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Yorodumi- PDB-8bf4: Crystal structure of Mouse Plexin-B1 (20-535) in complex with VHH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bf4 | ||||||
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Title | Crystal structure of Mouse Plexin-B1 (20-535) in complex with VHH15 and VHH14 | ||||||
Components |
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Keywords | SIGNALING PROTEIN / Complex / inhibitor / VHH / nanobody / Plexin / semaphorin / allosteric | ||||||
Function / homology | Function and homology information 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 / : / semaphorin-plexin signaling pathway involved in axon guidance / G alpha (12/13) signalling events / negative regulation of osteoblast proliferation / inhibitory synapse assembly / semaphorin receptor complex ...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 / : / semaphorin-plexin signaling pathway involved in axon guidance / G alpha (12/13) signalling events / negative regulation of osteoblast proliferation / inhibitory synapse assembly / semaphorin receptor complex / semaphorin receptor activity / negative regulation of cell adhesion / GTPase activating protein binding / ossification involved in bone maturation / regulation of cytoskeleton organization / positive regulation of axonogenesis / regulation of GTPase activity / 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 | Camelidae (mammal) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Cowan, R. / Hall, G. / Carr, M. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bf4.cif.gz | 322.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bf4.ent.gz | 234.7 KB | Display | PDB format |
PDBx/mmJSON format | 8bf4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bf/8bf4 ftp://data.pdbj.org/pub/pdb/validation_reports/bf/8bf4 | HTTPS FTP |
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-Related structure data
Related structure data | 8b3kC 8bb7SC 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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1 |
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2 |
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Unit cell |
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-Components
-Antibody , 2 types, 4 molecules DAEB
#1: Antibody | Mass: 13442.920 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Huarizo / Source: (gene. exp.) Camelidae (mammal) / Cell line (production host): Expi293-T / Production host: Homo sapiens (human) #3: Antibody | Mass: 14258.775 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Huarizo / Source: (gene. exp.) Camelidae (mammal) / Cell line (production host): Expi293-T / Production host: Homo sapiens (human) |
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-Protein / Sugars , 2 types, 9 molecules FC
#2: Protein | Mass: 56450.527 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Plxnb1, Kiaa0407 / Cell line (production host): Expi293-T / Production host: Homo sapiens (human) / References: UniProt: Q8CJH3 #4: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 394 molecules
#5: Chemical | ChemComp-CL / |
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#6: Chemical | ChemComp-EDO / |
#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: 2.95 Å3/Da / Density % sol: 58.4 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 15% (w/v) PEG 6000, 0.1 M sodium citrate, pH 5.5, 3% dextran sulphate (Mr 5000) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873127 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 6, 2018 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.873127 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2.149→95.653 Å / Num. obs: 76707 / % possible obs: 99.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 39.18 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.084 / Rrim(I) all: 0.121 / Net I/σ(I): 8.3 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8BB7 Resolution: 2.15→95.26 Å / SU ML: 0.2761 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 30.5551 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: 47.33 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→95.26 Å
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Refine LS restraints |
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LS refinement shell |
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