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Yorodumi- PDB-7ppb: 2.4 angstrom crystal structure of bone morphogenetic protein rece... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ppb | ||||||
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Title | 2.4 angstrom crystal structure of bone morphogenetic protein receptor type II (BMPRII) extracellular domain in complex with BMP10 | ||||||
Components |
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Keywords | SIGNALING PROTEIN / BMPRII BMP10 TGF-beta ligand and receptor Signalling complex | ||||||
Function / homology | Function and homology information semi-lunar valve development / atrial cardiac muscle tissue morphogenesis / regulation of cardiac muscle hypertrophy in response to stress / activin receptor activity, type II / negative regulation of chondrocyte proliferation / lymphatic endothelial cell differentiation / regulation of lung blood pressure / positive regulation of cell proliferation involved in heart morphogenesis / pulmonary valve development / positive regulation of sarcomere organization ...semi-lunar valve development / atrial cardiac muscle tissue morphogenesis / regulation of cardiac muscle hypertrophy in response to stress / activin receptor activity, type II / negative regulation of chondrocyte proliferation / lymphatic endothelial cell differentiation / regulation of lung blood pressure / positive regulation of cell proliferation involved in heart morphogenesis / pulmonary valve development / positive regulation of sarcomere organization / tricuspid valve morphogenesis / chondrocyte development / negative regulation of cell proliferation involved in heart valve morphogenesis / venous blood vessel development / aortic valve development / BMP binding / proteoglycan biosynthetic process / ventricular cardiac muscle cell development / negative regulation of muscle cell differentiation / atrial septum morphogenesis / endocardial cushion development / maternal placenta development / positive regulation of cartilage development / endochondral bone morphogenesis / transforming growth factor beta receptor activity / telethonin binding / lung vasculature development / lymphangiogenesis / mitral valve morphogenesis / negative regulation of cardiac muscle hypertrophy / BMP receptor activity / retina vasculature development in camera-type eye / positive regulation of axon extension involved in axon guidance / artery development / receptor protein serine/threonine kinase / Signaling by BMP / cellular response to BMP stimulus / activin receptor signaling pathway / endothelial cell apoptotic process / heart trabecula formation / receptor serine/threonine kinase binding / adult heart development / positive regulation of ossification / negative regulation of systemic arterial blood pressure / limb development / Molecules associated with elastic fibres / endothelial cell proliferation / negative regulation of endothelial cell migration / anterior/posterior pattern specification / cardiac muscle cell proliferation / ventricular cardiac muscle tissue morphogenesis / cell surface receptor protein serine/threonine kinase signaling pathway / negative regulation of vasoconstriction / sarcomere organization / ventricular septum morphogenesis / lung alveolus development / positive regulation of epithelial cell migration / positive regulation of cardiac muscle hypertrophy / blood vessel development / outflow tract morphogenesis / growth factor binding / positive regulation of SMAD protein signal transduction / mesoderm formation / regulation of cardiac muscle contraction / blood vessel remodeling / BMP signaling pathway / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / clathrin-coated pit / positive regulation of cardiac muscle cell proliferation / cellular response to starvation / negative regulation of cell migration / protein tyrosine kinase binding / basal plasma membrane / kidney development / cytokine activity / caveola / negative regulation of smooth muscle cell proliferation / adherens junction / growth factor activity / negative regulation of cell growth / hormone activity / cellular response to growth factor stimulus / Z disc / osteoblast differentiation / regulation of cell population proliferation / postsynaptic density / receptor complex / cell adhesion / cadherin binding / apical plasma membrane / phosphorylation / axon / neuronal cell body / dendrite / positive regulation of gene expression / positive regulation of DNA-templated transcription / cell surface / positive regulation of transcription by RNA polymerase II / extracellular space Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Guo, J. / Yu, M. / Li, W. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Crystal structures of BMPRII extracellular domain in binary and ternary receptor complexes with BMP10. Authors: Guo, J. / Liu, B. / Thorikay, M. / Yu, M. / Li, X. / Tong, Z. / Salmon, R.M. / Read, R.J. / Ten Dijke, P. / Morrell, N.W. / Li, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ppb.cif.gz | 111.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ppb.ent.gz | 71.4 KB | Display | PDB format |
PDBx/mmJSON format | 7ppb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pp/7ppb ftp://data.pdbj.org/pub/pdb/validation_reports/pp/7ppb | HTTPS FTP |
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-Related structure data
Related structure data | 7poiC 7pojC 7ppaSC 7ppcC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12177.185 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BMP10 / Cell line (production host): HEK EBNA / Production host: Homo sapiens (human) / References: UniProt: O95393 |
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#2: Protein | Mass: 13965.368 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BMPR2, PPH1 / Production host: Escherichia coli (E. coli) References: UniProt: Q13873, receptor protein serine/threonine kinase |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.7 % |
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Crystal grow | Temperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 14% PEG 3350 0.14 M KCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 23, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→42.82 Å / Num. obs: 8820 / % possible obs: 99 % / Redundancy: 6.9 % / Biso Wilson estimate: 35.96 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.217 / Rpim(I) all: 0.089 / Rrim(I) all: 0.234 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.048 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 887 / CC1/2: 0.745 / Rpim(I) all: 0.508 / Rrim(I) all: 1.284 / % possible all: 96.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7PPA Resolution: 2.4→42.82 Å / SU ML: 0.3479 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.5009 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.42 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→42.82 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -27.0589423588 Å / Origin y: 17.0557902789 Å / Origin z: 15.5973021841 Å
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Refinement TLS group | Selection details: all |