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Yorodumi- PDB-7vf3: Plexin B1 extracellular fragment in complex with lasso-grafted PB... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7vf3 | ||||||
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Title | Plexin B1 extracellular fragment in complex with lasso-grafted PB1m7 peptide | ||||||
Components |
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Keywords | SIGNALING PROTEIN / Plexin / Complex | ||||||
Function / homology | Function and homology information 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 / semaphorin-plexin signaling pathway involved in axon guidance / response to ozone / negative regulation of osteoblast proliferation ...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 / semaphorin-plexin signaling pathway involved in axon guidance / response to ozone / negative regulation of osteoblast proliferation / response to fibroblast growth factor / inhibitory synapse assembly / semaphorin receptor complex / semaphorin receptor activity / negative regulation of cell adhesion / RHOD GTPase cycle / Sema4D induced cell migration and growth-cone collapse / GTPase activating protein binding / Sema4D mediated inhibition of cell attachment and migration / ossification involved in bone maturation / regulation of cytoskeleton organization / positive regulation of Rho protein signal transduction / positive regulation of axonogenesis / semaphorin-plexin signaling pathway / negative regulation of type II interferon production / rough endoplasmic reticulum / T cell proliferation / regulation of cell migration / response to glucocorticoid / embryo implantation / negative regulation of T cell proliferation / regulation of mRNA stability / GTPase activator activity / neuron projection morphogenesis / secretory granule / response to cytokine / female pregnancy / positive regulation of GTPase activity / G alpha (12/13) signalling events / cell migration / transmembrane signaling receptor activity / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å | ||||||
Authors | Sugano, N.N. / Hirata, K. / Yamashita, K. / Yamamoto, M. / Arimori, T. / Takagi, J. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Structure / Year: 2022 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vf3.cif.gz | 489.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vf3.ent.gz | 331.3 KB | Display | PDB format |
PDBx/mmJSON format | 7vf3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vf/7vf3 ftp://data.pdbj.org/pub/pdb/validation_reports/vf/7vf3 | HTTPS FTP |
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-Related structure data
Related structure data | 7vg7C 1utgS 5b4wS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-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.) Homo sapiens (human) / Gene: PLXNB1, KIAA0407, PLXN5, SEP / Production host: Homo sapiens (human) / References: UniProt: O43157 #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.) Homo sapiens (human) / Gene: SCGB1A1, CC10, CCSP, UGB / Production host: Homo sapiens (human) / References: UniProt: P11684 |
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-Sugars , 1 types, 2 molecules
#3: Sugar |
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-Non-polymers , 4 types, 152 molecules
#4: Chemical | ChemComp-PEG / | ||
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#5: Chemical | ChemComp-PGE / | ||
#6: Chemical | ChemComp-PG4 / #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.22 % |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
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 |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
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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: 51.95 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.29→47.41 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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