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- PDB-8bf4: Crystal structure of Mouse Plexin-B1 (20-535) in complex with VHH... -

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Basic information

Entry
Database: PDB / ID: 8bf4
TitleCrystal structure of Mouse Plexin-B1 (20-535) in complex with VHH15 and VHH14
Components
  • Plexin-B1
  • VHH14
  • VHH15
KeywordsSIGNALING PROTEIN / Complex / inhibitor / VHH / nanobody / Plexin / semaphorin / allosteric
Function / homology
Function and homology information


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 / semaphorin receptor complex / semaphorin receptor activity / negative regulation of cell adhesion / positive regulation of axonogenesis / inhibitory synapse assembly ...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 / semaphorin receptor complex / semaphorin receptor activity / negative regulation of cell adhesion / positive regulation of axonogenesis / inhibitory synapse assembly / GTPase activating protein binding / ossification involved in bone maturation / positive regulation of Rho protein signal transduction / regulation of cytoskeleton organization / semaphorin-plexin signaling pathway / positive regulation of GTPase activity / neuron projection morphogenesis / regulation of cell shape / postsynaptic membrane / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / glutamatergic synapse / plasma membrane
Similarity search - Function
Plexin-B, PSI domain / Plexin, TIG domain 2 / TIG domain found in plexin / Plexin A/B, PSI domain / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RasGAP domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RasGAP domain / Plexin cytoplasmic RhoGTPase-binding domain ...Plexin-B, PSI domain / Plexin, TIG domain 2 / TIG domain found in plexin / Plexin A/B, PSI domain / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RasGAP domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RasGAP domain / Plexin cytoplasmic RhoGTPase-binding domain / Plexin family / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / IPT/TIG domain / ig-like, plexins, transcription factors / Rho GTPase activation protein / IPT domain / PSI domain / domain found in Plexins, Semaphorins and Integrins / Immunoglobulin E-set / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesCamelidae (mammal)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsCowan, R. / Hall, G. / Carr, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other private United Kingdom
CitationJournal: 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
DepositionOct 24, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1May 31, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.accession_code / _pdbx_initial_refinement_model.source_name / _pdbx_initial_refinement_model.type
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: VHH14
F: Plexin-B1
E: VHH15
A: VHH14
C: Plexin-B1
B: VHH15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,95015
Polymers168,3046
Non-polymers1,6469
Water7,062392
1
D: VHH14
F: Plexin-B1
E: VHH15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,0738
Polymers84,1523
Non-polymers9205
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: VHH14
C: Plexin-B1
B: VHH15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,8787
Polymers84,1523
Non-polymers7264
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.267, 109.233, 95.478
Angle α, β, γ (deg.)90.000, 90.700, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

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Antibody , 2 types, 4 molecules DAEB

#1: Antibody VHH14


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 VHH15


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 Plexin-B1


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 / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 394 molecules

#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.4 %
Crystal growTemperature: 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)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873127 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873127 Å / Relative weight: 1
ReflectionResolution: 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

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
11.89-95.4730.0456630.9250.0450.063
2.48-2.543.40.67944820.3660.6450.938

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8BB7

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
RfactorNum. reflection% reflection
Rfree0.2278 2019 2.63 %
Rwork0.2114 74662 -
obs0.2118 76681 72.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.33 Å2
Refinement stepCycle: LAST / Resolution: 2.15→95.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10920 0 103 392 11415
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004611276
X-RAY DIFFRACTIONf_angle_d0.800615349
X-RAY DIFFRACTIONf_chiral_restr0.12231722
X-RAY DIFFRACTIONf_plane_restr0.01272017
X-RAY DIFFRACTIONf_dihedral_angle_d16.34334048
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.20.2459130.2981394X-RAY DIFFRACTION5.4
2.2-2.260.3554290.3163980X-RAY DIFFRACTION13.36
2.26-2.330.3458490.32311835X-RAY DIFFRACTION24.91
2.33-2.40.325930.31423327X-RAY DIFFRACTION45.3
2.4-2.490.33351260.31344342X-RAY DIFFRACTION58.94
2.49-2.590.31611420.31075529X-RAY DIFFRACTION74.31
2.59-2.710.33541700.30546476X-RAY DIFFRACTION88.03
2.71-2.850.29811930.27637231X-RAY DIFFRACTION98.19
2.85-3.030.29881960.26247400X-RAY DIFFRACTION99.91
3.03-3.260.28421970.23837393X-RAY DIFFRACTION99.91
3.26-3.590.24312070.20367379X-RAY DIFFRACTION99.91
3.59-4.110.19592020.18187418X-RAY DIFFRACTION99.9
4.11-5.180.16322030.1517451X-RAY DIFFRACTION99.84
5.18-95.260.17191990.18177507X-RAY DIFFRACTION99.52

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