+Open data
-Basic information
Entry | Database: PDB / ID: 7poi | ||||||
---|---|---|---|---|---|---|---|
Title | Prodomain bound BMP10 crystal form 1 | ||||||
Components | (Bone morphogenetic protein 10) x 2 | ||||||
Keywords | CYTOKINE / BMP10 bone morphogenetic protein prodomain TGFbeta signalling | ||||||
Function / homology | Function and homology information atrial cardiac muscle tissue morphogenesis / regulation of cardiac muscle hypertrophy in response to stress / positive regulation of sarcomere organization / positive regulation of cell proliferation involved in heart morphogenesis / ventricular cardiac muscle cell development / positive regulation of cartilage development / telethonin binding / negative regulation of cardiac muscle hypertrophy / Signaling by BMP / activin receptor signaling pathway ...atrial cardiac muscle tissue morphogenesis / regulation of cardiac muscle hypertrophy in response to stress / positive regulation of sarcomere organization / positive regulation of cell proliferation involved in heart morphogenesis / ventricular cardiac muscle cell development / positive regulation of cartilage development / telethonin binding / negative regulation of cardiac muscle hypertrophy / Signaling by BMP / activin receptor signaling pathway / heart trabecula formation / receptor serine/threonine kinase binding / adult heart development / Molecules associated with elastic fibres / negative regulation of endothelial cell migration / ventricular cardiac muscle tissue morphogenesis / cardiac muscle cell proliferation / sarcomere organization / positive regulation of cardiac muscle hypertrophy / positive regulation of SMAD protein signal transduction / regulation of cardiac muscle contraction / BMP signaling pathway / positive regulation of cardiac muscle cell proliferation / negative regulation of cell migration / kidney development / cytokine activity / growth factor activity / hormone activity / negative regulation of cell growth / Z disc / cell adhesion / positive regulation of gene expression / positive regulation of DNA-templated transcription / cell surface / extracellular space / extracellular region / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Guo, J. / Yu, M. / Li, W. | ||||||
Funding support | United Kingdom, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7poi.cif.gz | 262.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7poi.ent.gz | 177.2 KB | Display | PDB format |
PDBx/mmJSON format | 7poi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7poi_validation.pdf.gz | 482.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7poi_full_validation.pdf.gz | 484.6 KB | Display | |
Data in XML | 7poi_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | 7poi_validation.cif.gz | 24.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/po/7poi ftp://data.pdbj.org/pub/pdb/validation_reports/po/7poi | HTTPS FTP |
-Related structure data
Related structure data | 7pojC 7ppaC 7ppbC 7ppcC 4yciS 6sf3S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
|
-Components
#1: Protein | Mass: 12177.185 Da / Num. of mol.: 2 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 #2: Protein | Mass: 33813.500 Da / Num. of mol.: 2 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 #3: Chemical | ChemComp-TAR / | #4: Sugar | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.88 % |
---|---|
Crystal grow | Temperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: 19% PEG 3350 0.15 M Ammonium tartrate dibasic 0.02 M Sodium cacodylate trihydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91589 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 13, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91589 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→107.02 Å / Num. obs: 19024 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 91.59 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.048 / Rrim(I) all: 0.173 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.9→3.08 Å / Redundancy: 12.8 % / Rmerge(I) obs: 3.761 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 3033 / CC1/2: 0.482 / Rpim(I) all: 1.094 / Rrim(I) all: 3.919 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6SF3, 4YCI Resolution: 2.9→107.02 Å / SU ML: 0.5248 / Cross valid method: FREE R-VALUE / σ(F): 0.34 / Phase error: 34.0263 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 112.09 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→107.02 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -3.41330751624 Å / Origin y: -22.6833408638 Å / Origin z: 19.663638474 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |