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- PDB-7vf3: Plexin B1 extracellular fragment in complex with lasso-grafted PB... -

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Basic information

Entry
Database: PDB / ID: 7vf3
TitlePlexin B1 extracellular fragment in complex with lasso-grafted PB1m7 peptide
Components
  • Plexin-B1
  • Uteroglobin,PB1m7 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 / phospholipase A2 inhibitor activity / semaphorin receptor binding / response to silicon dioxide / response to ozone / negative regulation of osteoblast proliferation / response to fibroblast growth factor ...polychlorinated biphenyl binding / negative regulation of interleukin-4 production / negative regulation of interleukin-5 production / negative regulation of interleukin-13 production / phospholipase A2 inhibitor activity / semaphorin receptor binding / response to silicon dioxide / response to ozone / negative regulation of osteoblast proliferation / response to fibroblast growth factor / semaphorin receptor complex / semaphorin receptor activity / negative regulation of cell adhesion / RHOD GTPase cycle / Sema4D induced cell migration and growth-cone collapse / positive regulation of axonogenesis / inhibitory synapse assembly / GTPase activating protein binding / Sema4D mediated inhibition of cell attachment and migration / ossification involved in bone maturation / positive regulation of Rho protein signal transduction / regulation of cytoskeleton organization / semaphorin-plexin signaling pathway / negative regulation of type II interferon production / positive regulation of GTPase activity / T cell proliferation / synapse assembly / negative regulation of T cell proliferation / neuron projection morphogenesis / response to cytokine / regulation of mRNA stability / embryo implantation / GTPase activator activity / regulation of cell migration / response to glucocorticoid / secretory granule / female pregnancy / transmembrane signaling receptor activity / nuclear envelope / cell migration / G alpha (12/13) signalling events / regulation of cell shape / regulation of inflammatory response / response to lipopolysaccharide / postsynaptic membrane / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / intracellular signal transduction / response to xenobiotic stimulus / glutamatergic synapse / 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. / Uteroglobin / Plexin-B, PSI domain / Secretoglobin superfamily / Plexin, TIG domain 2 / TIG domain found in plexin ...Uteroglobin / Secretoglobin family 1C-like / Secretoglobin / Uteroglobin family / Secretoglobin (SCGB) family profile. / Uteroglobin / Plexin-B, PSI domain / Secretoglobin superfamily / 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
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Plexin-B1 / Uteroglobin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 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 10, 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
Revision 1.4Nov 20, 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

Downloads & links

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Assembly

Deposited unit
A: Plexin-B1
B: Uteroglobin,PB1m7 peptide,Uteroglobin
C: Plexin-B1
D: Uteroglobin,PB1m7 peptide,Uteroglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,75212
Polymers148,2774
Non-polymers1,4768
Water2,630146
1
A: Plexin-B1
B: Uteroglobin,PB1m7 peptide,Uteroglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4664
Polymers74,1382
Non-polymers3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint6 kcal/mol
Surface area22960 Å2
MethodPISA
2
C: Plexin-B1
D: Uteroglobin,PB1m7 peptide,Uteroglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2878
Polymers74,1382
Non-polymers1,1486
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-3 kcal/mol
Surface area21530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)263.591, 263.591, 108.379
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11C-721-

HOH

21C-775-

HOH

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Plexin-B1 / Semaphorin receptor SEP


Mass: 56661.395 Da / Num. of mol.: 2
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,PB1m7 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: 17477.010 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PB1m7-grafted uteroglobin / Source: (gene. exp.) Homo sapiens (human) / Gene: SCGB1A1, CC10, CCSP, UGB / Production host: Homo sapiens (human) / References: UniProt: P11684

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Sugars , 1 types, 2 molecules

#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: isolated from a natural source / 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 , 4 types, 152 molecules

#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C8H18O5 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 3.17 Å3/Da / Density % sol: 61.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1M sodium acetate buffer, 20% PEG 400, 0.2M Calcium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.29→47.41 Å / Num. obs: 84660 / % possible obs: 99.9 % / Redundancy: 13.9 % / Biso Wilson estimate: 44.88 Å2 / CC1/2: 0.998 / Net I/σ(I): 11.45
Reflection shellResolution: 2.29→2.43 Å / Redundancy: 13.7 % / Mean I/σ(I) obs: 1.24 / Num. unique obs: 13445 / CC1/2: 0.663 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERv2.8.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B4W, 1UTG

5b4w

1utg


Resolution: 2.29→47.41 Å / SU ML: 0.3053 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.6512
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2257 4229 5 %
Rwork0.196 80286 -
obs0.1975 84515 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.95 Å2
Refinement stepCycle: LAST / Resolution: 2.29→47.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7754 0 97 146 7997
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00738045
X-RAY DIFFRACTIONf_angle_d0.931910960
X-RAY DIFFRACTIONf_chiral_restr0.05531212
X-RAY DIFFRACTIONf_plane_restr0.00821439
X-RAY DIFFRACTIONf_dihedral_angle_d7.34171161
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.320.31441350.32462559X-RAY DIFFRACTION96.77
2.32-2.350.33211410.31762655X-RAY DIFFRACTION99.57
2.35-2.380.37941380.32222639X-RAY DIFFRACTION99.75
2.38-2.410.34991400.30292652X-RAY DIFFRACTION99.82
2.41-2.440.3451390.30022633X-RAY DIFFRACTION99.71
2.44-2.470.31161410.28322674X-RAY DIFFRACTION99.75
2.47-2.510.29121370.26412626X-RAY DIFFRACTION99.71
2.51-2.540.28581400.25332651X-RAY DIFFRACTION99.82
2.54-2.580.27711400.25442674X-RAY DIFFRACTION99.79
2.58-2.630.29541400.24632647X-RAY DIFFRACTION99.82
2.63-2.670.32621390.24912644X-RAY DIFFRACTION99.96
2.67-2.720.28391400.24972666X-RAY DIFFRACTION99.89
2.72-2.770.28171410.2482670X-RAY DIFFRACTION99.75
2.77-2.830.25561390.24242644X-RAY DIFFRACTION99.78
2.83-2.890.27481410.24492668X-RAY DIFFRACTION99.75
2.89-2.960.29551400.2462655X-RAY DIFFRACTION99.89
2.96-3.030.27281420.24222692X-RAY DIFFRACTION99.89
3.03-3.110.28091390.23082649X-RAY DIFFRACTION100
3.11-3.210.26861410.21732680X-RAY DIFFRACTION99.96
3.21-3.310.26061410.20572668X-RAY DIFFRACTION100
3.31-3.430.24051410.1932685X-RAY DIFFRACTION99.93
3.43-3.560.22281400.19582681X-RAY DIFFRACTION99.89
3.56-3.730.1961420.17962697X-RAY DIFFRACTION100
3.73-3.920.17511420.15862691X-RAY DIFFRACTION100
3.92-4.170.18451420.14952697X-RAY DIFFRACTION99.96
4.17-4.490.17141430.13752718X-RAY DIFFRACTION100
4.49-4.940.14941430.13242717X-RAY DIFFRACTION99.93
4.94-5.660.1951440.15812734X-RAY DIFFRACTION100
5.66-7.120.20111460.18072765X-RAY DIFFRACTION100
7.12-47.410.18161520.18332855X-RAY DIFFRACTION98.75
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.486415385960.2483733465180.7233493629032.264717184780.3417791643413.062954399470.0364923257504-0.107813207973-0.144751960544-0.04556458942710.01592685919470.2116985046140.300439298937-0.371223582337-0.06220394159230.272446081183-0.00137856884380.04738706305190.3430079231620.02050036495530.28063032896225.5810401886-6.3697913490123.8155123299
21.26210076963-0.383648975690.4909137220821.46376395636-0.4264901373082.54788919884-0.02794496003160.172174062554-0.0413143166005-0.102737322992-0.01244824306020.002123708659970.1130323240010.03422795632410.05118609075120.2830784038740.001660816802250.03031910190430.346655332489-0.01399972490370.25162549716430.63966446245.032001567380.46606819008
32.910931668061.418150785170.1292131274182.1499294609-0.2526624114471.606489440760.046226379153-0.1433027566190.1349545961840.274645670726-0.0784813223127-0.255857847192-0.04679187694770.5559054458090.0257898753770.2755608423740.04895673160470.007549124881950.5780356657850.002403093167830.38521017715455.70235964557.634514967122.9802615403
42.91742532359-1.264881417422.567591160982.06156055657-0.2589674570642.735434311870.408469938222-0.33240921134-1.12195965948-0.02311922131590.3529768490760.4012057536382.35865623465-0.921037679168-0.5173161715640.840997794852-0.0701207299573-0.1086804144550.71328092461-0.0367036683210.67710375954837.6779729124-14.96342648595.95108544395
58.487511375210.66804333657-5.088327985380.9402631495260.2914890880623.57369373105-0.0170757919780.473171229987-0.854406287126-0.565874129422-0.0132444855281-0.8100603252111.469546829610.1442970358420.07177343627160.5715158670230.1307022703840.09050095204490.367285820741-0.04554099010070.48541466457641.6930703242-13.072219389913.9290125472
61.563035548520.3691856296551.097137688232.662160176070.3035519522312.89073040720.0837643108035-0.233283331324-0.05499980682730.0627925917263-0.05811592893690.2387600712980.233480961716-0.220578668012-0.01340212695740.2263064009910.002187001886270.06039615941210.3580551044160.01720474987040.26610876976728.5367579003-3.7709443888-30.9533882657
73.02073344079-0.268905826589-1.166378841591.627791947210.4225899887444.51178014635-0.1383462216260.0202378645392-0.07949491183960.09929363570170.10215998150.3670190856980.398548717972-0.4329232165180.0520353780750.226557990133-0.000273239310841-0.01653760228260.3011442881940.02181220152620.26410371768526.92013560151.2250939066-46.9792158142
82.21747713857-1.50523129820.9910415888812.55598870039-0.4749230325413.274144334510.02276782199520.1348228598470.0747866458611-0.120578953511-0.0976012244362-0.157841229244-0.05588642387140.3124548295850.076262379180.192244589864-0.018081572340.06441362463910.2997020682570.008349232778330.26681955258237.55089561079.49565215642-57.0817311973
92.527610638141.301062661170.3144721165381.24462958463-0.09032754197921.483790236090.0765894077372-0.2639586870480.1413915374180.0965467424085-0.0698470540871-0.142153068224-0.09612628589930.504779321782-0.0342406962450.2860039835110.04987472145340.02725117700010.63424330495-0.02796179929760.40394926396159.56299535217.37348210704-31.2589176055
109.030758534925.312425262311.883226027283.515757006782.588673066495.966357763620.245600820347-0.255802243872-1.56563945610.3231665858110.0366234529790.1320640356832.28779232247-0.992936442498-0.3783050655820.749077734291-0.0396959592704-0.05532511413360.582621404052-0.0255842926630.68911586816540.008636718-13.3572197774-48.5837241351
115.51855168402-0.538487037799-1.512102452458.615735376660.5645740790382.160990591260.2062902544380.2844325325-0.258337512489-0.0726184058919-0.0361874420254-0.2352162635211.31840892049-0.233625543044-0.1773176498130.492933374820.06484313244950.03504601305220.480955265590.01001577213670.40468064678444.2436348195-11.9506932615-40.7776644987
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 24 through 158 )AA24 - 1581 - 135
22chain 'A' and (resid 159 through 397 )AA159 - 397136 - 360
33chain 'A' and (resid 398 through 534 )AA398 - 534361 - 494
44chain 'B' and (resid 100 through 106 )BB100 - 1061 - 7
55chain 'B' and (resid 107 through 114 )BB107 - 1148 - 15
66chain 'C' and (resid 24 through 170 )CC24 - 1701 - 147
77chain 'C' and (resid 171 through 235 )CC171 - 235148 - 212
88chain 'C' and (resid 236 through 397 )CC236 - 397213 - 361
99chain 'C' and (resid 398 through 534 )CC398 - 534362 - 494
1010chain 'D' and (resid 100 through 106 )DD100 - 1061 - 7
1111chain 'D' and (resid 107 through 114 )DD107 - 1148 - 15

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