[English] 日本語
![](img/lk-miru.gif)
- PDB-7vf3: Plexin B1 extracellular fragment in complex with lasso-grafted PB... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7vf3 | ||||||
---|---|---|---|---|---|---|---|
Title | Plexin B1 extracellular fragment in complex with lasso-grafted PB1m7 peptide | ||||||
![]() |
| ||||||
![]() | SIGNALING PROTEIN / Plexin / Complex | ||||||
Function / homology | ![]() polychlorinated biphenyl binding / negative regulation of interleukin-4 production / negative regulation of interleukin-5 production / negative regulation of interleukin-13 production / semaphorin receptor binding / response to silicon dioxide / phospholipase A2 inhibitor activity / response to ozone / negative regulation of osteoblast proliferation / response to fibroblast growth factor ...polychlorinated biphenyl binding / negative regulation of interleukin-4 production / negative regulation of interleukin-5 production / negative regulation of interleukin-13 production / semaphorin receptor binding / response to silicon dioxide / phospholipase A2 inhibitor activity / response to ozone / negative regulation of osteoblast proliferation / response to fibroblast growth factor / inhibitory synapse assembly / semaphorin-plexin signaling pathway involved in axon guidance / semaphorin receptor activity / negative regulation of cell adhesion / RHOD GTPase cycle / semaphorin receptor complex / axon extension / Sema4D induced cell migration and growth-cone collapse / GTPase activating protein binding / ossification involved in bone maturation / Sema4D mediated inhibition of cell attachment and migration / positive regulation of axonogenesis / positive regulation of Rho protein signal transduction / regulation of cytoskeleton organization / semaphorin-plexin signaling pathway / negative regulation of type II interferon production / T cell proliferation / negative regulation of T cell proliferation / rough endoplasmic reticulum / response to glucocorticoid / regulation of cell migration / regulation of mRNA stability / embryo implantation / GTPase activator activity / neuron projection morphogenesis / positive regulation of GTPase activity / secretory granule / response to cytokine / female pregnancy / transmembrane signaling receptor activity / G alpha (12/13) signalling events / cell migration / nuclear envelope / regulation of cell shape / regulation of inflammatory response / response to lipopolysaccharide / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / intracellular signal transduction / response to xenobiotic stimulus / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular exosome / extracellular region / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sugano, N.N. / Hirata, K. / Yamashita, K. / Yamamoto, M. / Arimori, T. / Takagi, J. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: De novo Fc-based receptor dimerizers differentially modulate PlexinB1 function. Authors: Sugano-Nakamura, N. / Matoba, K. / Hirose, M. / Bashiruddin, N.K. / Matsunaga, Y. / Yamashita, K. / Hirata, K. / Yamamoto, M. / Arimori, T. / Suga, H. / Takagi, J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 489.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 331.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 507.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 515.9 KB | Display | |
Data in XML | ![]() | 37.1 KB | Display | |
Data in CIF | ![]() | 52.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7vg7C ![]() 1utgS ![]() 5b4wS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
2 | ![]()
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-
Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 56661.395 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein | Mass: 17477.010 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: PB1m7-grafted uteroglobin / Source: (gene. exp.) ![]() ![]() |
---|
-Sugars , 1 types, 2 molecules ![](data/chem/img/NAG.gif)
#3: Sugar |
---|
-Non-polymers , 4 types, 152 molecules ![](data/chem/img/PEG.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-PEG / | ||
---|---|---|---|
#5: Chemical | ChemComp-PGE / | ||
#6: Chemical | ChemComp-PG4 / #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.22 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.1M sodium acetate buffer, 20% PEG 400, 0.2M Calcium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 12, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→47.41 Å / Num. obs: 84660 / % possible obs: 99.9 % / Redundancy: 13.9 % / Biso Wilson estimate: 44.88 Å2 / CC1/2: 0.998 / Net I/σ(I): 11.45 |
Reflection shell | Resolution: 2.29→2.43 Å / Redundancy: 13.7 % / Mean I/σ(I) obs: 1.24 / Num. unique obs: 13445 / CC1/2: 0.663 / % possible all: 99.4 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5B4W, 1UTG Resolution: 2.29→47.41 Å / SU ML: 0.3053 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.6512 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: 51.95 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.29→47.41 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
|