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- PDB-3sua: Crystal structure of the intracellular domain of Plexin-B1 in com... -

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Basic information

Entry
Database: PDB / ID: 3sua
TitleCrystal structure of the 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


semaphorin receptor binding / regulation of respiratory burst / negative regulation of osteoblast proliferation / 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 ...semaphorin receptor binding / regulation of respiratory burst / negative regulation of osteoblast proliferation / 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 / negative regulation of cell adhesion / 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 / GTPase activating protein binding / RHOD GTPase cycle / motor neuron axon guidance / Nef and signal transduction / sphingosine-1-phosphate receptor signaling pathway / inhibitory synapse assembly / Sema4D induced cell migration and growth-cone collapse / positive regulation of axonogenesis / 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 / ossification involved in bone maturation / 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 / regulation of cytoskeleton organization / 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 / synapse assembly / 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 / positive regulation of GTPase activity / substrate adhesion-dependent cell spreading / GTPase activator activity / neuron projection morphogenesis / 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
Similarity search - Function
Plexin-B, PSI domain / 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-B, PSI domain / 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 / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / Immunoglobulin E-set / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like fold / P-loop containing nucleoside triphosphate hydrolase
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: 4.39 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 7, 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 / 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_asym_id / _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_asym_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
B: Ras-related C3 botulinum toxin substrate 1
C: Ras-related C3 botulinum toxin substrate 1
D: Plexin-B1
E: Plexin-B1
F: Plexin-B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)281,53012
Polymers279,8916
Non-polymers1,6406
Water00
1
A: Ras-related C3 botulinum toxin substrate 1
D: Plexin-B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,8434
Polymers93,2972
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-25 kcal/mol
Surface area32190 Å2
MethodPISA
2
B: Ras-related C3 botulinum toxin substrate 1
E: Plexin-B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,8434
Polymers93,2972
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-25 kcal/mol
Surface area32330 Å2
MethodPISA
3
C: Ras-related C3 botulinum toxin substrate 1
F: Plexin-B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,8434
Polymers93,2972
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-25 kcal/mol
Surface area32380 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12360 Å2
ΔGint-97 kcal/mol
Surface area91780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.340, 224.250, 258.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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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.: 3 / 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: 72628.016 Da / Num. of mol.: 3 / 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.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 3 / 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: 3.68 Å3/Da / Density % sol: 66.58 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 4.39→50 Å / Num. obs: 25525 / Biso Wilson estimate: 171.72 Å2

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Processing

SoftwareName: BUSTER / Version: 2.9.2 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.39→47.81 Å / Cor.coef. Fo:Fc: 0.7814 / Cor.coef. Fo:Fc free: 0.7482 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2638 1318 5.16 %RANDOM
Rwork0.2336 ---
obs0.2351 25522 --
all-25522 --
Displacement parametersBiso mean: 124.57 Å2
Baniso -1Baniso -2Baniso -3
1-37.5289 Å20 Å20 Å2
2--16.0763 Å20 Å2
3----53.6052 Å2
Refine analyzeLuzzati coordinate error obs: 1.106 Å
Refinement stepCycle: LAST / Resolution: 4.39→47.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16394 0 99 0 16493
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00916840HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1622892HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5886SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes396HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2378HARMONIC5
X-RAY DIFFRACTIONt_it16840HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.25
X-RAY DIFFRACTIONt_other_torsion22.76
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2194SEMIHARMONIC5
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_contact19665SEMIHARMONIC4
LS refinement shellResolution: 4.39→4.57 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2673 137 4.89 %
Rwork0.2513 2662 -
all0.2521 2799 -
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)
10.659-0.00471.16530.32291.128100.09550.182-0.12180.2568-0.04830.01480.0246-0.0151-0.0473-0.0341-0.1484-0.2226-0.06550.19260.0478-2.144233.848-17.7339
23.12660.7293-1.5881.0941-0.22850.3920.60410.17320.7204-0.2524-0.1196-0.32130.0926-0.3406-0.4844-0.4470.11540.304-0.1550.04310.6079-20.593686.0822-60.6926
30-1.6995-0.80351.41150.60950.06780.2434-0.2716-0.0255-0.3332-0.2413-0.1988-0.1028-0.2214-0.0021-0.26110.13970.0796-0.1786-0.08410.4569-20.087417.6546-84.8482
401.4701-2.27681.7865-2.879800.21780.2359-0.00310.5554-0.14960.2615-0.30320.1834-0.0682-0.09860.1831-0.07710.1801-0.2077-0.148-32.266356.9827-24.6399
50-0.5380.75553.00350.676300.22370.16050.15570.37210.1939-0.04660.20440.1632-0.4176-0.41890.07560.0042-0.1121-0.12460.5297-44.448257.261-71.6564
62.81680.06090.5910.08320.35372.11620.35920.13670.13460.2041-0.4665-0.22560.133-0.19440.1073-0.2654-0.1101-0.0295-0.2076-0.01620.3462-33.913914.9102-48.8671
70-0.3191-0.22170-0.13731.4689-0.15950.06680.04730.38190.3409-0.43550.2273-0.5275-0.1813-0.31510.3040.28090.4337-0.1413-0.0493-52.994680.274-26.57
82.44430.0421-1.51962.95670.55930.56320.23530.5564-0.11150.55260.16550.0406-0.2129-0.0358-0.4008-0.52690.1616-0.05070.0546-0.12890.2142-62.944436.3024-85.4289
900.6148-1.47550-0.29150.0688-0.19730.3674-0.14080.28790.3539-0.07620.1071-0.2288-0.1566-0.1479-0.3040.3040.2050.21260.0901-43.56727.6169-20.1306
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ D|1563 - D|1745 D|1916 - D|2023 D|2033 - D|2129 }D1563 - 1745
2X-RAY DIFFRACTION1{ D|1563 - D|1745 D|1916 - D|2023 D|2033 - D|2129 }D1916 - 2023
3X-RAY DIFFRACTION1{ D|1563 - D|1745 D|1916 - D|2023 D|2033 - D|2129 }D2033 - 2129
4X-RAY DIFFRACTION2{ E|1563 - E|1745 E|1914 - E|2023 E|2033 - E|2129 }E1563 - 1745
5X-RAY DIFFRACTION2{ E|1563 - E|1745 E|1914 - E|2023 E|2033 - E|2129 }E1914 - 2023
6X-RAY DIFFRACTION2{ E|1563 - E|1745 E|1914 - E|2023 E|2033 - E|2129 }E2033 - 2129
7X-RAY DIFFRACTION3{ F|1563 - F|1745 F|1913 - F|2023 F|2033 - F|2129 }F1563 - 1745
8X-RAY DIFFRACTION3{ F|1563 - F|1745 F|1913 - F|2023 F|2033 - F|2129 }F1913 - 2023
9X-RAY DIFFRACTION3{ F|1563 - F|1745 F|1913 - F|2023 F|2033 - F|2129 }F2033 - 2129
10X-RAY DIFFRACTION4{ D|1746 - D|1757 D|1764 - D|1854 D|1880 - D|1890 }D1746 - 1757
11X-RAY DIFFRACTION4{ D|1746 - D|1757 D|1764 - D|1854 D|1880 - D|1890 }D1764 - 1854
12X-RAY DIFFRACTION4{ D|1746 - D|1757 D|1764 - D|1854 D|1880 - D|1890 }D1880 - 1890
13X-RAY DIFFRACTION5{ E|1746 - E|1757 E|1764 - E|1854 E|1880 - E|1890 }E1746 - 1757
14X-RAY DIFFRACTION5{ E|1746 - E|1757 E|1764 - E|1854 E|1880 - E|1890 }E1764 - 1854
15X-RAY DIFFRACTION5{ E|1746 - E|1757 E|1764 - E|1854 E|1880 - E|1890 }E1880 - 1890
16X-RAY DIFFRACTION6{ F|1746 - F|1757 F|1764 - F|1854 F|1880 - F|1890 }F1746 - 1757
17X-RAY DIFFRACTION6{ F|1746 - F|1757 F|1764 - F|1854 F|1880 - F|1890 }F1764 - 1854
18X-RAY DIFFRACTION6{ F|1746 - F|1757 F|1764 - F|1854 F|1880 - F|1890 }F1880 - 1890
19X-RAY DIFFRACTION7{ A|1 - A|178 A|200 - A|201 }A1 - 178
20X-RAY DIFFRACTION7{ A|1 - A|178 A|200 - A|201 }A200 - 201
21X-RAY DIFFRACTION8{ B|1 - B|178 B|200 - B|201 }B1 - 178
22X-RAY DIFFRACTION8{ B|1 - B|178 B|200 - B|201 }B200 - 201
23X-RAY DIFFRACTION9{ C|1 - C|178 C|200 - C|201 }C1 - 178
24X-RAY DIFFRACTION9{ C|1 - C|178 C|200 - C|201 }C200 - 201

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