / cellular response to BMP stimulus / activin receptor signaling pathway / SMAD protein signal transduction / gastrulation with mouth forming second / regulation of nitric oxide biosynthetic process / determination of left/right symmetry / anterior/posterior pattern specification / odontogenesis of dentin-containing tooth / growth factor binding / mesoderm development / positive regulation of SMAD protein signal transduction / regulation of signal transduction / positive regulation of osteoblast differentiation / BMP signaling pathway / positive regulation of bone mineralization / coreceptor activity / positive regulation of erythrocyte differentiation / PDZ domain binding / cellular response to growth factor stimulus / autophagy / male gonad development / : / spermatogenesis / receptor complex / positive regulation of protein phosphorylation / phosphorylation / protein serine/threonine kinase activity / cell surface / positive regulation of transcription by RNA polymerase II / ATP binding / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.5 Å | |||||||||
Authors | Greenwald, J. / Fischer, W. / Vale, W. / Choe, S. | |||||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1999 Title: Three-finger toxin fold for the extracellular ligand-binding domain of the type II activin receptor serine kinase. Authors: Greenwald, J. / Fischer, W.H. / Vale, W.W. / Choe, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bte.cif.gz | 52.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bte.ent.gz | 40.8 KB | Display | PDB format |
PDBx/mmJSON format | 1bte.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bt/1bte ftp://data.pdbj.org/pub/pdb/validation_reports/bt/1bte | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.8945, -0.4458, -0.0349), Vector: |
-Components
#1: Protein | Mass: 11507.803 Da / Num. of mol.: 2 / Fragment: LIGAND-BINDING DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PPIC9K / Production host: Pichia pastoris (fungus) / Strain (production host): SMD1168 References: UniProt: P27038, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor #2: Sugar | ChemComp-NAG / #3: Water | ChemComp-HOH / | Compound details | GLYCOSYLATION FROM HOST EXPRESSION SYSTEM WAS REMOVED USING ENDOGLYCOSIDASE H, LEAVING BEHIND THE N- ...GLYCOSYLAT | Nonpolymer details | O6 OF NAG A 124 AND NAG B 124 IS MODELED IN TWO ALTERNATIV | Sequence details | THE NUMBERING OF RESIDUES IN THE PDB FILE IS BASED ON THE SEQUENCE WITHOUT THE SIGNAL PEPTIDE. THE ...THE NUMBERING OF RESIDUES IN THE PDB FILE IS BASED ON THE SEQUENCE WITHOUT THE SIGNAL PEPTIDE. THE MOLECULE IN THE CRYSTAL IS LACKING THE 14 C-TERMINAL RESIDUES WHICH HAVE BEEN REMOVED BY TREATMENT WITH ENDOPROTEI | |
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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: 2.4 Å3/Da / Density % sol: 42 % | ||||||||||||||||||||||||
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Crystal grow | pH: 4.5 Details: 100 MM SODIUM ACETATE, PH 4.5, 5% PEG 8000, 0.5M NACL | ||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 43 % | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97 |
Detector | Type: ADSC / Detector: CCD / Date: Jan 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 30005 / % possible obs: 83.9 % / Redundancy: 4.2 % / Biso Wilson estimate: 18.1 Å2 / Rsym value: 0.034 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.5→1.54 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 0.3 / Rsym value: 0.295 / % possible all: 37.3 |
Reflection | *PLUS Rmerge(I) obs: 0.034 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 1.5→20 Å / SU ML: 0.063 / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.092
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Displacement parameters | Biso mean: 23.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.5 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.181 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 23.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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