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- PDB-8b3k: Crystal structure of human Plexin-B1 (20-535) in the unbound state -

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Basic information

Entry
Database: PDB / ID: 8b3k
TitleCrystal structure of human Plexin-B1 (20-535) in the unbound state
ComponentsPlexin-B1
KeywordsSIGNALING PROTEIN / receptor / unbound / guidance / adherence / neurodevelopment / axonogenesis
Function / homology
Function and homology information


semaphorin receptor binding / semaphorin-plexin signaling pathway involved in axon guidance / negative regulation of osteoblast proliferation / 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 ...semaphorin receptor binding / semaphorin-plexin signaling pathway involved in axon guidance / negative regulation of osteoblast proliferation / 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 / regulation of cell migration / GTPase activator activity / neuron projection morphogenesis / positive regulation of GTPase activity / G alpha (12/13) signalling events / cell migration / transmembrane signaling receptor activity / regulation of cell shape / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / intracellular signal transduction / extracellular region / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.685 Å
AuthorsCowan, R. / Hall, G. / Carr, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
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
DepositionSep 16, 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 1.2Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Plexin-B1
A: Plexin-B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,97518
Polymers112,9582
Non-polymers2,01616
Water3,783210
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-49 kcal/mol
Surface area41580 Å2
Unit cell
Length a, b, c (Å)266.692, 266.692, 108.728
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Plexin-B1 / Semaphorin receptor SEP


Mass: 56479.238 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLXNB1, KIAA0407, PLXN5, SEP / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: O43157
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Cd
#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.: 2 / 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.: 210 / 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: 2.14150262 Å3/Da / Density % sol: 42.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 1.0 M sodium acetate, 0.2 M cadmium sulphate, 0.1 M HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.685→188.58 Å / Num. obs: 48266 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 0.993 / Rmerge(I) obs: 0.374 / Rpim(I) all: 0.152 / Rrim(I) all: 0.403 / Net I/σ(I): 5.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
11.2-188.5811.60.0638620.9980.0260.068
2.8-2.89144.0943820.6121.644.409

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Cootmodel building
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OL2

3ol2


Resolution: 2.685→66.67 Å / Cross valid method: FREE R-VALUE / Phase error: 24.4571
RfactorNum. reflection% reflectionSelection details
Rfree0.2451 1901 4.99 %Random Selection
Rwork0.1993 ---
obs-36173 69.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 47.35 Å2
Refinement stepCycle: LAST / Resolution: 2.685→66.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7461 0 42 210 7713
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection Rwork% reflection obs (%)
2.685-2.750.528655.050.331942.58
2.75-2.830.306135.060.31042446.67
2.83-2.910.3219194.760.322738010.46
2.91-30.4063405.160.310473520.29
3-3.110.41099650.3139182449.5
3.11-3.240.34051604.990.2628304783.21
3.24-3.380.31831914.980.2507364495.84
3.38-3.560.282619450.2011368599.97
3.56-3.780.23441955.020.1843368799.95
3.78-4.080.20221944.980.1667369999.97
4.08-4.490.18261975.020.14743727100
4.49-5.130.17371964.980.1408374099.97
5.14-6.470.22371984.990.1985376799.97
6.47-66.670.27962034.950.2298390098.96

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