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- PDB-7vg7: Plexin B1 extracellular fragment in complex with lasso-grafted PB... -

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Basic information

Entry
Database: PDB / ID: 7vg7
TitlePlexin B1 extracellular fragment in complex with lasso-grafted PB1m6A9 peptide
Components
  • Plexin-B1
  • Uteroglobin,PB1m6A9 peptide,Uteroglobin
KeywordsSIGNALING PROTEIN / Plexin / complex
Function / homology
Function and homology information


polychlorinated biphenyl binding / negative regulation of interleukin-4 production / negative regulation of interleukin-5 production / negative regulation of interleukin-13 production / semaphorin receptor binding / response to silicon dioxide / phospholipase A2 inhibitor activity / semaphorin-plexin signaling pathway involved in axon guidance / response to ozone / negative regulation of osteoblast proliferation ...polychlorinated biphenyl binding / negative regulation of interleukin-4 production / negative regulation of interleukin-5 production / negative regulation of interleukin-13 production / semaphorin receptor binding / response to silicon dioxide / phospholipase A2 inhibitor activity / semaphorin-plexin signaling pathway involved in axon guidance / response to ozone / negative regulation of osteoblast proliferation / response to fibroblast growth factor / 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 / negative regulation of type II interferon production / rough endoplasmic reticulum / T cell proliferation / regulation of cell migration / response to glucocorticoid / embryo implantation / negative regulation of T cell proliferation / regulation of mRNA stability / GTPase activator activity / neuron projection morphogenesis / secretory granule / response to cytokine / female pregnancy / positive regulation of GTPase activity / G alpha (12/13) signalling events / cell migration / transmembrane signaling receptor activity / nuclear envelope / regulation of cell shape / regulation of inflammatory response / response to lipopolysaccharide / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / intracellular signal transduction / response to xenobiotic stimulus / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular exosome / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
Uteroglobin / Secretoglobin family 1C-like / Secretoglobin / Uteroglobin family / Secretoglobin (SCGB) family profile. / Secretoglobin superfamily / Plexin, TIG domain 2 / TIG domain found in plexin / Plexin, TIG domain 1 / TIG domain ...Uteroglobin / Secretoglobin family 1C-like / Secretoglobin / Uteroglobin family / Secretoglobin (SCGB) family profile. / Secretoglobin superfamily / 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
TRIETHYLENE GLYCOL / Plexin-B1 / Uteroglobin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSugano, N.N. / Hirata, K. / Yamashita, K. / Yamamoto, M. / Arimori, T. / Takagi, J.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP20am0101075 Japan
CitationJournal: Structure / Year: 2022
Title: De novo Fc-based receptor dimerizers differentially modulate PlexinB1 function.
Authors: Sugano-Nakamura, N. / Matoba, K. / Hirose, M. / Bashiruddin, N.K. / Matsunaga, Y. / Yamashita, K. / Hirata, K. / Yamamoto, M. / Arimori, T. / Suga, H. / Takagi, J.
History
DepositionSep 14, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.2Oct 19, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Plexin-B1
B: Uteroglobin,PB1m6A9 peptide,Uteroglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3334
Polymers74,9612
Non-polymers3712
Water1,802100
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.190, 62.490, 82.600
Angle α, β, γ (deg.)90.000, 111.922, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Plexin-B1 / Semaphorin receptor SEP


Mass: 56661.395 Da / Num. of mol.: 1 / Mutation: T19S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLXNB1, KIAA0407, PLXN5, SEP / Production host: Homo sapiens (human) / References: UniProt: O43157
#2: Protein Uteroglobin,PB1m6A9 peptide,Uteroglobin / Clara cell phospholipid-binding protein / CCPBP / Clara cells 10 kDa secretory protein / CC10 / ...Clara cell phospholipid-binding protein / CCPBP / Clara cells 10 kDa secretory protein / CC10 / Secretoglobin family 1A member 1 / Urinary protein 1 / UP-1 / UP1 / Urine protein 1


Mass: 18300.041 Da / Num. of mol.: 1 / Mutation: A21S
Source method: isolated from a genetically manipulated source
Details: PB1m6A9-grafted uteroglobin / Source: (gene. exp.) Homo sapiens (human) / Gene: SCGB1A1, CC10, CCSP, UGB / Production host: Homo sapiens (human) / References: UniProt: P11684
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.21 Å3/Da / Density % sol: 44.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M MES or HEPES, 14-16% PEG 3350 / PH range: 6.5 - 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→76.6 Å / Num. obs: 22866 / % possible obs: 99.8 % / Redundancy: 19.7 % / Biso Wilson estimate: 24.31 Å2 / CC1/2: 0.975 / Rrim(I) all: 0.473 / Net I/σ(I): 6.43
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 18.5 % / Num. unique obs: 3621 / CC1/2: 0.678 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
PHASERv2.8.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B4W, 1UTG

5b4w

1utg


Resolution: 2.5→44.78 Å / SU ML: 0.3054 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.0224 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2432 1121 4.91 %
Rwork0.1805 21729 -
obs0.1837 22850 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.01 Å2
Refinement stepCycle: LAST / Resolution: 2.5→44.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4923 0 24 100 5047
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00995071
X-RAY DIFFRACTIONf_angle_d1.13786908
X-RAY DIFFRACTIONf_chiral_restr0.0526771
X-RAY DIFFRACTIONf_plane_restr0.0073906
X-RAY DIFFRACTIONf_dihedral_angle_d10.34053061
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.610.28751250.22682674X-RAY DIFFRACTION99.64
2.61-2.750.34671420.22842719X-RAY DIFFRACTION99.97
2.75-2.920.27421480.21842677X-RAY DIFFRACTION100
2.92-3.150.30381370.21042719X-RAY DIFFRACTION100
3.15-3.470.25611430.1782701X-RAY DIFFRACTION100
3.47-3.970.23391380.15852707X-RAY DIFFRACTION100
3.97-50.17441410.14212731X-RAY DIFFRACTION100
5-44.780.20361470.16992801X-RAY DIFFRACTION100

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