[English] 日本語
Yorodumi- PDB-5iv3: Crystal structure of human soluble adenylyl cyclase in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5iv3 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human soluble adenylyl cyclase in complex with alpha,beta-methyleneadenosine-5'-triphosphate and the allosteric inhibitor LRE1 | ||||||
Components | Adenylate cyclase type 10 | ||||||
Keywords | LYASE / human soluble adenylyl cyclase hsAC complex alpha / beta-methyleneadenosine-5'-triphosphate / allosteric inhibitor LRE1 | ||||||
Function / homology | Function and homology information negative regulation of cardiac muscle cell contraction / astrocyte end-foot / mitochondrial ATP transmembrane transport / bicarbonate binding / epithelial cilium movement involved in extracellular fluid movement / neuron projection retraction / positive regulation of glycogen catabolic process / : / central region of growth cone / glucose catabolic process ...negative regulation of cardiac muscle cell contraction / astrocyte end-foot / mitochondrial ATP transmembrane transport / bicarbonate binding / epithelial cilium movement involved in extracellular fluid movement / neuron projection retraction / positive regulation of glycogen catabolic process / : / central region of growth cone / glucose catabolic process / regulation of mitophagy / regulation of membrane repolarization / adenylate cyclase / basal part of cell / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cAMP biosynthetic process / positive regulation of ossification / adenylate cyclase activity / positive regulation of protein targeting to mitochondrion / positive regulation of reactive oxygen species biosynthetic process / neuron projection extension / positive regulation of vascular associated smooth muscle cell apoptotic process / positive regulation of mitochondrial depolarization / positive regulation of ATP biosynthetic process / positive regulation of cardiac muscle hypertrophy / positive regulation of cardiac muscle cell apoptotic process / negative regulation of mitochondrial membrane potential / spermatid development / positive regulation of axon extension / Hedgehog 'off' state / negative regulation of reactive oxygen species biosynthetic process / neuron projection maintenance / positive regulation of peptidyl-threonine phosphorylation / cilium / manganese ion binding / ATPase binding / cytoskeleton / intracellular signal transduction / apical plasma membrane / neuronal cell body / dendrite / perinuclear region of cytoplasm / magnesium ion binding / mitochondrion / extracellular region / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | ||||||
Authors | Kleinboelting, S. / Steegborn, C. | ||||||
Funding support | Germany, 1items
| ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2016 Title: Discovery of LRE1 as a specific and allosteric inhibitor of soluble adenylyl cyclase. Authors: Ramos-Espiritu, L. / Kleinboelting, S. / Navarrete, F.A. / Alvau, A. / Visconti, P.E. / Valsecchi, F. / Starkov, A. / Manfredi, G. / Buck, H. / Adura, C. / Zippin, J.H. / van den Heuvel, J. ...Authors: Ramos-Espiritu, L. / Kleinboelting, S. / Navarrete, F.A. / Alvau, A. / Visconti, P.E. / Valsecchi, F. / Starkov, A. / Manfredi, G. / Buck, H. / Adura, C. / Zippin, J.H. / van den Heuvel, J. / Glickman, J.F. / Steegborn, C. / Levin, L.R. / Buck, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5iv3.cif.gz | 119 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5iv3.ent.gz | 88 KB | Display | PDB format |
PDBx/mmJSON format | 5iv3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5iv3_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5iv3_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 5iv3_validation.xml.gz | 22.7 KB | Display | |
Data in CIF | 5iv3_validation.cif.gz | 32.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iv/5iv3 ftp://data.pdbj.org/pub/pdb/validation_reports/iv/5iv3 | HTTPS FTP |
-Related structure data
Related structure data | 5iv4C 4clkS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 54269.664 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Cys255 modified by BME CME = Cys+BME / Source: (gene. exp.) Homo sapiens (human) / Gene: ADCY10, SAC / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96PN6, adenylate cyclase |
---|
-Non-polymers , 9 types, 278 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-LRI / | #5: Chemical | ChemComp-APC / | #6: Chemical | ChemComp-CA / | #7: Chemical | ChemComp-PEG / | #8: Chemical | ChemComp-EDO / | #9: Chemical | ChemComp-CL / | #10: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % / Description: rockets |
---|---|
Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100 mM sodium acetate pH 4.8 200 mM tri-sodium-citrate 15% (w/v) PEG 4000 10% (v/v) glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 8, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918409 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→44.61 Å / Num. obs: 46795 / % possible obs: 99.9 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 1.86→1.98 Å / Redundancy: 4.4 % / Rmerge(I) obs: 1.281 / Mean I/σ(I) obs: 1.3 / % possible all: 99.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4clk Resolution: 1.86→44.61 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.027 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.126 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.4 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.86→44.61 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|