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- PDB-8bb7: Crystal structure of Mouse Plexin-B1 (20-535) in complex with VHH15 -

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Basic information

Entry
Database: PDB / ID: 8bb7
TitleCrystal structure of Mouse Plexin-B1 (20-535) in complex with VHH15
Components
  • Plexin-B1
  • VHH15 Nanobody
KeywordsSIGNALING 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
Plexin, TIG domain 2 / TIG domain found in plexin / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RhoGTPase-binding domain / Plexin, cytoplasmic RasGAP domain / Plexin cytoplasmic RasGAP domain / Plexin family / Plexin repeat ...Plexin, TIG domain 2 / TIG domain found in plexin / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RhoGTPase-binding domain / Plexin, cytoplasmic RasGAP domain / Plexin cytoplasmic RasGAP 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 / PSI domain / domain found in Plexins, Semaphorins and Integrins / IPT domain / Immunoglobulin E-set / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Camelidae (mammal)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 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 12, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Plexin-B1
D: VHH15 Nanobody
A: Plexin-B1
C: VHH15 Nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,18812
Polymers141,4194
Non-polymers1,7708
Water3,999222
1
B: Plexin-B1
D: VHH15 Nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3735
Polymers70,7092
Non-polymers6643
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Plexin-B1
C: VHH15 Nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8157
Polymers70,7092
Non-polymers1,1065
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.544, 108.988, 94.043
Angle α, β, γ (deg.)90.000, 90.370, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: 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
#2: Antibody VHH15 Nanobody


Mass: 14258.775 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Huarizo / Source: (gene. exp.) Camelidae (mammal) / Production host: Homo sapiens (human)
#3: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8 / 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.39 Å3/Da / Density % sol: 63.8 %
Crystal growTemperature: 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)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 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

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
10.57-47.155.90.0878960.9920.0570.104
3.05-3.196.62.35843830.3551.522.815

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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: 3OL2

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
RfactorNum. reflection% reflection
Rfree0.2293 1700 5.01 %
Rwork0.2026 32203 -
obs0.2039 33903 84.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.18 Å2
Refinement stepCycle: LAST / Resolution: 2.95→47.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9171 0 112 222 9505
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00749496
X-RAY DIFFRACTIONf_angle_d1.10712940
X-RAY DIFFRACTIONf_chiral_restr0.1141464
X-RAY DIFFRACTIONf_plane_restr0.01911700
X-RAY DIFFRACTIONf_dihedral_angle_d16.72993432
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.030.3762170.2811312X-RAY DIFFRACTION9.89
3.04-3.130.3355750.3051241X-RAY DIFFRACTION39.94
3.13-3.240.33371290.28972381X-RAY DIFFRACTION75.42
3.24-3.370.32121530.26832932X-RAY DIFFRACTION93.83
3.37-3.530.29361660.24553117X-RAY DIFFRACTION99.27
3.53-3.710.27571650.2193152X-RAY DIFFRACTION99.91
3.71-3.950.25851580.20433165X-RAY DIFFRACTION99.94
3.95-4.250.20391720.17493180X-RAY DIFFRACTION99.85
4.25-4.680.14351650.15233129X-RAY DIFFRACTION99.76
4.68-5.350.18061570.16023186X-RAY DIFFRACTION99.97
5.35-6.740.21691670.19843191X-RAY DIFFRACTION99.79
6.74-47.150.18911760.19563217X-RAY DIFFRACTION99.44

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