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- PDB-4c02: Crystal structure of human ACVR1 (ALK2) in complex with FKBP12.6 ... -
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Basic information
Entry | Database: PDB / ID: 4c02 | |||||||||
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Title | Crystal structure of human ACVR1 (ALK2) in complex with FKBP12.6 and dorsomorphin | |||||||||
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![]() | TRANSFERASE/ISOMERASE / TRANSFERASE-ISOMERASE COMPLEX / TRANSFERASE / DORSOMORPHIN | |||||||||
Function / homology | ![]() endocardial cushion cell fate commitment / mitral valve morphogenesis / endocardial cushion fusion / BMP receptor complex / BMP receptor activity / atrial septum primum morphogenesis / cardiac muscle cell fate commitment / acute inflammatory response / activin receptor activity, type I / positive regulation of cardiac epithelial to mesenchymal transition ...endocardial cushion cell fate commitment / mitral valve morphogenesis / endocardial cushion fusion / BMP receptor complex / BMP receptor activity / atrial septum primum morphogenesis / cardiac muscle cell fate commitment / acute inflammatory response / activin receptor activity, type I / positive regulation of cardiac epithelial to mesenchymal transition / positive regulation of determination of dorsal identity / transforming growth factor beta receptor activity, type I / activin receptor complex / endocardial cushion formation / smooth muscle cell differentiation / receptor protein serine/threonine kinase / transmembrane receptor protein serine/threonine kinase activity / pharyngeal system development / activin binding / cellular response to BMP stimulus / activin receptor signaling pathway / negative regulation of activin receptor signaling pathway / positive regulation of sequestering of calcium ion / cyclic nucleotide binding / negative regulation of calcium-mediated signaling / transforming growth factor beta binding / embryonic heart tube morphogenesis / negative regulation of insulin secretion involved in cellular response to glucose stimulus / gastrulation with mouth forming second / dorsal/ventral pattern formation / negative regulation of release of sequestered calcium ion into cytosol / neuronal action potential propagation / insulin secretion involved in cellular response to glucose stimulus / determination of left/right symmetry / neural crest cell migration / response to redox state / atrioventricular valve morphogenesis / protein maturation by protein folding / 'de novo' protein folding / negative regulation of heart rate / branching involved in blood vessel morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / ventricular septum morphogenesis / FK506 binding / positive regulation of axon regeneration / channel regulator activity / SMAD binding / germ cell development / peptide hormone binding / positive regulation of SMAD protein signal transduction / mesoderm formation / smooth muscle contraction / regulation of ossification / response to vitamin E / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / BMP signaling pathway / positive regulation of osteoblast differentiation / positive regulation of bone mineralization / negative regulation of signal transduction / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / T cell proliferation / release of sequestered calcium ion into cytosol / Ion homeostasis / regulation of cytosolic calcium ion concentration / sarcoplasmic reticulum membrane / calcium channel complex / transforming growth factor beta receptor signaling pathway / protein tyrosine kinase binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / negative regulation of extrinsic apoptotic signaling pathway / calcium-mediated signaling / response to hydrogen peroxide / Stimuli-sensing channels / cellular response to growth factor stimulus / Z disc / positive regulation of peptidyl-tyrosine phosphorylation / apical part of cell / heart development / positive regulation of cytosolic calcium ion concentration / protein refolding / in utero embryonic development / transmembrane transporter binding / protein kinase activity / positive regulation of cell migration / cadherin binding / signaling receptor binding / protein serine/threonine kinase activity / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / ATP binding / membrane / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Williams, E. / Riesebos, E. / Vollmar, M. / Krojer, T. / Bradley, A. / Shrestha, L. / Kupinska, K. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. ...Williams, E. / Riesebos, E. / Vollmar, M. / Krojer, T. / Bradley, A. / Shrestha, L. / Kupinska, K. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A. | |||||||||
![]() | ![]() Title: Crystal Structure of Human Acvr1 (Alk2) in Complex with Fkbp12.6 And Dorsomorphin Authors: Williams, E. / Riesebos, E. / Vollmar, M. / Krojer, T. / Bradley, A. / Shrestha, L. / Kupinska, K. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 190.8 KB | Display | ![]() |
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PDB format | ![]() | 150.3 KB | Display | ![]() |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 37398.746 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 172-499 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q04771, non-specific protein-tyrosine kinase, receptor protein serine/threonine kinase |
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#2: Protein | Mass: 11798.501 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 4 types, 253 molecules ![](data/chem/img/FLC.gif)
![](data/chem/img/TAK.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/TAK.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-FLC / #4: Chemical | ChemComp-TAK / | #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | N TERMINAL METHIONINE |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.11 Å3/Da / Density % sol: 75.95 % / Description: NONE |
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Crystal grow | pH: 7.2 / Details: 1.8M AMMONIUM CITRATE, pH 7.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 2.17→40 Å / Num. obs: 169113 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 9 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.17→2.23 Å / Redundancy: 9.3 % / Rmerge(I) obs: 1.07 / Mean I/σ(I) obs: 2 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 1C9H AND 3H9R Resolution: 2.17→39.82 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.949 / SU B: 6.385 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES WITH TLS ADDED DISORDERED REGIONS WERE NOT MODELED AND RELEVANT LOOPS DELETED FROM STRUCTURE.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.836 Å2
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Refinement step | Cycle: LAST / Resolution: 2.17→39.82 Å
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