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- PDB-3ryt: The Plexin A1 intracellular region in complex with Rac1 -

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Basic information

Entry
Database: PDB / ID: 3ryt
TitleThe Plexin A1 intracellular region in complex with Rac1
Components
  • Plexin-A1
  • Ras-related C3 botulinum toxin substrate 1
KeywordsSIGNALING PROTEIN / plexin / RasGAP / GTPase activating protein / Rac
Function / homology
Function and homology information


olfactory nerve formation / Other semaphorin interactions / CRMPs in Sema3A signaling / Sema3A PAK dependent Axon repulsion / neuron projection guidance / RHOD GTPase cycle / dichotomous subdivision of terminal units involved in salivary gland branching / gonadotrophin-releasing hormone neuronal migration to the hypothalamus / RND1 GTPase cycle / regulation of respiratory burst ...olfactory nerve formation / Other semaphorin interactions / CRMPs in Sema3A signaling / Sema3A PAK dependent Axon repulsion / neuron projection guidance / RHOD GTPase cycle / dichotomous subdivision of terminal units involved in salivary gland branching / gonadotrophin-releasing hormone neuronal migration to the hypothalamus / RND1 GTPase cycle / regulation of respiratory burst / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / regulation of neutrophil migration / negative regulation of interleukin-23 production / localization within membrane / Activated NTRK2 signals through CDK5 / regulation of hydrogen peroxide metabolic process / negative regulation of receptor-mediated endocytosis / ruffle assembly / NTRK2 activates RAC1 / NADPH oxidase complex / Inactivation of CDC42 and RAC1 / semaphorin receptor complex / respiratory burst / WNT5:FZD7-mediated leishmania damping / cortical cytoskeleton organization / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / hepatocyte growth factor receptor signaling pathway / semaphorin receptor activity / ruffle organization / cell projection assembly / positive regulation of bicellular tight junction assembly / thioesterase binding / regulation of stress fiber assembly / regulation of lamellipodium assembly / negative regulation of fibroblast migration / RHO GTPases activate CIT / regulation of nitric oxide biosynthetic process / regulation of smooth muscle cell migration / motor neuron axon guidance / Nef and signal transduction / sphingosine-1-phosphate receptor signaling pathway / PCP/CE pathway / Activation of RAC1 / RHO GTPases activate KTN1 / MET activates RAP1 and RAC1 / DCC mediated attractive signaling / Azathioprine ADME / positive regulation of cell-substrate adhesion / positive regulation of neutrophil chemotaxis / Sema4D mediated inhibition of cell attachment and migration / Ephrin signaling / CD28 dependent Vav1 pathway / superoxide anion generation / Wnt signaling pathway, planar cell polarity pathway / lamellipodium assembly / neuron projection extension / Activation of RAC1 downstream of NMDARs / small GTPase-mediated signal transduction / NRAGE signals death through JNK / regulation of cell size / positive regulation of Rho protein signal transduction / Rho GDP-dissociation inhibitor binding / establishment or maintenance of cell polarity / Rac protein signal transduction / RHO GTPases activate PAKs / semaphorin-plexin signaling pathway / ficolin-1-rich granule membrane / Sema3A PAK dependent Axon repulsion / RHO GTPases Activate NADPH Oxidases / EPH-ephrin mediated repulsion of cells / positive regulation of focal adhesion assembly / anatomical structure morphogenesis / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of lamellipodium assembly / RHO GTPases activate PKNs / GPVI-mediated activation cascade / positive regulation of stress fiber assembly / positive regulation of microtubule polymerization / actin filament polymerization / EPHB-mediated forward signaling / RAC1 GTPase cycle / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of endothelial cell migration / substrate adhesion-dependent cell spreading / regulation of cell migration / secretory granule membrane / small monomeric GTPase / actin filament organization / cell-matrix adhesion / Signal transduction by L1 / VEGFR2 mediated vascular permeability / cell projection / Translocation of SLC2A4 (GLUT4) to the plasma membrane / cell chemotaxis / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation
Similarity search - Function
Plexin-A1, Sema domain / GTPase Activation - p120GAP; domain 1 / GTPase Activation - p120gap; domain 1 / Plexin A/B, PSI domain / Plexin, TIG domain 2 / TIG domain found in plexin / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RasGAP domain / Plexin, cytoplasmic RhoGTPase-binding domain ...Plexin-A1, Sema domain / GTPase Activation - p120GAP; domain 1 / GTPase Activation - p120gap; domain 1 / Plexin A/B, PSI domain / Plexin, TIG domain 2 / TIG domain found in plexin / 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 / Small GTPase Rho / small GTPase Rho family profile. / ig-like, plexins, transcription factors / 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 / Ras-related C3 botulinum toxin substrate 1 / Plexin-A1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.582 Å
AuthorsZhang, X. / He, H.
CitationJournal: Sci.Signal. / Year: 2012
Title: Plexins Are GTPase-Activating Proteins for Rap and Are Activated by Induced Dimerization.
Authors: Wang, Y. / He, H. / Srivastava, N. / Vikarunnessa, S. / Chen, Y.B. / Jiang, J. / Cowan, C.W. / Zhang, X.
History
DepositionMay 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_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: Plexin-A1
B: Plexin-A1
C: Ras-related C3 botulinum toxin substrate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,2915
Polymers163,7443
Non-polymers5472
Water00
1
A: Plexin-A1
C: Ras-related C3 botulinum toxin substrate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,4134
Polymers91,8662
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-27 kcal/mol
Surface area32560 Å2
MethodPISA
2
B: Plexin-A1


Theoretical massNumber of molelcules
Total (without water)71,8781
Polymers71,8781
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)110.783, 110.783, 265.628
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Plexin-A1 / Plex 1 / Plexin-1


Mass: 71877.953 Da / Num. of mol.: 2 / Fragment: intracellular region (UNP residues 1269-1894)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kiaa4053, Plexin A1, Plxna1 / Plasmid: modified pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Arcticexpress / References: UniProt: P70206
#2: Protein Ras-related C3 botulinum toxin substrate 1 / Rac1 / Cell migration-inducing gene 5 protein / Ras-like protein TC25 / p21-Rac1


Mass: 19988.107 Da / Num. of mol.: 1 / Fragment: UNP residues 1-177 / Mutation: Q61L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MIG5, RAC1, TC25 / Plasmid: modified pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P63000
#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

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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: 2.49 Å3/Da / Density % sol: 50.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15% PEG1500, 100 mM SPG buffer, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 7, 2008
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 3.582→49.568 Å / Num. all: 20160 / Num. obs: 20090 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rsym value: 0.103
Reflection shellResolution: 3.6→3.73 Å / % possible all: 98.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3IG3 AND 1MH1

3ig3

1mh1


Resolution: 3.582→49.544 Å / SU ML: 0.54 / σ(F): 1 / Phase error: 33.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3397 879 4.75 %RANDOM
Rwork0.2703 ---
all0.2736 20090 --
obs0.2703 18508 91.42 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 216.613 Å2 / ksol: 0.327 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.1635 Å20 Å2-0 Å2
2--6.1635 Å20 Å2
3----12.3269 Å2
Refinement stepCycle: LAST / Resolution: 3.582→49.544 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9079 0 33 0 9112
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049288
X-RAY DIFFRACTIONf_angle_d0.49412682
X-RAY DIFFRACTIONf_dihedral_angle_d11.3253121
X-RAY DIFFRACTIONf_chiral_restr0.0311510
X-RAY DIFFRACTIONf_plane_restr0.0021617
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5821-3.80640.46641500.43812538X-RAY DIFFRACTION82
3.8064-4.10020.411310.34652729X-RAY DIFFRACTION87
4.1002-4.51250.33481150.29282898X-RAY DIFFRACTION92
4.5125-5.16490.33291670.24313002X-RAY DIFFRACTION94
5.1649-6.50490.38591530.31633098X-RAY DIFFRACTION95
6.5049-49.54840.29221630.21833364X-RAY DIFFRACTION98
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)
12.3238-1.469-0.55391.02760.73240.7873-0.1031-0.0641-0.1239-1.07780.183-1.6811.57450.35210.13212.9086-0.4565-0.23090.23090.03541.0862-56.1463-32.1374-12.6168
25.5552.9228-0.54180.9944-0.313.9151-0.2902-0.0319-0.28590.19530.3814-0.15370.0376-0.1458-0.06170.3405-0.031-0.16040.00660.06090.3892-47.52924.0723-7.8453
30.4986-0.62420.81652.9867-1.16911.1759-1.1208-0.6985-0.2744-1.34120.0313-0.3832-0.3006-0.08080.44160.46110.4943-0.82271.8218-0.9260.4441-71.491324.7354-41.4615
40.26531.14662.88852.87160.9990.1744-0.3026-0.87990.14790.16160.07230.0330.9385-0.24610.20210.39880.184-0.0650.8747-0.15860.2495-52.0406-6.5281-42.0105
52.4305-1.3415-2.02050.48890.58713.85390.23840.67410.1663-0.1947-0.6956-0.8286-0.89180.31490.1521.17810.21370.00590.2233-0.12050.4154-56.7357-65.0011-17.6968
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resseq 1472:1657A1472 - 1657
2X-RAY DIFFRACTION2chain A and (resseq 1278:1471 and resseq 1676:1890)A0
3X-RAY DIFFRACTION3chain B and resid 1472:1656B1472 - 1656
4X-RAY DIFFRACTION4chain B and (resseq 1277:1471 and resseq 1673:1891)B0
5X-RAY DIFFRACTION5chain C and (resseq 2:176 or resname GNP or resname MG)C2 - 176
6X-RAY DIFFRACTION5chain C and (resseq 2:176 or resname GNP or resname MG)C2 - 176
7X-RAY DIFFRACTION5chain C and (resseq 2:176 or resname GNP or resname MG)C2 - 176

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