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- PDB-3su8: Crystal structure of a truncated intracellular domain of Plexin-B... -

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Basic information

Entry
Database: PDB / ID: 3su8
TitleCrystal structure of a truncated intracellular domain of Plexin-B1 in complex with Rac1
Components
  • Plexin-B1
  • Ras-related C3 botulinum toxin substrate 1
KeywordsAPOPTOSIS/SIGNALING PROTEIN / Axon guidance / signal transduction / APOPTOSIS-SIGNALING PROTEIN complex
Function / homology
Function and homology information


negative regulation of osteoblast proliferation / semaphorin receptor binding / regulation of respiratory burst / positive regulation of ovarian follicle development / regulation of neutrophil migration / negative regulation of interleukin-23 production / Activated NTRK2 signals through CDK5 / negative regulation of fibroblast migration / ruffle assembly / localization within membrane ...negative regulation of osteoblast proliferation / semaphorin receptor binding / regulation of respiratory burst / positive regulation of ovarian follicle development / regulation of neutrophil migration / negative regulation of interleukin-23 production / Activated NTRK2 signals through CDK5 / negative regulation of fibroblast migration / ruffle assembly / localization within membrane / kinocilium / regulation of cell adhesion involved in heart morphogenesis / NTRK2 activates RAC1 / NADPH oxidase complex / Inactivation of CDC42 and RAC1 / regulation of hydrogen peroxide metabolic process / Rac protein signal transduction / engulfment of apoptotic cell / semaphorin receptor complex / positive regulation of axonogenesis / superoxide anion generation / WNT5:FZD7-mediated leishmania damping / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / respiratory burst / motor neuron axon guidance / negative regulation of cell adhesion / ruffle organization / semaphorin receptor activity / positive regulation of bicellular tight junction assembly / GTP-dependent protein binding / midbrain dopaminergic neuron differentiation / regulation of lamellipodium assembly / thioesterase binding / regulation of stress fiber assembly / RHO GTPases activate CIT / regulation of nitric oxide biosynthetic process / RHOD GTPase cycle / Nef and signal transduction / Activation of RAC1 / PCP/CE pathway / Sema4D induced cell migration and growth-cone collapse / hepatocyte growth factor receptor signaling pathway / RHO GTPases activate KTN1 / forebrain development / sphingosine-1-phosphate receptor signaling pathway / DCC mediated attractive signaling / MET activates RAP1 and RAC1 / Azathioprine ADME / Sema4D mediated inhibition of cell attachment and migration / lamellipodium assembly / CD28 dependent Vav1 pathway / Ephrin signaling / positive regulation of neutrophil chemotaxis / inhibitory synapse assembly / Wnt signaling pathway, planar cell polarity pathway / GTPase activating protein binding / positive regulation of ruffle assembly / regulation of receptor signaling pathway via JAK-STAT / ossification involved in bone maturation / NRAGE signals death through JNK / Rho GDP-dissociation inhibitor binding / small GTPase-mediated signal transduction / Activation of RAC1 downstream of NMDARs / regulation of cytoskeleton organization / positive regulation of Rho protein signal transduction / pericentriolar material / establishment or maintenance of cell polarity / semaphorin-plexin signaling pathway / RHO GTPases activate PAKs / Sema3A PAK dependent Axon repulsion / SRC activates STAT3 in a quantitative manner, through Cadherin-11 (CDH11), RAC1 and gp130 (IL6ST) / EPH-ephrin mediated repulsion of cells / regulation of postsynapse assembly / ficolin-1-rich granule membrane / positive regulation of GTPase activity / positive regulation of focal adhesion assembly / RHO GTPases Activate NADPH Oxidases / positive regulation of substrate adhesion-dependent cell spreading / anatomical structure morphogenesis / positive regulation of stress fiber assembly / regulation of synaptic vesicle endocytosis / RHO GTPases Activate WASPs and WAVEs / substrate adhesion-dependent cell spreading / positive regulation of lamellipodium assembly / cell-matrix adhesion / RHO GTPases activate IQGAPs / GPVI-mediated activation cascade / RHO GTPases activate PKNs / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / phagocytic cup / actin filament polymerization / RAC1 GTPase cycle / EPHB-mediated forward signaling / synapse assembly / regulation of cell migration / positive regulation of endothelial cell migration / neuron projection morphogenesis / GTPase activator activity / Activation of STAT3 by cadherin engagement / cell motility
Similarity search - Function
GTPase Activation - p120GAP; domain 1 / GTPase Activation - p120gap; domain 1 / : / 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 ...GTPase Activation - p120GAP; domain 1 / GTPase Activation - p120gap; domain 1 / : / 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 / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / Plexin repeat / Plexin repeat / IPT/TIG domain / Small GTPase Rho / ig-like, plexins, transcription factors / Small GTPase Rho domain profile. / Rho GTPase activation protein / IPT domain / PSI domain / domain found in Plexins, Semaphorins and Integrins / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Ubiquitin-like (UB roll) / Small GTP-binding protein domain / Immunoglobulin E-set / P-loop containing nucleotide triphosphate hydrolases / WD40/YVTN repeat-like-containing domain superfamily / Roll / Immunoglobulin-like fold / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Plexin-B1 / Ras-related C3 botulinum toxin substrate 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsBell, C.H. / Aricescu, A.R. / Jones, E.Y. / Siebold, C.
CitationJournal: Plos Biol. / Year: 2011
Title: A Dual Binding Mode for RhoGTPases in Plexin Signalling.
Authors: Bell, C.H. / Aricescu, A.R. / Jones, E.Y. / Siebold, C.
History
DepositionJul 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2011Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ras-related C3 botulinum toxin substrate 1
X: Plexin-B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,0764
Polymers90,5302
Non-polymers5472
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-26 kcal/mol
Surface area36310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.450, 63.810, 84.550
Angle α, β, γ (deg.)90.00, 107.53, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ras-related C3 botulinum toxin substrate 1 / Cell migration-inducing gene 5 protein / Ras-like protein TC25 / p21-Rac1


Mass: 20668.826 Da / Num. of mol.: 1 / Fragment: UNP residues 1-177
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAC1, TC25, MIG5 / Production host: Escherichia coli (E. coli) / References: UniProt: P63000
#2: Protein Plexin-B1 / Semaphorin receptor SEP


Mass: 69860.766 Da / Num. of mol.: 1 / Fragment: UNP residues 1533-2135
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLXNB1, KIAA0407, PLXN5, SEP / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O43157
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
Sequence detailsS1625T CONFLICT IN UNP ENTRY O43157

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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: 2.61 Å3/Da / Density % sol: 52.81 %

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Data collection

Diffraction
IDCrystal-ID
RCSB0666571
11
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 15655 / Biso Wilson estimate: 72.26 Å2

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Processing

SoftwareName: BUSTER / Version: 2.9.2 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→45.89 Å / Cor.coef. Fo:Fc: 0.9043 / Cor.coef. Fo:Fc free: 0.8542 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2377 786 5.02 %RANDOM
Rwork0.2066 ---
all0.2082 16434 --
obs0.2082 15648 --
Displacement parametersBiso mean: 66.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.707 Å20 Å210.6322 Å2
2---2.312 Å20 Å2
3---1.605 Å2
Refine analyzeLuzzati coordinate error obs: 0.678 Å
Refinement stepCycle: LAST / Resolution: 3.2→45.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5729 0 33 0 5762
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0085885HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.937997HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2069SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes139HARMONIC2
X-RAY DIFFRACTIONt_gen_planes837HARMONIC5
X-RAY DIFFRACTIONt_it5885HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.6
X-RAY DIFFRACTIONt_other_torsion18.52
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion760SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6397SEMIHARMONIC4
LS refinement shellResolution: 3.2→3.42 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2956 123 4.38 %
Rwork0.2528 2684 -
all0.2547 2807 -
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)
11.63450.295-0.11041.64040.51443.3850.17530.0027-0.20150.3594-0.01680.2888-0.0877-0.4187-0.1585-0.00090.03170.1005-0.12070.0395-0.073422.4945-18.842631.646
21.99181.32670.90472.5341.03582.50950.0474-0.0902-0.3226-0.31240.00920.32090.0419-0.4128-0.0566-0.1318-0.068-0.07870.06380.062-0.11418.1161-35.0871-6.5955
32.3308-2.3222-4.26524.2102-3.51443.64570.00650.27610.1682-0.1570.07990.0653-0.153-0.0743-0.08640.17040.08820.0811-0.01490.12550.114242.9258-54.84115.6567
41.7625-0.1447-0.56992.61731.31333.53660.0983-0.07070.08740.08330.0985-0.3179-0.32150.058-0.1968-0.01630.01750.0908-0.1167-0.0084-0.136238.7754-19.882114.5173
52.39260.6145-1.05542.5630.68814.25210.2215-0.1683-0.01240.29660.0559-0.0036-0.08650.0262-0.2774-0.15290.0962-0.0279-0.26540.0791-0.189430.0475-18.897126.5785
66.68663.6071.3456.73270.89284.091-0.1325-0.1743-0.0456-0.3893-0.11960.137-0.08390.06680.2521-0.3039-0.1633-0.1876-0.181-0.036-0.0549-4.6276-50.4964-29.858
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ X|1560 - X|1699 }X1560 - 1699
2X-RAY DIFFRACTION2{ X|1700 - X|1890 }X1700 - 1890
3X-RAY DIFFRACTION3{ X|1891 - X|1908 }X1891 - 1908
4X-RAY DIFFRACTION4{ X|1909 - X|1999 }X1909 - 1999
5X-RAY DIFFRACTION5{ X|2000 - X|2129 }X2000 - 2129
6X-RAY DIFFRACTION6{ A|1 - A|178 }A1 - 178

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