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- PDB-8bb7: Crystal structure of Mouse Plexin-B1 (20-535) in complex with VHH15 -
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Open data
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Basic information
Entry | Database: PDB / ID: 8bb7 | ||||||
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Title | Crystal structure of Mouse Plexin-B1 (20-535) in complex with VHH15 | ||||||
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![]() | SIGNALING PROTEIN / Complex / inhibitor / VHH / nanobody / Plexin / semaphorin / allosteric | ||||||
Function / homology | ![]() semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis / Sema4D mediated inhibition of cell attachment and migration / Sema4D induced cell migration and growth-cone collapse / RHOD GTPase cycle / : / G alpha (12/13) signalling events / negative regulation of osteoblast proliferation / inhibitory synapse assembly / semaphorin-plexin signaling pathway involved in axon guidance / semaphorin receptor activity ...semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis / Sema4D mediated inhibition of cell attachment and migration / Sema4D induced cell migration and growth-cone collapse / RHOD GTPase cycle / : / G alpha (12/13) signalling events / negative regulation of osteoblast proliferation / inhibitory synapse assembly / semaphorin-plexin signaling pathway involved in axon guidance / semaphorin receptor activity / negative regulation of cell adhesion / semaphorin receptor complex / GTPase activating protein binding / ossification involved in bone maturation / positive regulation of axonogenesis / regulation of GTPase activity / regulation of cytoskeleton organization / semaphorin-plexin signaling pathway / regulation of cell migration / neuron projection morphogenesis / positive regulation of GTPase activity / regulation of cell shape / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cowan, R. / Hall, G. / Carr, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Nanobody inhibitors of Plexin-B1 identify allostery in plexin-semaphorin interactions and signaling. Authors: Cowan, R. / Trokter, M. / Oleksy, A. / Fedorova, M. / Sawmynaden, K. / Worzfeld, T. / Offermanns, S. / Matthews, D. / Carr, M.D. / Hall, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 271.2 KB | Display | ![]() |
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PDB format | ![]() | 197.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 492.4 KB | Display | ![]() |
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Full document | ![]() | 514 KB | Display | |
Data in XML | ![]() | 47.3 KB | Display | |
Data in CIF | ![]() | 65.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8b3kC ![]() 8bf4C ![]() 3ol2S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 56450.527 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Antibody | Mass: 14258.775 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Huarizo / Source: (gene. exp.) ![]() ![]() #3: Sugar | ChemComp-NAG / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.39 Å3/Da / Density % sol: 63.8 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 8% (w/v) PEG 8000, 0.1 M Sodium Citrate, pH 5.0, 1% (w/v) dextran-sulphate (Mr 5000) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 27, 2018 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2.948→47.194 Å / Num. obs: 36092 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 42.66 Å2 / CC1/2: 0.953 / Rmerge(I) obs: 0.42 / Rpim(I) all: 0.274 / Rrim(I) all: 0.504 / Net I/σ(I): 5.6 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3OL2 Resolution: 2.95→47.15 Å / SU ML: 0.3244 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.0364 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.18 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.95→47.15 Å
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Refine LS restraints |
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LS refinement shell |
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